Matteo Pellegrini

Title(s)Professor, Molecular, Cell and Developmental Biology
SchoolCollege of Letters and Science
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    Other Positions
    Title(s)Professor, Human Genetics

    Title(s)Professor, CA NanoSystems

    Title(s)Professor, Medicine


    Collapse Research 
    Collapse Research Activities and Funding
    Metabolic and epigenetic reprogramming of vital organs in SARS-CoV-2 induced systemic toxicity
    NIH R01DK132735Sep 17, 2021 - Aug 31, 2024
    Role: Co-Principal Investigator
    Bruins in Genomics: Dental, Oral & Craniofacial Research Training Program (BIG DOC)
    NIH R25DE030117Jan 15, 2021 - Dec 31, 2025
    Role: Co-Principal Investigator
    Role of collagen heterogeneity in remodeling of acute and chronic heart scars
    NIH R01HL149687Jul 1, 2020 - Jun 30, 2024
    Role: Co-Principal Investigator
    Enhancing the International Molecular Exchange (IMEx): Providing an Improved Community-Oriented Molecular Interactions Resource
    NIH R01GM123126Mar 1, 2018 - Feb 28, 2022
    Role: Principal Investigator
    Epigenetic clock for measuring the DNA methylation age of mouse tissues
    NIH R21AG049400May 1, 2016 - Apr 30, 2018
    Role: Co-Principal Investigator
    Biomedical Big Data Training Grant
    NIH T32LM012424May 1, 2015 - Jun 30, 2020
    Role: Principal Investigator
    Biomedical Big Data Training Grant
    NIH T32CA201160May 1, 2015 - Apr 30, 2020
    Role: Principal Investigator
    DNA methylation and its relationship to gene expression and physiologic traits
    NIH R01GM095656Jul 1, 2011 - Mar 31, 2016
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. The Multi-State Epigenetic Pacemaker enables the identification of combinations of factors that influence DNA methylation. Geroscience. 2024 Nov 16. Farrell C, Tandon K, Ferrari R, Lapborisuth K, Modi R, Snir S, Pellegrini M. PMID: 39549198.
      View in: PubMed   Mentions:    Fields:    
    2. Complete genome of Variovorax sp. EBFNA2, isolated from a surface-sterilized fava bean nodule. Microbiol Resour Announc. 2024 Nov 11; e0076224. Hirsch AM, Humm E, Rubbi L, Del Vecchio G, Ha SM, Pellegrini M, Gunsalus RP. PMID: 39526792.
      View in: PubMed   Mentions:
    3. PD-1 blockade plus cisplatin-based chemotherapy in patients with small cell/neuroendocrine bladder and prostate cancers. Cell Rep Med. 2024 Nov 06; 101824. Gu Y, Ly A, Rodriguez S, Zhang H, Kim J, Mao Z, Sachdeva A, Zomorodian N, Pellegrini M, Li G, Liu S, Drakaki A, Rettig MB, Chin AI. PMID: 39536751.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCTClinical Trials
    4. A humanized monoclonal antibody targeting an ectonucleotidase rescues cardiac metabolism and heart function after myocardial infarction. Cell Rep Med. 2024 Oct 17; 101795. Li S, Tao B, Wan J, Montecino-Rodriguez E, Wang P, Ma F, Sun B, Gu Y, Ramadoss S, Su L, Sun Q, Hoeve JT, Stiles L, Collins J, van Dam RM, Tamboline M, Taschereau R, Shirihai O, Kitchen DB, Pellegrini M, Graeber T, Dorshkind K, Xu S, Deb A. PMID: 39454569.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    5. An epigenetic human cytomegalovirus infection score predicts viremia risk in seropositive lung transplant recipients. Epigenetics. 2024 Dec; 19(1):2408843. Hsu FM, Mohanty RP, Rubbi L, Thompson M, Pickering H, Reed EF, Greenland JR, Schaenman JM, Pellegrini M. PMID: 39360678; PMCID: PMC11451273.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    6. Single cell and TCR analysis of immune cells from AAV gene therapy-dosed Duchenne muscular dystrophy patients. Mol Ther Methods Clin Dev. 2024 Dec 12; 32(4):101349. Emami MR, Brimble MA, Espinoza A, Owens J, Whiteley LO, Casinghino S, Lanz TA, Farahat PK, Pellegrini M, Young CS, Thomas PG, McNally EM, Villalta SA, Schattgen SA, Spencer MJ. PMID: 39524974; PMCID: PMC11546459.
      View in: PubMed   Mentions:
    7. Genome of Dietzia cinnamea 55, a desert-isolated microbe with plant growth-promoting properties for grain crops. Microbiol Resour Announc. 2024 Oct 10; 13(10):e0025724. Hirsch AM, Khan N, Humm E, Rubbi M, Del Vecchio G, Ha SM, Pellegrini M, Gunsalus RP. PMID: 39254331; PMCID: PMC11465666.
      View in: PubMed   Mentions:
    8. Adenovirus small E1A directs activation of Alu transcription at YAP/TEAD- and AP-1-bound enhancers through interactions with the EP400 chromatin remodeler. Nucleic Acids Res. 2024 Sep 09; 52(16):9481-9500. Cantarella S, Vezzoli M, Carnevali D, Morselli M, Zemke NR, Montanini B, Daussy CF, Wodrich H, Teichmann M, Pellegrini M, Berk AJ, Dieci G, Ferrari R. PMID: 39011896; PMCID: PMC11381368.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    9. The evolution of computational research in a data-centric world. Cell. 2024 Aug 22; 187(17):4449-4457. Deshpande D, Chhugani K, Ramesh T, Pellegrini M, Shiffman S, Abedalthagafi MS, Alqahtani S, Ye J, Liu XS, Leek JT, Brazma A, Ophoff RA, Rao G, Butte AJ, Moore JH, Katritch V, Mangul S. PMID: 39178828.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    10. The response to influenza vaccination is associated with DNA methylation-driven regulation of T cell innate antiviral pathways. Clin Epigenetics. 2024 Aug 21; 16(1):114. Fu H, Pickering H, Rubbi L, Ross TM, Zhou W, Reed EF, Pellegrini M. PMID: 39169387; PMCID: PMC11340180.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCellsPHPublic Health
    11. Non-coding RNA yREX3 from human extracellular vesicles exerts macrophage-mediated cardioprotection via a novel gene-methylating mechanism. Eur Heart J. 2024 Aug 03; 45(29):2660-2673. Ciullo A, Li L, Li C, Tsi K, Farrell C, Pellegrini M, Marbán E, Ibrahim AGE. PMID: 38865332; PMCID: PMC11297535.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    12. Role of Forkhead Box P3 in IFNγ-Mediated PD-L1 Expression and Bladder Cancer Epithelial-to-Mesenchymal Transition. Cancer Res Commun. 2024 Aug 01; 4(8):2228-2241. Zhang H, Ly A, Chou E, Wang L, Zhang P, Prado K, Gu Y, Pellegrini M, Chin AI. PMID: 39099201; PMCID: PMC11345674.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    13. Age-correlated changes in the canine oral microbiome. Front Microbiol. 2024; 15:1426691. Kislik G, Zhou L, Rubbi L, Pellegrini M. PMID: 39081893; PMCID: PMC11287893.
      View in: PubMed   Mentions:
    14. Co-analysis of methylation platforms for signatures of biological aging in the domestic dog reveals previously unexplored confounding factors. Aging (Albany NY). 2024 Jul 09; 16(13):10724-10748. Armero AS, Buckley RM, Mboning L, Spatola GJ, Horvath S, Pellegrini M, Ostrander EA. PMID: 38985449; PMCID: PMC11272130.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    15. Complete genomes of two Variovorax endophytes isolated from surface-sterilized alfalfa nodules. Microbiol Resour Announc. 2024 Aug 13; 13(8):e0033624. Hirsch AM, Humm E, Rubbi M, Del Vecchio G, Ha SM, Pellegrini M, Gunsalus RP. PMID: 38967468; PMCID: PMC11320970.
      View in: PubMed   Mentions:
    16. Single-stranded pre-methylated 5mC adapters uncover the methylation profile of plasma ultrashort Single-stranded cell-free DNA. Nucleic Acids Res. 2024 Jun 24; 52(11):e50. Cheng JC, Swarup N, Morselli M, Huang WL, Aziz M, Caggiano C, Kordi M, Patel AA, Chia D, Kim Y, Li F, Wei F, Zaitlen N, Krysan K, Dubinett S, Pellegrini M, Wong DTW. PMID: 38797520; PMCID: PMC11194076.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    17. The response to influenza vaccination is associated with DNA methylation-driven regulation of T cell innate antiviral pathways. Res Sq. 2024 May 23. Fu H, Pickering H, Rubbi L, Ross TM, Zhou W, Reed EF, Pellegrini M. PMID: 38826189; PMCID: PMC11142309.
      View in: PubMed   Mentions:
    18. Novel DNA methylation-based epigenetic signatures in colorectal cancer from peripheral blood leukocytes. Am J Cancer Res. 2024; 14(5):2253-2271. Jung SY, Yu H, Tan X, Pellegrini M. PMID: 38859857; PMCID: PMC11162685.
      View in: PubMed   Mentions:
    19. Generation of allogeneic CAR-NKT cells from hematopoietic stem and progenitor cells using a clinically guided culture method. Nat Biotechnol. 2024 May 14. Li YR, Zhou Y, Yu J, Kim YJ, Li M, Lee D, Zhou K, Chen Y, Zhu Y, Wang YC, Li Z, Yu Y, Dunn ZS, Guo W, Cen X, Husman T, Bajpai A, Kramer A, Wilson M, Fang Y, Huang J, Li S, Zhou Y, Zhang Y, Hahn Z, Zhu E, Ma F, Pan C, Lusis AJ, Zhou JJ, Seet CS, Kohn DB, Wang P, Zhou XJ, Pellegrini M, Puliafito BR, Larson SM, Yang L. PMID: 38744947.
      View in: PubMed   Mentions: 4     Fields:    
    20. Editorial: Computational methods for analysis of DNA methylation data, volume II. Front Bioinform. 2024; 4:1415791. Di Lena P, Nardini C, Pellegrini M. PMID: 38766648; PMCID: PMC11099281.
      View in: PubMed   Mentions:
    21. Enhanced CTLA-4 blockade anti-tumor immunity with APG-157 combination in a murine head and neck cancer. Cancer Med. 2024 May; 13(9):e7212. Shin DS, Basak S, Veena MS, Comin-Anduix B, Bhattacharya A, Dong TS, Ko A, Han P, Jacobs J, Moatamed NA, Avila L, Pellegrini M, Wang M, Srivatsan ES. PMID: 38686626; PMCID: PMC11058674.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    22. Protocol for isolating amnion cells from human and non-human primate placenta for flow cytometry and transcriptomics. STAR Protoc. 2024 Jun 21; 5(2):103044. Cappelletti M, Short D, Morselli M, Pellegrini M, Johnson MR, Afshar Y, Kallapur SG, Presicce P. PMID: 38678572; PMCID: PMC11068923.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    23. BayesAge: A maximum likelihood algorithm to predict epigenetic age. Front Bioinform. 2024; 4:1329144. Mboning L, Rubbi L, Thompson M, Bouchard LS, Pellegrini M. PMID: 38638123; PMCID: PMC11024280.
      View in: PubMed   Mentions: 2  
    24. D-2-HG Inhibits IDH1mut Glioma Growth via FTO Inhibition and Resultant m6A Hypermethylation. Cancer Res Commun. 2024 Mar 22; 4(3):876-894. Pianka ST, Li T, Prins TJ, Eldred BSC, Kevan BM, Liang H, Zapanta Rinonos S, Kornblum HI, Nathanson DA, Pellegrini M, Liau LM, Nghiemphu PL, Cloughesy TF, Lai A. PMID: 38445960; PMCID: PMC10959073.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimals
    25. Gigaxonin Suppresses Epithelial-to-Mesenchymal Transition of Human Cancer Through Downregulation of Snail. Cancer Res Commun. 2024 03 08; 4(3):706-722. Veena MS, Gahng JJ, Alani M, Ko AY, Basak SK, Liu IY, Hwang KJ, Chatoff JR, Venkatesan N, Morselli M, Yan W, Ali I, Kaczor-Urbanowicz KE, Gowda BS, Frost P, Pellegrini M, Moatamed NA, Wilczynski SP, Bomont P, Wang MB, Shin DS, Srivatsan ES. PMID: 38421310; PMCID: PMC10921914.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    26. Single-cell sequencing reveals Hippo signaling as a driver of fibrosis in hidradenitis suppurativa. J Clin Invest. 2024 Feb 01; 134(3). van Straalen KR, Ma F, Tsou PS, Plazyo O, Gharaee-Kermani M, Calbet M, Xing X, Sarkar MK, Uppala R, Harms PW, Wasikowski R, Nahlawi L, Nakamura M, Eshaq M, Wang C, Dobry C, Kozlow JH, Cherry-Bukowiec J, Brodie WD, Wolk K, Uluçkan Ö, Mattichak MN, Pellegrini M, Modlin RL, Maverakis E, Sabat R, Kahlenberg JM, Billi AC, Tsoi LC, Gudjonsson JE. PMID: 38051587; PMCID: PMC10836805.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    27. Longitudinal analysis of influenza vaccination implicates regulation of RIG-I signaling by DNA methylation. Sci Rep. 2024 01 17; 14(1):1455. Fu H, Pickering H, Rubbi L, Ross TM, Reed EF, Pellegrini M. PMID: 38228690; PMCID: PMC10791625.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCellsPHPublic Health
    28. Identifying epigenetic aging moderators using the epigenetic pacemaker. Front Bioinform. 2023; 3:1308680. Farrell C, Hu C, Lapborisuth K, Pu K, Snir S, Pellegrini M. PMID: 38235295; PMCID: PMC10791860.
      View in: PubMed   Mentions:
    29. Systems-based identification of the Hippo pathway for promoting fibrotic mesenchymal differentiation in systemic sclerosis. Nat Commun. 2024 Jan 03; 15(1):210. Ma F, Tsou PS, Gharaee-Kermani M, Plazyo O, Xing X, Kirma J, Wasikowski R, Hile GA, Harms PW, Jiang Y, Xing E, Nakamura M, Ochocki D, Brodie WD, Pillai S, Maverakis E, Pellegrini M, Modlin RL, Varga J, Tsoi LC, Lafyatis R, Kahlenberg JM, Billi AC, Khanna D, Gudjonsson JE. PMID: 38172207; PMCID: PMC10764940.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    30. Design and Construction of a Designed Ankyrin Repeat Protein (DARPin) Display Library. Curr Protoc. 2024 Jan; 4(1):e960. Morselli M, Holton TR, Pellegrini M, Yeates TO, Arbing MA. PMID: 38206591.
      View in: PubMed   Mentions: 2     Fields:    
    31. Exponential dynamics of DNA methylation with age. J Theor Biol. 2024 02 21; 579:111697. Dufek G, Katriel G, Snir S, Pellegrini M. PMID: 38142045.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    32. Fasting-Mimicking Diet Inhibits Autophagy and Synergizes with Chemotherapy to Promote T-Cell-Dependent Leukemia-Free Survival. Cancers (Basel). 2023 Dec 16; 15(24). Buono R, Tucci J, Cutri R, Guidi N, Mangul S, Raucci F, Pellegrini M, Mittelman SD, Longo VD. PMID: 38136414; PMCID: PMC10741737.
      View in: PubMed   Mentions: 1  
    33. Whole blood transcriptomics identifies subclasses of pediatric septic shock. Crit Care. 2023 12 08; 27(1):486. Yang JO, Zinter MS, Pellegrini M, Wong MY, Gala K, Markovic D, Nadel B, Peng K, Do N, Mangul S, Nadkarni VM, Karlsberg A, Deshpande D, Butte MJ, Asaro L, Agus M, Sapru A, Study Site Investigators for CAF-PINT. PMID: 38066613; PMCID: PMC10709863.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    34. Epigenetic aging in cows is accelerated by milk production. Epigenetics. 2023 12; 18(1):2240188. Ratan P, Rubbi L, Thompson M, Naresh K, Waddell J, Jones B, Pellegrini M. PMID: 37533239; PMCID: PMC10402850.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    35. Age-associated DNA methylation changes in Xenopus frogs. Epigenetics. 2023 12; 18(1):2201517. Morselli M, Bennett R, Shaidani NI, Horb M, Peshkin L, Pellegrini M. PMID: 37092296; PMCID: PMC10128463.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    36. Unlocking the potential of allogeneic Vδ2 T cells for ovarian cancer therapy through CD16 biomarker selection and CAR/IL-15 engineering. Nat Commun. 2023 11 08; 14(1):6942. Lee D, Dunn ZS, Guo W, Rosenthal CJ, Penn NE, Yu Y, Zhou K, Li Z, Ma F, Li M, Song TC, Cen X, Li YR, Zhou JJ, Pellegrini M, Wang P, Yang L. PMID: 37938576; PMCID: PMC10632431.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    37. A ketogenic diet can mitigate SARS-CoV-2 induced systemic reprogramming and inflammation. Commun Biol. 2023 11 03; 6(1):1115. Palermo A, Li S, Ten Hoeve J, Chellappa A, Morris A, Dillon B, Ma F, Wang Y, Cao E, Shabane B, Acín-Perez R, Petcherski A, Lusis AJ, Hazen S, Shirihai OS, Pellegrini M, Arumugaswami V, Graeber TG, Deb A. PMID: 37923961; PMCID: PMC10624922.
      View in: PubMed   Mentions: 1  Translation:AnimalsCells
    38. Distinct Features of Plasma Ultrashort Single-Stranded Cell-Free DNA as Biomarkers for Lung Cancer Detection. Clin Chem. 2023 11 02; 69(11):1270-1282. Cheng J, Swarup N, Li F, Kordi M, Lin CC, Yang SC, Huang WL, Aziz M, Kim Y, Chia D, Yeh YM, Wei F, Zheng D, Zhang L, Pellegrini M, Su WC, Wong DTW. PMID: 37725931; PMCID: PMC10644908.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    39. Rtf1-dependent transcriptional pausing regulates cardiogenesis. bioRxiv. 2023 Oct 15. Langenbacher AD, Lu F, Tsang L, Huang ZYS, Keer B, Tian Z, Eide A, Pellegrini M, Nakano H, Nakano A, Chen JN. PMID: 37873297; PMCID: PMC10592831.
      View in: PubMed   Mentions:
    40. Amnion responses to intrauterine inflammation and effects of inhibition of TNF signaling in preterm Rhesus macaque. iScience. 2023 Nov 17; 26(11):108118. Presicce P, Cappelletti M, Morselli M, Ma F, Senthamaraikannan P, Protti G, Nadel BB, Aryan L, Eghbali M, Salwinski L, Pithia N, De Franco E, Miller LA, Pellegrini M, Jobe AH, Chougnet CA, Kallapur SG. PMID: 37953944; PMCID: PMC10637919.
      View in: PubMed   Mentions: 1  
    41. The methylome of buccal epithelial cells is influenced by age, sex, and physiological properties. Physiol Genomics. 2023 Dec 01; 55(12):618-633. Protti G, Rubbi L, Gören T, Sabirli R, Civlan S, Kurt Ö, Türkçüer I, Köseler A, Pellegrini M. PMID: 37781740.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    42. IL-1β-mediated inflammatory signaling drives ineffective erythropoiesis in early-stage myelodysplastic syndromes. bioRxiv. 2023 Sep 30. Adema V, Ganan-Gomez I, Ma F, Rodriguez-Sevilla JJ, Chien K, Yang H, Thongon N, Kanagal-Shamanna R, Loghavi S, Montalban-Bravo G, Hammond D, Gu Y, Tan R, Tan L, Lorenzi P, Al-Atrash G, Clise-Dwyer K, Bejar R, Pellegrini M, Garcia-Manero G, Colla S. PMID: 37808770; PMCID: PMC10557725.
      View in: PubMed   Mentions:
    43. Fibroblasts in heart scar tissue directly regulate cardiac excitability and arrhythmogenesis. Science. 2023 09 29; 381(6665):1480-1487. Wang Y, Li Q, Tao B, Angelini M, Ramadoss S, Sun B, Wang P, Krokhaleva Y, Ma F, Gu Y, Espinoza A, Yamauchi K, Pellegrini M, Novitch B, Olcese R, Qu Z, Song Z, Deb A. PMID: 37769108; PMCID: PMC10768850.
      View in: PubMed   Mentions: 16     Fields:    Translation:AnimalsCells
    44. Whole Blood Transcriptomics Identifies Subclasses of Pediatric Septic Shock. Res Sq. 2023 Aug 28. Yang JO, Zinter MS, Pellegrini M, Wong MY, Gala K, Markovic D, Nadel B, Peng K, Do N, Mangul S, Nadkarni VM, Karlsberg A, Deshpande D, Butte MJ, Asaro L, Agus M, Sapru A. PMID: 37693502; PMCID: PMC10491329.
      View in: PubMed   Mentions:
    45. DNA methylation networks underlying mammalian traits. Science. 2023 08 11; 381(6658):eabq5693. Haghani A, Li CZ, Robeck TR, Zhang J, Lu AT, Ablaeva J, Acosta-Rodríguez VA, Adams DM, Alagaili AN, Almunia J, Aloysius A, Amor NMS, Ardehali R, Arneson A, Baker CS, Banks G, Belov K, Bennett NC, Black P, Blumstein DT, Bors EK, Breeze CE, Brooke RT, Brown JL, Carter G, Caulton A, Cavin JM, Chakrabarti L, Chatzistamou I, Chavez AS, Chen H, Cheng K, Chiavellini P, Choi OW, Clarke S, Cook JA, Cooper LN, Cossette ML, Day J, DeYoung J, Dirocco S, Dold C, Dunnum JL, Ehmke EE, Emmons CK, Emmrich S, Erbay E, Erlacher-Reid C, Faulkes CG, Fei Z, Ferguson SH, Finno CJ, Flower JE, Gaillard JM, Garde E, Gerber L, Gladyshev VN, Goya RG, Grant MJ, Green CB, Hanson MB, Hart DW, Haulena M, Herrick K, Hogan AN, Hogg CJ, Hore TA, Huang T, Izpisua Belmonte JC, Jasinska AJ, Jones G, Jourdain E, Kashpur O, Katcher H, Katsumata E, Kaza V, Kiaris H, Kobor MS, Kordowitzki P, Koski WR, Krützen M, Kwon SB, Larison B, Lee SG, Lehmann M, Lemaître JF, Levine AJ, Li X, Li C, Lim AR, Lin DTS, Lindemann DM, Liphardt SW, Little TJ, Macoretta N, Maddox D, Matkin CO, Mattison JA, McClure M, Mergl J, Meudt JJ, Montano GA, Mozhui K, Munshi-South J, Murphy WJ, Naderi A, Nagy M, Narayan P, Nathanielsz PW, Nguyen NB, Niehrs C, Nyamsuren B, O'Brien JK, Ginn PO, Odom DT, Ophir AG, Osborn S, Ostrander EA, Parsons KM, Paul KC, Pedersen AB, Pellegrini M, Peters KJ, Petersen JL, Pietersen DW, Pinho GM, Plassais J, Poganik JR, Prado NA, Reddy P, Rey B, Ritz BR, Robbins J, Rodriguez M, Russell J, Rydkina E, Sailer LL, Salmon AB, Sanghavi A, Schachtschneider KM, Schmitt D, Schmitt T, Schomacher L, Schook LB, Sears KE, Seifert AW, Shafer ABA, Shindyapina AV, Simmons M, Singh K, Sinha I, Slone J, Snell RG, Soltanmohammadi E, Spangler ML, Spriggs M, Staggs L, Stedman N, Steinman KJ, Stewart DT, Sugrue VJ, Szladovits B, Takahashi JS, Takasugi M, Teeling EC, Thompson MJ, Van Bonn B, Vernes SC, Villar D, Vinters HV, Vu H, Wallingford MC, Wang N, Wilkinson GS, Williams RW, Yan Q, Yao M, Young BG, Zhang B, Zhang Z, Zhao Y, Zhao P, Zhou W, Zoller JA, Ernst J, Seluanov A, Gorbunova V, Yang XW, Raj K, Horvath S. PMID: 37561875; PMCID: PMC11180965.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansAnimalsCells
    46. Pan-primate studies of age and sex. Geroscience. 2023 12; 45(6):3187-3209. Horvath S, Haghani A, Zoller JA, Lu AT, Ernst J, Pellegrini M, Jasinska AJ, Mattison JA, Salmon AB, Raj K, Horvath M, Paul KC, Ritz BR, Robeck TR, Spriggs M, Ehmke EE, Jenkins S, Li C, Nathanielsz PW. PMID: 37493860; PMCID: PMC10643767.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    47. Innate and adaptive AAV-mediated immune responses in a mouse model of Duchenne muscular dystrophy. Mol Ther Methods Clin Dev. 2023 Sep 14; 30:90-102. Emami MR, Espinoza A, Young CS, Ma F, Farahat PK, Felgner PL, Chamberlain JS, Xu X, Pyle AD, Pellegrini M, Villalta SA, Spencer MJ. PMID: 37746243; PMCID: PMC10512012.
      View in: PubMed   Mentions: 4  
    48. Single cell and spatial sequencing define processes by which keratinocytes and fibroblasts amplify inflammatory responses in psoriasis. Nat Commun. 2023 06 12; 14(1):3455. Ma F, Plazyo O, Billi AC, Tsoi LC, Xing X, Wasikowski R, Gharaee-Kermani M, Hile G, Jiang Y, Harms PW, Xing E, Kirma J, Xi J, Hsu JE, Sarkar MK, Chung Y, Di Domizio J, Gilliet M, Ward NL, Maverakis E, Klechevsky E, Voorhees JJ, Elder JT, Lee JH, Kahlenberg JM, Pellegrini M, Modlin RL, Gudjonsson JE. PMID: 37308489; PMCID: PMC10261041.
      View in: PubMed   Mentions: 38     Fields:    Translation:HumansCells
    49. Genetic architecture of heart mitochondrial proteome influencing cardiac hypertrophy. Elife. 2023 06 05; 12. Chella Krishnan K, El Hachem EJ, Keller MP, Patel SG, Carroll L, Vegas AD, Gerdes Gyuricza I, Light C, Cao Y, Pan C, Kaczor-Urbanowicz KE, Shravah V, Anum D, Pellegrini M, Lee CF, Seldin MM, Rosenthal NA, Churchill GA, Attie AD, Parker B, James DE, Lusis AJ. PMID: 37276142; PMCID: PMC10241513.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
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    101. Synergistic Effects of Genetic Variants of Glucose Homeostasis and Lifelong Exposures to Cigarette Smoking, Female Hormones, and Dietary Fat Intake on Primary Colorectal Cancer Development in African and Hispanic/Latino American Women. Front Oncol. 2021; 11:760243. Jung SY, Sobel EM, Pellegrini M, Yu H, Papp JC. PMID: 34692549; PMCID: PMC8529283.
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    102. Molecular Biology Networks and Key Gene Regulators for Inflammatory Biomarkers Shared by Breast Cancer Development: Multi-Omics Systems Analysis. Biomolecules. 2021 09 18; 11(9). Jung SY, Papp JC, Pellegrini M, Yu H, Sobel EM. PMID: 34572592; PMCID: PMC8469138.
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    103. The induction of preterm labor in rhesus macaques is determined by the  strength of immune response to intrauterine infection. PLoS Biol. 2021 09; 19(9):e3001385. Cappelletti M, Presicce P, Feiyang M, Senthamaraikannan P, Miller LA, Pellegrini M, Sim MS, Jobe AH, Divanovic S, Way SS, Chougnet CA, Kallapur SG. PMID: 34495952; PMCID: PMC8452070.
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    104. Identification of Genes Encoding Antimicrobial Proteins in Langerhans Cells. Front Immunol. 2021; 12:695373. Oulee A, Ma F, Teles RMB, de Andrade Silva BJ, Pellegrini M, Klechevsky E, Harman AN, Rhodes JW, Modlin RL. PMID: 34512625; PMCID: PMC8426439.
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    105. NOTUM promotes thermogenic capacity and protects against diet-induced obesity in male mice. Sci Rep. 2021 08 12; 11(1):16409. Guo F, Seldin M, Péterfy M, Charugundla S, Zhou Z, Lee SD, Mouton A, Rajbhandari P, Zhang W, Pellegrini M, Tontonoz P, Lusis AJ, Shih DM. PMID: 34385484; PMCID: PMC8361163.
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    106. Early adaptive chromatin remodeling events precede pathologic phenotypes and are reinforced in the failing heart. J Mol Cell Cardiol. 2021 11; 160:73-86. Chapski DJ, Cabaj M, Morselli M, Mason RJ, Soehalim E, Ren S, Pellegrini M, Wang Y, Vondriska TM, Rosa-Garrido M. PMID: 34273410; PMCID: PMC9181638.
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    107. The cellular architecture of the antimicrobial response network in human leprosy granulomas. Nat Immunol. 2021 07; 22(7):839-850. Ma F, Hughes TK, Teles RMB, Andrade PR, de Andrade Silva BJ, Plazyo O, Tsoi LC, Do T, Wadsworth MH, Oulee A, Ochoa MT, Sarno EN, Iruela-Arispe ML, Klechevsky E, Bryson B, Shalek AK, Bloom BR, Gudjonsson JE, Pellegrini M, Modlin RL. PMID: 34168371; PMCID: PMC8579511.
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    108. Targeting monoamine oxidase A-regulated tumor-associated macrophage polarization for cancer immunotherapy. Nat Commun. 2021 06 10; 12(1):3530. Wang YC, Wang X, Yu J, Ma F, Li Z, Zhou Y, Zeng S, Ma X, Li YR, Neal A, Huang J, To A, Clarke N, Memarzadeh S, Pellegrini M, Yang L. PMID: 34112755; PMCID: PMC8192781.
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    109. Single-cell RNA sequencing of batch Chlamydomonas cultures reveals heterogeneity in their diurnal cycle phase. Plant Cell. 2021 05 31; 33(4):1042-1057. Ma F, Salomé PA, Merchant SS, Pellegrini M. PMID: 33585940; PMCID: PMC8226295.
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    110. Targeting monoamine oxidase A for T cell-based cancer immunotherapy. Sci Immunol. 2021 05 14; 6(59). Wang X, Li B, Kim YJ, Wang YC, Li Z, Yu J, Zeng S, Ma X, Choi IY, Di Biase S, Smith DJ, Zhou Y, Li YR, Ma F, Huang J, Clarke N, To A, Gong L, Pham AT, Moon H, Pellegrini M, Yang L. PMID: 33990379.
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    111. Single Cell Transcriptomic Analyses Reveal the Impact of bHLH Factors on Human Retinal Organoid Development. Front Cell Dev Biol. 2021; 9:653305. Zhang X, Mandric I, Nguyen KH, Nguyen TTT, Pellegrini M, Grove JCR, Barnes S, Yang XJ. PMID: 34055784; PMCID: PMC8155690.
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    112. BiSulfite Bolt: A bisulfite sequencing analysis platform. Gigascience. 2021 05 08; 10(5). Farrell C, Thompson M, Tosevska A, Oyetunde A, Pellegrini M. PMID: 33966074; PMCID: PMC8106542.
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    113. Single-cell sequencing of human white adipose tissue identifies new cell states in health and obesity. Nat Immunol. 2021 05; 22(5):639-653. Hildreth AD, Ma F, Wong YY, Sun R, Pellegrini M, O'Sullivan TE. PMID: 33907320; PMCID: PMC8102391.
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    114. GLUT1 overexpression enhances glucose metabolism and promotes neonatal heart regeneration. Sci Rep. 2021 04 21; 11(1):8669. Fajardo VM, Feng I, Chen BY, Perez-Ramirez CA, Shi B, Clark P, Tian R, Lien CL, Pellegrini M, Christofk H, Nakano H, Nakano A. PMID: 33883682; PMCID: PMC8060418.
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    115. Genetically determined elevated C-reactive protein associated with primary colorectal cancer risk: Mendelian randomization with lifestyle interactions. Am J Cancer Res. 2021; 11(4):1733-1753. Jung SY, Yu H, Pellegrini M, Papp JC, Sobel EM, Zhang ZF. PMID: 33948386; PMCID: PMC8085861.
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    116. IRAK2 Has a Critical Role in Promoting Feed-Forward Amplification of Epidermal Inflammatory Responses. J Invest Dermatol. 2021 10; 141(10):2436-2448. Shao S, Tsoi LC, Swindell WR, Chen J, Uppala R, Billi AC, Xing X, Zeng C, Sarkar MK, Wasikowski R, Jiang Y, Kirma J, Sun J, Plazyo O, Wang G, Harms PW, Voorhees JJ, Ward NL, Ma F, Pellegrini M, Merleev A, Perez White BE, Modlin RL, Andersen B, Maverakis E, Weidinger S, Kahlenberg JM, Gudjonsson JE. PMID: 33864770; PMCID: PMC9423738.
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    117. Species-Specific Relationships between DNA and Chromatin Properties of CpG Islands in Embryonic Stem Cells and Differentiated Cells. Stem Cell Reports. 2021 04 13; 16(4):899-912. Langerman J, Lopez D, Pellegrini M, Smale ST. PMID: 33770494; PMCID: PMC8072027.
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    118. Human DNA methylation signatures differentiate persistent from resolving MRSA bacteremia. Proc Natl Acad Sci U S A. 2021 03 09; 118(10). Chang YL, Rossetti M, Gjertson DW, Rubbi L, Thompson M, Montoya DJ, Morselli M, Ruffin F, Hoffmann A, Pellegrini M, Fowler VG, Yeaman MR, Reed EF, with the MRSA Systems Immunology Group. PMID: 33649198; PMCID: PMC7958259.
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    119. The Gene Expression Deconvolution Interactive Tool (GEDIT): accurate cell type quantification from gene expression data. Gigascience. 2021 02 16; 10(2). Nadel BB, Lopez D, Montoya DJ, Ma F, Waddel H, Khan MM, Mangul S, Pellegrini M. PMID: 33590863; PMCID: PMC7931818.
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    120. Comparative analysis of embryo proper and suspensor transcriptomes in plant embryos with different morphologies. Proc Natl Acad Sci U S A. 2021 02 09; 118(6). Chen M, Lin JY, Wu X, Apuya NR, Henry KF, Le BH, Bui AQ, Pelletier JM, Cokus S, Pellegrini M, Harada JJ, Goldberg RB. PMID: 33536344; PMCID: PMC8017943.
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    121. Genetically Predicted C-Reactive Protein Associated With Postmenopausal Breast Cancer Risk: Interrelation With Estrogen and Cancer Molecular Subtypes Using Mendelian Randomization. Front Oncol. 2020; 10:630994. Jung SY, Papp JC, Sobel EM, Pellegrini M, Yu H, Zhang ZF. PMID: 33614510; PMCID: PMC7888276.
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    122. Integrative analysis of chloroplast DNA methylation in a marine alga-Saccharina japonica. Plant Mol Biol. 2021 Apr; 105(6):611-623. Teng L, Han W, Fan X, Zhang X, Xu D, Wang Y, Rahman S, Pellegrini M, Mock T, Ye N. PMID: 33528753.
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    123. Metabolic reprogramming and epigenetic changes of vital organs in SARS-CoV-2-induced systemic toxicity. JCI Insight. 2021 01 25; 6(2). Li S, Ma F, Yokota T, Garcia G, Palermo A, Wang Y, Farrell C, Wang YC, Wu R, Zhou Z, Pan C, Morselli M, Teitell MA, Ryazantsev S, Fishbein GA, Hoeve JT, Arboleda VA, Bloom J, Dillon B, Pellegrini M, Lusis AJ, Graeber TG, Arumugaswami V, Deb A. PMID: 33284134; PMCID: PMC7934846.
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    124. Extracellular traps released by antimicrobial TH17 cells contribute to host defense. J Clin Invest. 2021 01 19; 131(2). Agak GW, Mouton A, Teles RM, Weston T, Morselli M, Andrade PR, Pellegrini M, Modlin RL. PMID: 33211671; PMCID: PMC7810473.
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    125. Pro-inflammatory cytokine polymorphisms and interactions with dietary alcohol and estrogen, risk factors for invasive breast cancer using a post genome-wide analysis for gene-gene and gene-lifestyle interaction. Sci Rep. 2021 01 13; 11(1):1058. Jung SY, Papp JC, Sobel EM, Pellegrini M, Yu H, Zhang ZF. PMID: 33441805; PMCID: PMC7807068.
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    126. Inhibition of microbiota-dependent TMAO production attenuates chronic kidney disease in mice. Sci Rep. 2021 01 12; 11(1):518. Zhang W, Miikeda A, Zuckerman J, Jia X, Charugundla S, Zhou Z, Kaczor-Urbanowicz KE, Magyar C, Guo F, Wang Z, Pellegrini M, Hazen SL, Nicholas SB, Lusis AJ, Shih DM. PMID: 33436815; PMCID: PMC7804188.
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    127. Cardiac fibroblast proliferation rates and collagen expression mature early and are unaltered with advancing age. JCI Insight. 2020 12 17; 5(24). Wu R, Ma F, Tosevska A, Farrell C, Pellegrini M, Deb A. PMID: 33180747; PMCID: PMC7819745.
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    128. Towards a unified open access dataset of molecular interactions. Nat Commun. 2020 12 01; 11(1):6144. Porras P, Barrera E, Bridge A, Del-Toro N, Cesareni G, Duesbury M, Hermjakob H, Iannuccelli M, Jurisica I, Kotlyar M, Licata L, Lovering RC, Lynn DJ, Meldal B, Nanduri B, Paneerselvam K, Panni S, Pastrello C, Pellegrini M, Perfetto L, Rahimzadeh N, Ratan P, Ricard-Blum S, Salwinski L, Shirodkar G, Shrivastava A, Orchard S. PMID: 33262342; PMCID: PMC7708836.
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    129. Dynamic changes in chromatin accessibility, altered adipogenic gene expression, and total versus de novo fatty acid synthesis in subcutaneous adipose stem cells of normal-weight polycystic ovary syndrome (PCOS) women during adipogenesis: evidence of cellular programming. Clin Epigenetics. 2020 11 23; 12(1):181. Leung KL, Sanchita S, Pham CT, Davis BA, Okhovat M, Ding X, Dumesic P, Grogan TR, Williams KJ, Morselli M, Ma F, Carbone L, Li X, Pellegrini M, Dumesic DA, Chazenbalk GD. PMID: 33228780; PMCID: PMC7686698.
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    130. A High-Content Screen Identifies Drugs That Restrict Tumor Cell Extravasation across the Endothelial Barrier. Cancer Res. 2021 02 01; 81(3):619-633. Hilfenhaus G, Mompeón A, Freshman J, Prajapati DP, Hernandez G, Freitas VM, Ma F, Langenbacher AD, Mirkov S, Song D, Cho BK, Goo YA, Pellegrini M, Chen JN, Damoiseaux R, Iruela-Arispe ML. PMID: 33218969; PMCID: PMC7916904.
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    131. β-Globin Lentiviral Vectors Have Reduced Titers due to Incomplete Vector RNA Genomes and Lowered Virion Production. Stem Cell Reports. 2021 01 12; 16(1):198-211. Han J, Tam K, Ma F, Tam C, Aleshe B, Wang X, Quintos JP, Morselli M, Pellegrini M, Hollis RP, Kohn DB. PMID: 33186538; PMCID: PMC7897704.
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    132. A rat epigenetic clock recapitulates phenotypic aging and co-localizes with heterochromatin. Elife. 2020 11 12; 9. Levine M, McDevitt RA, Meer M, Perdue K, Di Francesco A, Meade T, Farrell C, Thrush K, Wang M, Dunn C, Pellegrini M, de Cabo R, Ferrucci L. PMID: 33179594; PMCID: PMC7661040.
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    133. X chromosome dosage of histone demethylase KDM5C determines sex differences in adiposity. J Clin Invest. 2020 11 02; 130(11):5688-5702. Link JC, Wiese CB, Chen X, Avetisyan R, Ronquillo E, Ma F, Guo X, Yao J, Allison M, Chen YI, Rotter JI, El-Sayed Moustafa JS, Small KS, Iwase S, Pellegrini M, Vergnes L, Arnold AP, Reue K. PMID: 32701509; PMCID: PMC7598065.
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    134. The Epigenetic Pacemaker: modeling epigenetic states under an evolutionary framework. Bioinformatics. 2020 11 01; 36(17):4662-4663. Farrell C, Snir S, Pellegrini M. PMID: 32573701; PMCID: PMC7750963.
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    135. Cell-free DNA Methylation and Transcriptomic Signature Prediction of Pregnancies with Adverse Outcomes. Epigenetics. 2021 06; 16(6):642-661. Del Vecchio G, Li Q, Li W, Thamotharan S, Tosevska A, Morselli M, Sung K, Janzen C, Zhou X, Pellegrini M, Devaskar SU. PMID: 33045922; PMCID: PMC8143248.
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    136. Dysregulation of hsa-miR-34a and hsa-miR-449a leads to overexpression of PACS-1 and loss of DNA damage response (DDR) in cervical cancer. J Biol Chem. 2020 12 11; 295(50):17169-17186. Veena MS, Raychaudhuri S, Basak SK, Venkatesan N, Kumar P, Biswas R, Chakrabarti R, Lu J, Su T, Gallagher-Jones M, Morselli M, Fu H, Pellegrini M, Goldstein T, Aladjem MI, Rettig MB, Wilczynski SP, Shin DS, Srivatsan ES. PMID: 33028635; PMCID: PMC7863911.
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    137. Transcriptome Profiling of Human Monocyte-Derived Macrophages Upon CCL2 Neutralization Reveals an Association Between Activation of Innate Immune Pathways and Restriction of HIV-1 Gene Expression. Front Immunol. 2020; 11:2129. Covino DA, Kaczor-Urbanowicz KE, Lu J, Chiantore MV, Fiorucci G, Vescio MF, Catapano L, Purificato C, Galluzzo CM, Amici R, Andreotti M, Gauzzi MC, Pellegrini M, Fantuzzi L. PMID: 33072075; PMCID: PMC7531389.
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    138. Integrative Analysis of Glucometabolic Traits, Adipose Tissue DNA Methylation, and Gene Expression Identifies Epigenetic Regulatory Mechanisms of Insulin Resistance and Obesity in African Americans. Diabetes. 2020 12; 69(12):2779-2793. Sharma NK, Comeau ME, Montoya D, Pellegrini M, Howard TD, Langefeld CD, Das SK. PMID: 32928872; PMCID: PMC7679782.
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    139. Genome-wide Association Analysis of Proinflammatory Cytokines and Gene-lifestyle Interaction for Invasive Breast Cancer Risk: The WHI dbGaP Study. Cancer Prev Res (Phila). 2021 01; 14(1):41-54. Jung SY, Scott PA, Papp JC, Sobel EM, Pellegrini M, Yu H, Han S, Zhang ZF. PMID: 32928877; PMCID: PMC7956151.
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    140. Pro-inflammatory cytokine polymorphisms in ONECUT2 and HNF4A and primary colorectal carcinoma: a post genome-wide gene-lifestyle interaction study. Am J Cancer Res. 2020; 10(9):2955-2976. Jung SY, Papp JC, Sobel EM, Pellegrini M, Yu H, Zhang ZF. PMID: 33042629; PMCID: PMC7539781.
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    141. Targeted bisulfite sequencing for biomarker discovery. Methods. 2021 03; 187:13-27. Morselli M, Farrell C, Rubbi L, Fehling HL, Henkhaus R, Pellegrini M. PMID: 32755621; PMCID: PMC7855209.
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    142. Epigenetic Suppression of Transgenic T-cell Receptor Expression via Gamma-Retroviral Vector Methylation in Adoptive Cell Transfer Therapy. Cancer Discov. 2020 11; 10(11):1645-1653. Nowicki TS, Farrell C, Morselli M, Rubbi L, Campbell KM, Macabali MH, Berent-Maoz B, Comin-Anduix B, Pellegrini M, Ribas A. PMID: 32699033; PMCID: PMC7641915.
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    143. Type V Collagen in Scar Tissue Regulates the Size of Scar after Heart Injury. Cell. 2020 08 06; 182(3):545-562.e23. Yokota T, McCourt J, Ma F, Ren S, Li S, Kim TH, Kurmangaliyev YZ, Nasiri R, Ahadian S, Nguyen T, Tan XHM, Zhou Y, Wu R, Rodriguez A, Cohn W, Wang Y, Whitelegge J, Ryazantsev S, Khademhosseini A, Teitell MA, Chiou PY, Birk DE, Rowat AC, Crosbie RH, Pellegrini M, Seldin M, Lusis AJ, Deb A. PMID: 32621799; PMCID: PMC7415659.
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    144. Omega-3 fatty acids increase OXPHOS energy for immune therapy of Alzheimer disease patients. FASEB J. 2020 08; 34(8):9982-9994. Lau YCC, Ding JA, Simental A, Mirzoyan H, Lee W, Diamante G, Cely I, Tran M, Morselli M, Dang J, Kaczor-Urbanowicz KE, Sayre J, Stiles L, Yang X, Pellegrini M, Fiala M. PMID: 32614485.
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    145. Effects of sulforaphane on the oxidative response, apoptosis, and the transcriptional profile of human stomach mucosa cells in vitro. Mutat Res Genet Toxicol Environ Mutagen. 2020 Jun - Jul; 854-855:503201. Santos PW, Machado ART, De Grandis R, Ribeiro DL, Tuttis K, Morselli M, Aissa AF, Pellegrini M, Antunes LMG. PMID: 32660825.
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    146. EMP2 Is a Novel Regulator of Stemness in Breast Cancer Cells. Mol Cancer Ther. 2020 08; 19(8):1682-1695. Dillard C, Kiyohara M, Mah V, McDermott SP, Bazzoun D, Tsui J, Chan AM, Haddad G, Pellegrini M, Chang YL, Elshimali Y, Wu Y, Vadgama JV, Kim SR, Goodglick L, Law SM, Patel DD, Dhawan P, O'Brien NA, Gordon LK, Braun J, Lazar G, Wicha MS, Wadehra M. PMID: 32451329; PMCID: PMC7415657.
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    147. Phenotypic and functional characterization of corneal endothelial cells during in vitro expansion. Sci Rep. 2020 05 04; 10(1):7402. Frausto RF, Swamy VS, Peh GSL, Boere PM, Hanser EM, Chung DD, George BL, Morselli M, Kao L, Azimov R, Wu J, Pellegrini M, Kurtz I, Mehta JS, Aldave AJ. PMID: 32366916; PMCID: PMC7198491.
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    148. The dopamine receptor antagonist trifluoperazine prevents phenotype conversion and improves survival in mouse models of glioblastoma. Proc Natl Acad Sci U S A. 2020 05 19; 117(20):11085-11096. Bhat K, Saki M, Vlashi E, Cheng F, Duhachek-Muggy S, Alli C, Yu G, Medina P, He L, Damoiseaux R, Pellegrini M, Zemke NR, Nghiemphu PL, Cloughesy TF, Liau LM, Kornblum HI, Pajonk F. PMID: 32358191; PMCID: PMC7245100.
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    149. Molecular signatures for inflammation vary across cancer types and correlate significantly with tumor stage, sex and vital status of patients. PLoS One. 2020; 15(4):e0221545. So AR, Si JM, Lopez D, Pellegrini M. PMID: 32330128; PMCID: PMC7182171.
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    150. Impacts of ciliary neurotrophic factor on the retinal transcriptome in a mouse model of photoreceptor degeneration. Sci Rep. 2020 04 20; 10(1):6593. Wang Y, Rhee KD, Pellegrini M, Yang XJ. PMID: 32313077; PMCID: PMC7171121.
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    151. Creating New β-Globin-Expressing Lentiviral Vectors by High-Resolution Mapping of Locus Control Region Enhancer Sequences. Mol Ther Methods Clin Dev. 2020 Jun 12; 17:999-1013. Morgan RA, Ma F, Unti MJ, Brown D, Ayoub PG, Tam C, Lathrop L, Aleshe B, Kurita R, Nakamura Y, Senadheera S, Wong RL, Hollis RP, Pellegrini M, Kohn DB. PMID: 32426415; PMCID: PMC7225380.
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    152. ER Stress Regulates Immunosuppressive Function of Myeloid Derived Suppressor Cells in Leprosy that Can Be Overcome in the Presence of IFN-γ. iScience. 2020 May 22; 23(5):101050. Kelly-Scumpia KM, Choi A, Shirazi R, Bersabe H, Park E, Scumpia PO, Ochoa MT, Yu J, Ma F, Pellegrini M, Modlin RL. PMID: 32339990; PMCID: PMC7190750.
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    153. TNF-Signaling Modulates Neutrophil-Mediated Immunity at the Feto-Maternal Interface During LPS-Induced Intrauterine Inflammation. Front Immunol. 2020; 11:558. Presicce P, Cappelletti M, Senthamaraikannan P, Ma F, Morselli M, Jackson CM, Mukherjee S, Miller LA, Pellegrini M, Jobe AH, Chougnet CA, Kallapur SG. PMID: 32308656; PMCID: PMC7145904.
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    154. Expression of Stromal Progesterone Receptor and Differential Methylation Patterns in the Endometrium May Correlate with Response to Progesterone Therapy in Endometrial Complex Atypical Hyperplasia. Reprod Sci. 2020 09; 27(9):1778-1790. Neal AS, Nunez M, Lai T, Tosevska A, Morselli M, Amneus M, Zakhour M, Moatamed NA, Pellegrini M, Memarzadeh S. PMID: 32124398; PMCID: PMC7395059.
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    155. Cellular, Molecular, and Immunological Characteristics of Langhans Multinucleated Giant Cells Programmed by IL-15. J Invest Dermatol. 2020 09; 140(9):1824-1836.e7. Wang H, Jiang H, Teles RMB, Chen Y, Wu A, Lu J, Chen Z, Ma F, Pellegrini M, Modlin RL. PMID: 32092350; PMCID: PMC8223586.
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    156. A randomized, phase 1, placebo-controlled trial of APG-157 in oral cancer demonstrates systemic absorption and an inhibitory effect on cytokines and tumor-associated microbes. Cancer. 2020 04 15; 126(8):1668-1682. Basak SK, Bera A, Yoon AJ, Morselli M, Jeong C, Tosevska A, Dong TS, Eklund M, Russ E, Nasser H, Lagishetty V, Guo R, Sajed D, Mudgal S, Mehta P, Avila L, Srivastava M, Faull K, Jacobs J, Pellegrini M, Shin DS, Srivatsan ES, Wang MB. PMID: 32022261.
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    157. ACTINN: automated identification of cell types in single cell RNA sequencing. Bioinformatics. 2020 01 15; 36(2):533-538. Ma F, Pellegrini M. PMID: 31359028.
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    158. Telescope: an interactive tool for managing large-scale analysis from mobile devices. Gigascience. 2020 01 01; 9(1). Brito JJ, Mosqueiro T, Rotman J, Xue V, Chapski DJ, la Hoz J, Matias P, Martin LS, Zelikovsky A, Pellegrini M, Mangul S. PMID: 31972019; PMCID: PMC6977584.
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    159. Genome-wide DNA Methylation Profiling of Blood from Monozygotic Twins Discordant for Myocardial Infarction. In Vivo. 2020 Jan-Feb; 34(1):361-367. Koseler A, Ma F, Kilic ID, Morselli M, Kilic O, Pellegrini M. PMID: 31882500; PMCID: PMC6984093.
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    160. Omega-3 Fatty Acids Increase Amyloid-β Immunity, Energy, and Circadian Rhythm for Cognitive Protection of Alzheimer's Disease Patients Beyond Cholinesterase Inhibitors. J Alzheimers Dis. 2020; 75(3):993-1002. Fiala M, Lau YCC, Aghajani A, Bhargava S, Aminpour E, Kaczor-Urbanowicz KE, Mirzoyan H, Nichols I, Ko MW, Morselli M, Santana J, Dang J, Sayre J, Paul K, Pellegrini M. PMID: 32390637; PMCID: PMC10190202.
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    161. DNA Methylation Changes More Slowly Than Physiological States in Response to Weight Loss in Genetically Diverse Mouse Strains. Front Endocrinol (Lausanne). 2019; 10:882. Edillor CR, Parks BW, Mehrabian M, Lusis AJ, Pellegrini M. PMID: 31920990; PMCID: PMC6933503.
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    162. Transcriptome and DNA methylation changes modulated by sulforaphane induce cell cycle arrest, apoptosis, DNA damage, and suppression of proliferation in human liver cancer cells. Food Chem Toxicol. 2020 Feb; 136:111047. Dos Santos PWDS, Machado ART, De Grandis RA, Ribeiro DL, Tuttis K, Morselli M, Aissa AF, Pellegrini M, Antunes LMG. PMID: 31838189.
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    163. Activation of the HIF1α/PFKFB3 stress response pathway in beta cells in type 1 diabetes. Diabetologia. 2020 01; 63(1):149-161. Nomoto H, Pei L, Montemurro C, Rosenberger M, Furterer A, Coppola G, Nadel B, Pellegrini M, Gurlo T, Butler PC, Tudzarova S. PMID: 31720731; PMCID: PMC6945783.
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    164. Identification of a systemic interferon-γ inducible antimicrobial gene signature in leprosy patients undergoing reversal reaction. PLoS Negl Trop Dis. 2019 10; 13(10):e0007764. Teles RMB, Lu J, Tió-Coma M, Goulart IMB, Banu S, Hagge D, Bobosha K, Ottenhoff THM, Pellegrini M, Geluk A, Modlin RL. PMID: 31600201; PMCID: PMC6805014.
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    165. The size of cell-free mitochondrial DNA in blood is inversely correlated with tumor burden in cancer patients. Precis Clin Med. 2019 Sep; 2(3):131-139. An Q, Hu Y, Li Q, Chen X, Huang J, Pellegrini M, Zhou XJ, Rettig M, Fan G. PMID: 31598384; PMCID: PMC6770274.
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    166. Single-base methylome profiling of the giant kelp Saccharina japonica reveals significant differences in DNA methylation to microalgae and plants. New Phytol. 2020 Jan; 225(1):234-249. Fan X, Han W, Teng L, Jiang P, Zhang X, Xu D, Li C, Pellegrini M, Wu C, Wang Y, Kaczurowski MJS, Lin X, Tirichine L, Mock T, Ye N. PMID: 31419316; PMCID: PMC6916402.
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    167. Interactions between core histone marks and DNA methyltransferases predict DNA methylation patterns observed in human cells and tissues. Epigenetics. 2020 03; 15(3):272-282. Fu K, Bonora G, Pellegrini M. PMID: 31509087; PMCID: PMC7028327.
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    168. An in situ high-throughput screen identifies inhibitors of intracellular Burkholderia pseudomallei with therapeutic efficacy. Proc Natl Acad Sci U S A. 2019 09 10; 116(37):18597-18606. Bulterys PL, Toesca IJ, Norris MH, Maloy JP, Fitz-Gibbon ST, France B, Toffig B, Morselli M, Somprasong N, Pellegrini M, Schweizer HP, Tuanyok A, Damoiseaux R, French CT, Miller JF. PMID: 31439817; PMCID: PMC6744847.
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    169. Functional reprogramming of regulatory T cells in the absence of Foxp3. Nat Immunol. 2019 09; 20(9):1208-1219. Charbonnier LM, Cui Y, Stephen-Victor E, Harb H, Lopez D, Bleesing JJ, Garcia-Lloret MI, Chen K, Ozen A, Carmeliet P, Li MO, Pellegrini M, Chatila TA. PMID: 31384057; PMCID: PMC6707855.
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    170. The cell fate regulator NUPR1 is induced by Mycobacterium leprae via type I interferon in human leprosy. PLoS Negl Trop Dis. 2019 07; 13(7):e0007589. R Andrade P, Mehta M, Lu J, M B Teles R, Montoya D, O Scumpia P, Nunes Sarno E, Ochoa MT, Ma F, Pellegrini M, Modlin RL. PMID: 31344041; PMCID: PMC6684084.
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    171. The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata. BMC Genomics. 2019 Jul 23; 20(1):605. Armaleo D, Müller O, Lutzoni F, Andrésson ÓS, Blanc G, Bode HB, Collart FR, Dal Grande F, Dietrich F, Grigoriev IV, Joneson S, Kuo A, Larsen PE, Logsdon JM, Lopez D, Martin F, May SP, McDonald TR, Merchant SS, Miao V, Morin E, Oono R, Pellegrini M, Rubinstein N, Sanchez-Puerta MV, Savelkoul E, Schmitt I, Slot JC, Soanes D, Szövényi P, Talbot NJ, Veneault-Fourrey C, Xavier BB. PMID: 31337355; PMCID: PMC6652019.
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    172. Alu RNA Modulates the Expression of Cell Cycle Genes in Human Fibroblasts. Int J Mol Sci. 2019 Jul 05; 20(13). Cantarella S, Carnevali D, Morselli M, Conti A, Pellegrini M, Montanini B, Dieci G. PMID: 31284509; PMCID: PMC6651528.
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    173. H3K36 Methylation and the Chromodomain Protein Eaf3 Are Required for Proper Cotranscriptional Spliceosome Assembly. Cell Rep. 2019 06 25; 27(13):3760-3769.e4. Leung CS, Douglass SM, Morselli M, Obusan MB, Pavlyukov MS, Pellegrini M, Johnson TL. PMID: 31242410; PMCID: PMC6904931.
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    174. IL-1β Induces the Rapid Secretion of the Antimicrobial Protein IL-26 from Th17 Cells. J Immunol. 2019 08 15; 203(4):911-921. Weiss DI, Ma F, Merleev AA, Maverakis E, Gilliet M, Balin SJ, Bryson BD, Ochoa MT, Pellegrini M, Bloom BR, Modlin RL. PMID: 31235553; PMCID: PMC6684376.
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    175. ZEB1 insufficiency causes corneal endothelial cell state transition and altered cellular processing. PLoS One. 2019; 14(6):e0218279. Frausto RF, Chung DD, Boere PM, Swamy VS, Duong HNV, Kao L, Azimov R, Zhang W, Carrigan L, Wong D, Morselli M, Zakharevich M, Hanser EM, Kassels AC, Kurtz I, Pellegrini M, Aldave AJ. PMID: 31194824; PMCID: PMC6564028.
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    176. Human epigenetic ageing is logarithmic with time across the entire lifespan. Epigenetics. 2019 09; 14(9):912-926. Snir S, Farrell C, Pellegrini M. PMID: 31138013; PMCID: PMC6691990.
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    177. Correction: CRACR2A-Mediated TCR Signaling Promotes Local Effector Th1 and Th17 Responses. J Immunol. 2019 Jul 01; 203(1):293. Woo JS, Srikanth S, Kim KD, Elsaesser H, Lu J, Pellegrini M, Brooks DG, Sun Z, Gwack Y. PMID: 31127031.
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    178. DNA methylation estimation using methylation-sensitive restriction enzyme bisulfite sequencing (MREBS). PLoS One. 2019; 14(4):e0214368. Bonora G, Rubbi L, Morselli M, Ma F, Chronis C, Plath K, Pellegrini M. PMID: 30946758; PMCID: PMC6448829.
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    179. Dual RNA-Seq of Human Leprosy Lesions Identifies Bacterial Determinants Linked to Host Immune Response. Cell Rep. 2019 03 26; 26(13):3574-3585.e3. Montoya DJ, Andrade P, Silva BJA, Teles RMB, Ma F, Bryson B, Sadanand S, Noel T, Lu J, Sarno E, Arnvig KB, Young D, Lahiri R, Williams DL, Fortune S, Bloom BR, Pellegrini M, Modlin RL. PMID: 30917313; PMCID: PMC6508871.
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    180. Endocardially Derived Macrophages Are Essential for Valvular Remodeling. Dev Cell. 2019 03 11; 48(5):617-630.e3. Shigeta A, Huang V, Zuo J, Besada R, Nakashima Y, Lu Y, Ding Y, Pellegrini M, Kulkarni RP, Hsiai T, Deb A, Zhou B, Nakano H, Nakano A. PMID: 30799229; PMCID: PMC6440481.
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    181. A comparison between whole transcript and 3' RNA sequencing methods using Kapa and Lexogen library preparation methods. BMC Genomics. 2019 Jan 07; 20(1):9. Ma F, Fuqua BK, Hasin Y, Yukhtman C, Vulpe CD, Lusis AJ, Pellegrini M. PMID: 30616562; PMCID: PMC6323698.
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    182. Comparison of reprogramming factor targets reveals both species-specific and conserved mechanisms in early iPSC reprogramming. BMC Genomics. 2018 Dec 22; 19(1):956. Fu K, Chronis C, Soufi A, Bonora G, Edwards M, Smale ST, Zaret KS, Plath K, Pellegrini M. PMID: 30577748; PMCID: PMC6303873.
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    183. Plasticity of antimicrobial and phagocytic programs in human macrophages. Immunology. 2019 02; 156(2):164-173. Montoya D, Mehta M, Ferguson BG, Teles RMB, Krutzik SR, Cruz D, Pellegrini M, Modlin RL. PMID: 30357820; PMCID: PMC6328994.
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    184. A phylogenomic study quantifies competing mechanisms for pseudogenization in prokaryotes-The Mycobacterium leprae case. PLoS One. 2018; 13(11):e0204322. Avni E, Montoya D, Lopez D, Modlin R, Pellegrini M, Snir S. PMID: 30383852; PMCID: PMC6211624.
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    185. A multi-tissue full lifespan epigenetic clock for mice. Aging (Albany NY). 2018 10 21; 10(10):2832-2854. Thompson MJ, Chwialkowska K, Rubbi L, Lusis AJ, Davis RC, Srivastava A, Korstanje R, Churchill GA, Horvath S, Pellegrini M. PMID: 30348905; PMCID: PMC6224226.
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    186. A temporal transcriptome and methylome in human embryonic stem cell-derived cardiomyocytes identifies novel regulators of early cardiac development. Epigenetics. 2018; 13(10-11):1013-1026. Fu K, Nakano H, Morselli M, Chen T, Pappoe H, Nakano A, Pellegrini M. PMID: 30240284; PMCID: PMC6342070.
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    187. Metabolic repair through emergence of new pathways in Escherichia coli. Nat Chem Biol. 2018 11; 14(11):1005-1009. Pontrelli S, Fricke RCB, Teoh ST, Laviña WA, Putri SP, Fitz-Gibbon S, Chung M, Pellegrini M, Fukusaki E, Liao JC. PMID: 30327558.
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    188. Author Correction: Synaptic N6-methyladenosine (m6A) epitranscriptome reveals functional partitioning of localized transcripts. Nat Neurosci. 2018 Oct; 21(10):1493. Merkurjev D, Hong WT, Iida K, Oomoto I, Goldie BJ, Yamaguti H, Ohara T, Kawaguchi SY, Hirano T, Martin KC, Pellegrini M, Wang DO. PMID: 30097659.
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    189. Transposon-associated epigenetic silencing during Pleurotus ostreatus life cycle. DNA Res. 2018 Oct 01; 25(5):451-464. Borgognone A, Castanera R, Morselli M, López-Varas L, Rubbi L, Pisabarro AG, Pellegrini M, Ramírez L. PMID: 29893819; PMCID: PMC6191308.
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    190. Human antimicrobial cytotoxic T lymphocytes, defined by NK receptors and antimicrobial proteins, kill intracellular bacteria. Sci Immunol. 2018 08 31; 3(26). Balin SJ, Pellegrini M, Klechevsky E, Won ST, Weiss DI, Choi AW, Hakimian J, Lu J, Ochoa MT, Bloom BR, Lanier LL, Stenger S, Modlin RL. PMID: 30171080; PMCID: PMC6431239.
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    191. Seed genome hypomethylated regions are enriched in transcription factor genes. Proc Natl Acad Sci U S A. 2018 08 28; 115(35):E8315-E8322. Chen M, Lin JY, Hur J, Pelletier JM, Baden R, Pellegrini M, Harada JJ, Goldberg RB. PMID: 30104383; PMCID: PMC6126732.
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    192. Directed strain evolution restructures metabolism for 1-butanol production in minimal media. Metab Eng. 2018 09; 49:153-163. Pontrelli S, Fricke RCB, Sakurai SSM, Putri SP, Fitz-Gibbon S, Chung M, Wu HY, Chen YJ, Pellegrini M, Fukusaki E, Liao JC. PMID: 30107263.
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    193. GATA4 represses RANKL in osteoblasts via multiple long-range enhancers to regulate osteoclast differentiation. Bone. 2018 11; 116:78-86. Khalid AB, Slayden AV, Kumpati J, Perry CD, Berryhill SB, Crawford JA, Fatima I, Morselli M, Pellegrini M, Miranda-Carboni GA, Krum SA. PMID: 30031905; PMCID: PMC6158087.
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    194. Epigenome-wide association in adipose tissue from the METSIM cohort. Hum Mol Genet. 2018 07 15; 27(14):2586. Orozco LD, Farrell C, Hale C, Rubbi L, Rinaldi A, Civelek M, Pan C, Lam L, Montoya D, Edillor C, Seldin M, Boehnke M, Mohlke KL, Jacobsen S, Kuusisto J, Laakso M, Lusis AJ, Pellegrini M. PMID: 29893869; PMCID: PMC6030960.
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    197. Vav3-induced cytoskeletal dynamics contribute to heterotypic properties of endothelial barriers. J Cell Biol. 2018 08 06; 217(8):2813-2830. Hilfenhaus G, Nguyen DP, Freshman J, Prajapati D, Ma F, Song D, Ziyad S, Cuadrado M, Pellegrini M, Bustelo XR, Iruela-Arispe ML. PMID: 29858212; PMCID: PMC6080943.
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    199. The Memory of Environmental Chemical Exposure in C. elegans Is Dependent on the Jumonji Demethylases jmjd-2 and jmjd-3/utx-1. Cell Rep. 2018 05 22; 23(8):2392-2404. Camacho J, Truong L, Kurt Z, Chen YW, Morselli M, Gutierrez G, Pellegrini M, Yang X, Allard P. PMID: 29791850; PMCID: PMC6003705.
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    201. Loss of MECP2 Leads to Activation of P53 and Neuronal Senescence. Stem Cell Reports. 2018 05 08; 10(5):1453-1463. Ohashi M, Korsakova E, Allen D, Lee P, Fu K, Vargas BS, Cinkornpumin J, Salas C, Park JC, Germanguz I, Langerman J, Chronis C, Kuoy E, Tran S, Xiao X, Pellegrini M, Plath K, Lowry WE. PMID: 29742391; PMCID: PMC5995366.
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    202. Topological Arrangement of Cardiac Fibroblasts Regulates Cellular Plasticity. Circ Res. 2018 06 22; 123(1):73-85. Yu J, Seldin MM, Fu K, Li S, Lam L, Wang P, Wang Y, Huang D, Nguyen TL, Wei B, Kulkarni RP, Di Carlo D, Teitell M, Pellegrini M, Lusis AJ, Deb A. PMID: 29691232; PMCID: PMC6014922.
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    203. Mycobacterium tuberculosis Transfer RNA Induces IL-12p70 via Synergistic Activation of Pattern Recognition Receptors within a Cell Network. J Immunol. 2018 05 01; 200(9):3244-3258. Keegan C, Krutzik S, Schenk M, Scumpia PO, Lu J, Pang YLJ, Russell BS, Lim KS, Shell S, Prestwich E, Su D, Elashoff D, Hershberg RM, Bloom BR, Belisle JT, Fortune S, Dedon PC, Pellegrini M, Modlin RL. PMID: 29610140; PMCID: PMC5916334.
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    204. Genetic Mechanisms of Immune Evasion in Colorectal Cancer. Cancer Discov. 2018 06; 8(6):730-749. Grasso CS, Giannakis M, Wells DK, Hamada T, Mu XJ, Quist M, Nowak JA, Nishihara R, Qian ZR, Inamura K, Morikawa T, Nosho K, Abril-Rodriguez G, Connolly C, Escuin-Ordinas H, Geybels MS, Grady WM, Hsu L, Hu-Lieskovan S, Huyghe JR, Kim YJ, Krystofinski P, Leiserson MDM, Montoya DJ, Nadel BB, Pellegrini M, Pritchard CC, Puig-Saus C, Quist EH, Raphael BJ, Salipante SJ, Shin DS, Shinbrot E, Shirts B, Shukla S, Stanford JL, Sun W, Tsoi J, Upfill-Brown A, Wheeler DA, Wu CJ, Yu M, Zaidi SH, Zaretsky JM, Gabriel SB, Lander ES, Garraway LA, Hudson TJ, Fuchs CS, Ribas A, Ogino S, Peters U. PMID: 29510987; PMCID: PMC5984687.
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    205. Complete genomic sequences of Propionibacterium freudenreichii phages from Swiss cheese reveal greater diversity than Cutibacterium (formerly Propionibacterium) acnes phages. BMC Microbiol. 2018 03 01; 18(1):19. Cheng L, Marinelli LJ, Grosset N, Fitz-Gibbon ST, Bowman CA, Dang BQ, Russell DA, Jacobs-Sera D, Shi B, Pellegrini M, Miller JF, Gautier M, Hatfull GF, Modlin RL. PMID: 29490612; PMCID: PMC5831693.
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    206. CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data. Bioinformatics. 2018 02 01; 34(3):381-387. Guo W, Zhu P, Pellegrini M, Zhang MQ, Wang X, Ni Z. PMID: 28968643; PMCID: PMC6454434.
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    207. High-throughput sequencing of the chloroplast and mitochondrion of Chlamydomonas reinhardtii to generate improved de novo assemblies, analyze expression patterns and transcript speciation, and evaluate diversity among laboratory strains and wild isolates. Plant J. 2018 02; 93(3):545-565. Gallaher SD, Fitz-Gibbon ST, Strenkert D, Purvine SO, Pellegrini M, Merchant SS. PMID: 29172250; PMCID: PMC5775909.
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    208. Immunotherapy of Mild Cognitive Impairment by ω-3 Supplementation: Why Are Amyloid-β Antibodies and ω-3 Not Working in Clinical Trials? J Alzheimers Dis. 2018; 62(3):1013-1022. Fiala M, Restrepo L, Pellegrini M. PMID: 29103035; PMCID: PMC5870008.
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    209. Glucose inhibits cardiac muscle maturation through nucleotide biosynthesis. Elife. 2017 12 12; 6. Nakano H, Minami I, Braas D, Pappoe H, Wu X, Sagadevan A, Vergnes L, Fu K, Morselli M, Dunham C, Ding X, Stieg AZ, Gimzewski JK, Pellegrini M, Clark PM, Reue K, Lusis AJ, Ribalet B, Kurdistani SK, Christofk H, Nakatsuji N, Nakano A. PMID: 29231167; PMCID: PMC5726851.
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    211. Similarity between soybean and Arabidopsis seed methylomes and loss of non-CG methylation does not affect seed development. Proc Natl Acad Sci U S A. 2017 11 07; 114(45):E9730-E9739. Lin JY, Le BH, Chen M, Henry KF, Hur J, Hsieh TF, Chen PY, Pelletier JM, Pellegrini M, Fischer RL, Harada JJ, Goldberg RB. PMID: 29078418; PMCID: PMC5692608.
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    213. Correction: In vivo targeting of de novo DNA methylation by histone modifications in yeast and mouse. Elife. 2017 08 31; 6. Morselli M, Pastor WA, Montanini B, Nee K, Ferrari R, Fu K, Bonora G, Rubbi L, Clark AT, Ottonello S, Jacobsen SE, Pellegrini M. PMID: 28858608; PMCID: PMC5578735.
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    215. Addressing the Digital Divide in Contemporary Biology: Lessons from Teaching UNIX. Trends Biotechnol. 2017 10; 35(10):901-903. Mangul S, Martin LS, Hoffmann A, Pellegrini M, Eskin E. PMID: 28720283.
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    217. Prenatal Growth Patterns and Birthweight Are Associated With Differential DNA Methylation and Gene Expression of Cardiometabolic Risk Genes in Human Placentas: A Discovery-Based Approach. Reprod Sci. 2018 04; 25(4):523-539. Chen PY, Chu A, Liao WW, Rubbi L, Janzen C, Hsu FM, Thamotharan S, Ganguly A, Lam L, Montoya D, Pellegrini M, Devaskar SU. PMID: 28693373; PMCID: PMC6348426.
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    219. Chromosome-level genome assembly and transcriptome of the green alga Chromochloris zofingiensis illuminates astaxanthin production. Proc Natl Acad Sci U S A. 2017 05 23; 114(21):E4296-E4305. Roth MS, Cokus SJ, Gallaher SD, Walter A, Lopez D, Erickson E, Endelman B, Westcott D, Larabell CA, Merchant SS, Pellegrini M, Niyogi KK. PMID: 28484037; PMCID: PMC5448231.
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    220. Abf1 and other general regulatory factors control ribosome biogenesis gene expression in budding yeast. Nucleic Acids Res. 2017 05 05; 45(8):4493-4506. Bosio MC, Fermi B, Spagnoli G, Levati E, Rubbi L, Ferrari R, Pellegrini M, Dieci G. PMID: 28158860; PMCID: PMC5416754.
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    221. Modulation of innate immunity of patients with Alzheimer's disease by omega-3 fatty acids. FASEB J. 2017 08; 31(8):3229-3239. Fiala M, Kooij G, Wagner K, Hammock B, Pellegrini M. PMID: 28420693; PMCID: PMC5503712.
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    222. An epigenetic aging clock for dogs and wolves. Aging (Albany NY). 2017 03 28; 9(3):1055-1068. Thompson MJ, vonHoldt B, Horvath S, Pellegrini M. PMID: 28373601; PMCID: PMC5391218.
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    223. Cytoreductive conditioning intensity predicts clonal diversity in ADA-SCID retroviral gene therapy patients. Blood. 2017 05 11; 129(19):2624-2635. Cooper AR, Lill GR, Shaw K, Carbonaro-Sarracino DA, Davila A, Sokolic R, Candotti F, Pellegrini M, Kohn DB. PMID: 28351939; PMCID: PMC5428461.
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    225. Altered methylation of specific DNA loci in the liver of Bhmt-null mice results in repression of Iqgap2 and F2rl2 and is associated with development of preneoplastic foci. FASEB J. 2017 05; 31(5):2090-2103. Lupu DS, Orozco LD, Wang Y, Cullen JM, Pellegrini M, Zeisel SH. PMID: 28179424; PMCID: PMC5388550.
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    226. Regulation of Marginal Zone B-Cell Differentiation by MicroRNA-146a. Front Immunol. 2016; 7:670. King JK, Ung NM, Paing MH, Contreras JR, Alberti MO, Fernando TR, Zhang K, Pellegrini M, Rao DS. PMID: 28138326; PMCID: PMC5237642.
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    227. Transcriptomic Modification in the Cerebral Cortex following Noninvasive Brain Stimulation: RNA-Sequencing Approach. Neural Plast. 2016; 2016:5942980. Holmes B, Jung SH, Lu J, Wagner JA, Rubbi L, Pellegrini M, Jankord R. PMID: 28119786; PMCID: PMC5227175.
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    228. Human Embryonic Stem Cells Do Not Change Their X Inactivation Status during Differentiation. Cell Rep. 2017 01 03; 18(1):54-67. Patel S, Bonora G, Sahakyan A, Kim R, Chronis C, Langerman J, Fitz-Gibbon S, Rubbi L, Skelton RJP, Ardehali R, Pellegrini M, Lowry WE, Clark AT, Plath K. PMID: 27989715; PMCID: PMC5214931.
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    229. Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype. Biotechnol Biofuels. 2016; 9:258. Traller JC, Cokus SJ, Lopez DA, Gaidarenko O, Smith SR, McCrow JP, Gallaher SD, Podell S, Thompson M, Cook O, Morselli M, Jaroszewicz A, Allen EE, Allen AE, Merchant SS, Pellegrini M, Hildebrand M. PMID: 27933100; PMCID: PMC5124317.
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    230. Cardiac Fibroblasts Adopt Osteogenic Fates and Can Be Targeted to Attenuate Pathological Heart Calcification. Cell Stem Cell. 2017 02 02; 20(2):218-232.e5. Pillai ICL, Li S, Romay M, Lam L, Lu Y, Huang J, Dillard N, Zemanova M, Rubbi L, Wang Y, Lee J, Xia M, Liang O, Xie YH, Pellegrini M, Lusis AJ, Deb A. PMID: 27867037; PMCID: PMC5291784.
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    231. A Statistical Framework to Identify Deviation from Time Linearity in Epigenetic Aging. PLoS Comput Biol. 2016 Nov; 12(11):e1005183. Snir S, vonHoldt BM, Pellegrini M. PMID: 27835646; PMCID: PMC5106012.
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    232. First Draft Assembly and Annotation of the Genome of a California Endemic Oak Quercus lobata Née (Fagaceae). G3 (Bethesda). 2016 Nov 08; 6(11):3485-3495. Sork VL, Fitz-Gibbon ST, Puiu D, Crepeau M, Gugger PF, Sherman R, Stevens K, Langley CH, Pellegrini M, Salzberg SL. PMID: 27621377; PMCID: PMC5100847.
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    233. Mergeomics: multidimensional data integration to identify pathogenic perturbations to biological systems. BMC Genomics. 2016 11 04; 17(1):874. Shu L, Zhao Y, Kurt Z, Byars SG, Tukiainen T, Kettunen J, Orozco LD, Pellegrini M, Lusis AJ, Ripatti S, Zhang B, Inouye M, Mäkinen VP, Yang X. PMID: 27814671; PMCID: PMC5097440.
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    234. Reversible Regulation of Promoter and Enhancer Histone Landscape by DNA Methylation in Mouse Embryonic Stem Cells. Cell Rep. 2016 09 27; 17(1):289-302. King AD, Huang K, Rubbi L, Liu S, Wang CY, Wang Y, Pellegrini M, Fan G. PMID: 27681438; PMCID: PMC5507178.
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    235. Increased intermediate M1-M2 macrophage polarization and improved cognition in mild cognitive impairment patients on ω-3 supplementation. FASEB J. 2017 01; 31(1):148-160. Famenini S, Rigali EA, Olivera-Perez HM, Dang J, Chang MT, Halder R, Rao RV, Pellegrini M, Porter V, Bredesen D, Fiala M. PMID: 27677546; PMCID: PMC5161513.
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    236. Cell-type deconvolution with immune pathways identifies gene networks of host defense and immunopathology in leprosy. JCI Insight. 2016 09 22; 1(15):e88843. Inkeles MS, Teles RM, Pouldar D, Andrade PR, Madigan CA, Lopez D, Ambrose M, Noursadeghi M, Sarno EN, Rea TH, Ochoa MT, Iruela-Arispe ML, Swindell WR, Ottenhoff TH, Geluk A, Bloom BR, Pellegrini M, Modlin RL. PMID: 27699251; PMCID: PMC5033757.
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    237. Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes. Elife. 2016 09 13; 5. Hasin-Brumshtein Y, Khan AH, Hormozdiari F, Pan C, Parks BW, Petyuk VA, Piehowski PD, Brümmer A, Pellegrini M, Xiao X, Eskin E, Smith RD, Lusis AJ, Smith DJ. PMID: 27623010; PMCID: PMC5053804.
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    238. Gestational food restriction decreases placental interleukin-10 expression and markers of autophagy and endoplasmic reticulum stress in murine intrauterine growth restriction. Nutr Res. 2016 10; 36(10):1055-1067. Chu A, Thamotharan S, Ganguly A, Wadehra M, Pellegrini M, Devaskar SU. PMID: 27865347; PMCID: PMC5119922.
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    239. An asthma-associated IL4R variant exacerbates airway inflammation by promoting conversion of regulatory T cells to TH17-like cells. Nat Med. 2016 09; 22(9):1013-22. Massoud AH, Charbonnier LM, Lopez D, Pellegrini M, Phipatanakul W, Chatila TA. PMID: 27479084; PMCID: PMC5014738.
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    240. Cutaneous wound healing through paradoxical MAPK activation by BRAF inhibitors. Nat Commun. 2016 08 01; 7:12348. Escuin-Ordinas H, Li S, Xie MW, Sun L, Hugo W, Huang RR, Jiao J, de-Faria FM, Realegeno S, Krystofinski P, Azhdam A, Komenan SM, Atefi M, Comin-Anduix B, Pellegrini M, Cochran AJ, Modlin RL, Herschman HR, Lo RS, McBride WH, Segura T, Ribas A. PMID: 27476449; PMCID: PMC4974650.
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    241. CRISPR/Cas9-Mediated Correction of the Sickle Mutation in Human CD34+ cells. Mol Ther. 2016 Sep; 24(9):1561-9. Hoban MD, Lumaquin D, Kuo CY, Romero Z, Long J, Ho M, Young CS, Mojadidi M, Fitz-Gibbon S, Cooper AR, Lill GR, Urbinati F, Campo-Fernandez B, Bjurstrom CF, Pellegrini M, Hollis RP, Kohn DB. PMID: 27406980; PMCID: PMC5113113.
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    242. Plant hydraulics as a central hub integrating plant and ecosystem function: meeting report for 'Emerging Frontiers in Plant Hydraulics' (Washington, DC, May 2015). Plant Cell Environ. 2016 09; 39(9):2085-94. Sack L, Ball MC, Brodersen C, Davis SD, Des Marais DL, Donovan LA, Givnish TJ, Hacke UG, Huxman T, Jansen S, Jacobsen AL, Johnson DM, Koch GW, Maurel C, McCulloh KA, McDowell NG, McElrone A, Meinzer FC, Melcher PJ, North G, Pellegrini M, Pockman WT, Pratt RB, Sala A, Santiago LS, Savage JA, Scoffoni C, Sevanto S, Sperry J, Tyerman SD, Way D, Holbrook NM. PMID: 27037757.
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    243. Novel features of telomere biology revealed by the absence of telomeric DNA methylation. Genome Res. 2016 08; 26(8):1047-56. Vega-Vaquero A, Bonora G, Morselli M, Vaquero-Sedas MI, Rubbi L, Pellegrini M, Vega-Palas MA. PMID: 27405804; PMCID: PMC4971770.
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    244. Astrocytes Can Adopt Endothelial Cell Fates in a p53-Dependent Manner. Mol Neurobiol. 2017 08; 54(6):4584-4596. Brumm AJ, Nunez S, Doroudchi MM, Kawaguchi R, Duan J, Pellegrini M, Lam L, Carmichael ST, Deb A, Hinman JD. PMID: 27389775; PMCID: PMC5219956.
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    245. Epigenetic changes in T-cell and monocyte signatures and production of neurotoxic cytokines in ALS patients. FASEB J. 2016 10; 30(10):3461-3473. Lam L, Chin L, Halder RC, Sagong B, Famenini S, Sayre J, Montoya D, Rubbi L, Pellegrini M, Fiala M. PMID: 27368295; PMCID: PMC5024692.
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    246. CRISPR-Mediated VHL Knockout Generates an Improved Model for Metastatic Renal Cell Carcinoma. Sci Rep. 2016 Jun 30; 6:29032. Schokrpur S, Hu J, Moughon DL, Liu P, Lin LC, Hermann K, Mangul S, Guan W, Pellegrini M, Xu H, Wu L. PMID: 27358011; PMCID: PMC4928183.
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    247. S100A12 Is Part of the Antimicrobial Network against Mycobacterium leprae in Human Macrophages. PLoS Pathog. 2016 06; 12(6):e1005705. Realegeno S, Kelly-Scumpia KM, Dang AT, Lu J, Teles R, Liu PT, Schenk M, Lee EY, Schmidt NW, Wong GC, Sarno EN, Rea TH, Ochoa MT, Pellegrini M, Modlin RL. PMID: 27355424; PMCID: PMC4927120.
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    248. A naïve Bayesian classifier for identifying plant microRNAs. Plant J. 2016 06; 86(6):481-92. Douglass S, Hsu SW, Cokus S, Goldberg RB, Harada JJ, Pellegrini M. PMID: 27061965.
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    249. Identification and Characterization of a cis-Regulatory Element for Zygotic Gene Expression in Chlamydomonas reinhardtii. G3 (Bethesda). 2016 06 01; 6(6):1541-8. Hamaji T, Lopez D, Pellegrini M, Umen J. PMID: 27172209; PMCID: PMC4889651.
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    250. Imatinib Triggers Phagolysosome Acidification and Antimicrobial Activity against Mycobacterium bovis Bacille Calmette-Guérin in Glucocorticoid-Treated Human Macrophages. J Immunol. 2016 07 01; 197(1):222-32. Steiger J, Stephan A, Inkeles MS, Realegeno S, Bruns H, Kröll P, de Castro Kroner J, Sommer A, Batinica M, Pitzler L, Kalscheuer R, Hartmann P, Plum G, Stenger S, Pellegrini M, Brachvogel B, Modlin RL, Fabri M. PMID: 27233968; PMCID: PMC5536119.
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    251. Biased Expression of the FOXP3Δ3 Isoform in Aggressive Bladder Cancer Mediates Differentiation and Cisplatin Chemotherapy Resistance. Clin Cancer Res. 2016 Nov 01; 22(21):5349-5361. Zhang H, Prado K, Zhang KX, Peek EM, Lee J, Wang X, Huang J, Li G, Pellegrini M, Chin AI. PMID: 27189164.
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    252. Epigenetic changes mediated by polycomb repressive complex 2 and E2a are associated with drug resistance in a mouse model of lymphoma. Genome Med. 2016 05 04; 8(1):54. Flinders C, Lam L, Rubbi L, Ferrari R, Fitz-Gibbon S, Chen PY, Thompson M, Christofk H, B Agus D, Ruderman D, Mallick P, Pellegrini M. PMID: 27146673; PMCID: PMC4857420.
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    253. Systems Nutrigenomics Reveals Brain Gene Networks Linking Metabolic and Brain Disorders. EBioMedicine. 2016 May; 7:157-66. Meng Q, Ying Z, Noble E, Zhao Y, Agrawal R, Mikhail A, Zhuang Y, Tyagi E, Zhang Q, Lee JH, Morselli M, Orozco L, Guo W, Kilts TM, Zhu J, Zhang B, Pellegrini M, Xiao X, Young MF, Gomez-Pinilla F, Yang X. PMID: 27322469; PMCID: PMC4909610.
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    254. Genetic Tagging During Human Mesoderm Differentiation Reveals Tripotent Lateral Plate Mesodermal Progenitors. Stem Cells. 2016 05; 34(5):1239-50. Chin CJ, Cooper AR, Lill GR, Evseenko D, Zhu Y, He CB, Casero D, Pellegrini M, Kohn DB, Crooks GM. PMID: 26934332; PMCID: PMC5052131.
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    255. Species-wide patterns of DNA methylation variation in Quercus lobata and their association with climate gradients. Mol Ecol. 2016 Apr; 25(8):1665-80. Gugger PF, Fitz-Gibbon S, PellEgrini M, Sork VL. PMID: 26833902.
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    256. Glycolytic-to-oxidative fiber-type switch and mTOR signaling activation are early-onset features of SBMA muscle modified by high-fat diet. Acta Neuropathol. 2016 07; 132(1):127-44. Rocchi A, Milioto C, Parodi S, Armirotti A, Borgia D, Pellegrini M, Urciuolo A, Molon S, Morbidoni V, Marabita M, Romanello V, Gatto P, Blaauw B, Bonaldo P, Sambataro F, Robins DM, Lieberman AP, Sorarù G, Vergani L, Sandri M, Pennuto M. PMID: 26971100; PMCID: PMC4911374.
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    257. Discovering communities in complex networks by edge label propagation. Sci Rep. 2016 Mar 01; 6:22470. Liu W, Jiang X, Pellegrini M, Wang X. PMID: 26926830; PMCID: PMC4772381.
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    258. Rapid Changes in the Translatome during the Conversion of Growth Cones to Synaptic Terminals. Cell Rep. 2016 Feb 09; 14(5):1258-1271. Zhang KX, Tan L, Pellegrini M, Zipursky SL, McEwen JM. PMID: 26832407.
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    259. The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves. Mol Ecol. 2016 Apr; 25(8):1838-55. Janowitz Koch I, Clark MM, Thompson MJ, Deere-Machemer KA, Wang J, Duarte L, Gnanadesikan GE, McCoy EL, Rubbi L, Stahler DR, Pellegrini M, Ostrander EA, Wayne RK, Sinsheimer JS, vonHoldt BM. PMID: 27112634; PMCID: PMC4849173.
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    260. DNA Methylation Indicates Susceptibility to Isoproterenol-Induced Cardiac Pathology and Is Associated With Chromatin States. Circ Res. 2016 Mar 04; 118(5):786-97. Chen H, Orozco LD, Wang J, Rau CD, Rubbi L, Ren S, Wang Y, Pellegrini M, Lusis AJ, Vondriska TM. PMID: 26838786; PMCID: PMC4779427.
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    261. A Designed Inhibitor of p53 Aggregation Rescues p53 Tumor Suppression in Ovarian Carcinomas. Cancer Cell. 2016 Jan 11; 29(1):90-103. Soragni A, Janzen DM, Johnson LM, Lindgren AG, Thai-Quynh Nguyen A, Tiourin E, Soriaga AB, Lu J, Jiang L, Faull KF, Pellegrini M, Memarzadeh S, Eisenberg DS. PMID: 26748848; PMCID: PMC4733364.
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    262. Anti-inflammatory therapies of amyotrophic lateral sclerosis guided by immune pathways. Am J Neurodegener Dis. 2015; 4(2):28-39. Lam L, Halder RC, Montoya DJ, Rubbi L, Rinaldi A, Sagong B, Weitzman S, Rubattino R, Singh RR, Pellegrini M, Fiala M. PMID: 26807342; PMCID: PMC4700124.
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    264. Dynamic Changes in the Transcriptome and Methylome of Chlamydomonas reinhardtii throughout Its Life Cycle. Plant Physiol. 2015 Dec; 169(4):2730-43. Lopez D, Hamaji T, Kropat J, De Hoff P, Morselli M, Rubbi L, Fitz-Gibbon S, Gallaher SD, Merchant SS, Umen J, Pellegrini M. PMID: 26450704; PMCID: PMC4677889.
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    265. Integrative analysis of human protein, function and disease networks. Sci Rep. 2015 Sep 24; 5:14344. Liu W, Wu A, Pellegrini M, Wang X. PMID: 26399914; PMCID: PMC4585831.
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    266. Distinct Shifts in Microbiota Composition during Drosophila Aging Impair Intestinal Function and Drive Mortality. Cell Rep. 2015 Sep 08; 12(10):1656-67. Clark RI, Salazar A, Yamada R, Fitz-Gibbon S, Morselli M, Alcaraz J, Rana A, Rera M, Pellegrini M, Ja WW, Walker DW. PMID: 26321641; PMCID: PMC4565751.
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    267. Chlamydomonas Genome Resource for Laboratory Strains Reveals a Mosaic of Sequence Variation, Identifies True Strain Histories, and Enables Strain-Specific Studies. Plant Cell. 2015 Sep; 27(9):2335-52. Gallaher SD, Fitz-Gibbon ST, Glaesener AG, Pellegrini M, Merchant SS. PMID: 26307380; PMCID: PMC4815092.
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    268. Comparison of the Mitochondrial Genomes and Steady State Transcriptomes of Two Strains of the Trypanosomatid Parasite, Leishmania tarentolae. PLoS Negl Trop Dis. 2015; 9(7):e0003841. Simpson L, Douglass SM, Lake JA, Pellegrini M, Li F. PMID: 26204118; PMCID: PMC4512693.
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    269. Erratum to: Endogenous CCL2 neutralization restricts HIV-1 replication in primary human macrophages by inhibiting viral DNA accumulation. Retrovirology. 2015 Jun 09; 12:47. Sabbatucci M, Covino DA, Purificato C, Mallano A, Federico M, Lu J, Rinaldi AO, Pellegrini M, Bona R, Michelini Z, Cara A, Vella S, Gessani S, Andreotti M, Fantuzzi L. PMID: 26054949; PMCID: PMC4459676.
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    271. Pancreatic cancer patient survival correlates with DNA methylation of pancreas development genes. PLoS One. 2015; 10(6):e0128814. Thompson MJ, Rubbi L, Dawson DW, Donahue TR, Pellegrini M. PMID: 26039411; PMCID: PMC4454596.
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    277. Genome-wide gene order distances support clustering the gram-positive bacteria. Front Microbiol. 2014; 5:785. House CH, Pellegrini M, Fitz-Gibbon ST. PMID: 25653643; PMCID: PMC4299520.
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    299. Nkx2-5 suppresses the proliferation of atrial myocytes and conduction system. Circ Res. 2014 Mar 28; 114(7):1103-13. Nakashima Y, Yanez DA, Touma M, Nakano H, Jaroszewicz A, Jordan MC, Pellegrini M, Roos KP, Nakano A. PMID: 24563458.
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    340. DNA methylation dynamics, metabolic fluxes, gene splicing, and alternative phenotypes in honey bees. Proc Natl Acad Sci U S A. 2012 Mar 27; 109(13):4968-73. Foret S, Kucharski R, Pellegrini M, Feng S, Jacobsen SE, Robinson GE, Maleszka R. PMID: 22416128; PMCID: PMC3324026.
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    341. Genome-wide evaluation of histone methylation changes associated with leaf senescence in Arabidopsis. PLoS One. 2012; 7(3):e33151. Brusslan JA, Rus Alvarez-Canterbury AM, Nair NU, Rice JC, Hitchler MJ, Pellegrini M. PMID: 22427974; PMCID: PMC3299739.
      View in: PubMed   Mentions: 40     Fields:    Translation:AnimalsCells
    342. Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas. J Biol Chem. 2012 May 04; 287(19):15811-25. Boyle NR, Page MD, Liu B, Blaby IK, Casero D, Kropat J, Cokus SJ, Hong-Hermesdorf A, Shaw J, Karpowicz SJ, Gallaher SD, Johnson S, Benning C, Pellegrini M, Grossman A, Merchant SS. PMID: 22403401; PMCID: PMC3346115.
      View in: PubMed   Mentions: 165     Fields:    Translation:Animals
    343. Impact of oxidative stress on ascorbate biosynthesis in Chlamydomonas via regulation of the VTC2 gene encoding a GDP-L-galactose phosphorylase. J Biol Chem. 2012 Apr 20; 287(17):14234-45. Urzica EI, Adler LN, Page MD, Linster CL, Arbing MA, Casero D, Pellegrini M, Merchant SS, Clarke SG. PMID: 22393048; PMCID: PMC3340187.
      View in: PubMed   Mentions: 41     Fields:    Translation:AnimalsCells
    344. Transcriptome sequencing identifies SPL7-regulated copper acquisition genes FRO4/FRO5 and the copper dependence of iron homeostasis in Arabidopsis. Plant Cell. 2012 Feb; 24(2):738-61. Bernal M, Casero D, Singh V, Wilson GT, Grande A, Yang H, Dodani SC, Pellegrini M, Huijser P, Connolly EL, Merchant SS, Krämer U. PMID: 22374396; PMCID: PMC3315244.
      View in: PubMed   Mentions: 128     Fields:    Translation:AnimalsCells
    345. Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression. BMC Genomics. 2012 Jan 17; 13:27. Vining KJ, Pomraning KR, Wilhelm LJ, Priest HD, Pellegrini M, Mockler TC, Freitag M, Strauss SH. PMID: 22251412; PMCID: PMC3298464.
      View in: PubMed   Mentions: 59     Fields:    Translation:AnimalsCells
    346. Epigenetic analysis: ChIP-chip and ChIP-seq. Methods Mol Biol. 2012; 802:377-87. Pellegrini M, Ferrari R. PMID: 22130894.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    347. Using phylogenetic profiles to predict functional relationships. Methods Mol Biol. 2012; 804:167-77. Pellegrini M. PMID: 22144153.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    348. Genome-wide binding map of the HIV-1 Tat protein to the human genome. PLoS One. 2011; 6(11):e26894. Marban C, Su T, Ferrari R, Li B, Vatakis D, Pellegrini M, Zack JA, Rohr O, Kurdistani SK. PMID: 22073215; PMCID: PMC3208564.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCells
    349. Regulation of the yeast metabolic cycle by transcription factors with periodic activities. BMC Syst Biol. 2011 Oct 12; 5:160. Rao AR, Pellegrini M. PMID: 21992532; PMCID: PMC3216092.
      View in: PubMed   Mentions: 7     Fields:    Translation:Animals
    350. Lethal iron deprivation induced by non-neutralizing antibodies targeting transferrin receptor 1 in malignant B cells. Leuk Lymphoma. 2011 Nov; 52(11):2169-78. Rodríguez JA, Luria-Pérez R, López-Valdés HE, Casero D, Daniels TR, Patel S, Avila D, Leuchter R, So S, Ortiz-Sánchez E, Bonavida B, Martínez-Maza O, Charles AC, Pellegrini M, Helguera G, Penichet ML. PMID: 21870996; PMCID: PMC3732792.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    351. Novel stem/progenitor cell population from murine tracheal submucosal gland ducts with multipotent regenerative potential. Stem Cells. 2011 Aug; 29(8):1283-93. Hegab AE, Ha VL, Gilbert JL, Zhang KX, Malkoski SP, Chon AT, Darmawan DO, Bisht B, Ooi AT, Pellegrini M, Nickerson DW, Gomperts BN. PMID: 21710468; PMCID: PMC3403816.
      View in: PubMed   Mentions: 70     Fields:    Translation:AnimalsCells
    352. Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data. BMC Bioinformatics. 2011 Jul 12; 12:282. Lopez D, Casero D, Cokus SJ, Merchant SS, Pellegrini M. PMID: 21749710; PMCID: PMC3144025.
      View in: PubMed   Mentions: 39     Fields:    Translation:Animals
    353. A comparative analysis of DNA methylation across human embryonic stem cell lines. Genome Biol. 2011 Jul 06; 12(7):R62. Chen PY, Feng S, Joo JW, Jacobsen SE, Pellegrini M. PMID: 21733148; PMCID: PMC3218824.
      View in: PubMed   Mentions: 51     Fields:    Translation:HumansCells
    354. Identification of novel targets of CSL-dependent Notch signaling in hematopoiesis. PLoS One. 2011; 6(5):e20022. Hamidi H, Gustafason D, Pellegrini M, Gasson J. PMID: 21637838; PMCID: PMC3102675.
      View in: PubMed   Mentions: 21     Fields:    Translation:AnimalsCells
    355. Systems biology approach in Chlamydomonas reveals connections between copper nutrition and multiple metabolic steps. Plant Cell. 2011 Apr; 23(4):1273-92. Castruita M, Casero D, Karpowicz SJ, Kropat J, Vieler A, Hsieh SI, Yan W, Cokus S, Loo JA, Benning C, Pellegrini M, Merchant SS. PMID: 21498682; PMCID: PMC3101551.
      View in: PubMed   Mentions: 103     Fields:    Translation:AnimalsCells
    356. Global phosphoproteomics reveals crosstalk between Bcr-Abl and negative feedback mechanisms controlling Src signaling. Sci Signal. 2011 Mar 29; 4(166):ra18. Rubbi L, Titz B, Brown L, Galvan E, Komisopoulou E, Chen SS, Low T, Tahmasian M, Skaggs B, Müschen M, Pellegrini M, Graeber TG. PMID: 21447799; PMCID: PMC4057100.
      View in: PubMed   Mentions: 30     Fields:    Translation:HumansCells
    357. A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii. Plant J. 2011 Jun; 66(5):770-80. Kropat J, Hong-Hermesdorf A, Casero D, Ent P, Castruita M, Pellegrini M, Merchant SS, Malasarn D. PMID: 21309872; PMCID: PMC3101321.
      View in: PubMed   Mentions: 132     Fields:    Translation:AnimalsCells
    358. Identification of genes required for de novo DNA methylation in Arabidopsis. Epigenetics. 2011 Mar; 6(3):344-54. Greenberg MV, Ausin I, Chan SW, Cokus SJ, Cuperus JT, Feng S, Law JA, Chu C, Pellegrini M, Carrington JC, Jacobsen SE. PMID: 21150311; PMCID: PMC3092683.
      View in: PubMed   Mentions: 44     Fields:    Translation:AnimalsCells
    359. Determining DNA methylation profiles using sequencing. Methods Mol Biol. 2011; 733:223-38. Feng S, Rubbi L, Jacobsen SE, Pellegrini M. PMID: 21431774.
      View in: PubMed   Mentions: 28     Fields:    Translation:Cells
    360. Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli. Mol Syst Biol. 2010 Dec 21; 6:449. Atsumi S, Wu TY, Machado IM, Huang WC, Chen PY, Pellegrini M, Liao JC. PMID: 21179021; PMCID: PMC3018172.
      View in: PubMed   Mentions: 106     Fields:    Translation:Cells
    361. AID-induced genotoxic stress promotes B cell differentiation in the germinal center via ATM and LKB1 signaling. Mol Cell. 2010 Sep 24; 39(6):873-85. Sherman MH, Kuraishy AI, Deshpande C, Hong JS, Cacalano NA, Gatti RA, Manis JP, Damore MA, Pellegrini M, Teitell MA. PMID: 20864035; PMCID: PMC2945612.
      View in: PubMed   Mentions: 41     Fields:    Translation:HumansAnimalsCells
    362. Molecular analyses of human induced pluripotent stem cells and embryonic stem cells. Cell Stem Cell. 2010 Aug 06; 7(2):263-9. Chin MH, Pellegrini M, Plath K, Lowry WE. PMID: 20682452; PMCID: PMC3276111.
      View in: PubMed   Mentions: 75     Fields:    Translation:HumansCells
    363. RNA-seq analysis of sulfur-deprived Chlamydomonas cells reveals aspects of acclimation critical for cell survival. Plant Cell. 2010 Jun; 22(6):2058-84. González-Ballester D, Casero D, Cokus S, Pellegrini M, Merchant SS, Grossman AR. PMID: 20587772; PMCID: PMC2910963.
      View in: PubMed   Mentions: 128     Fields:    Translation:AnimalsCells
    364. Relationship between nucleosome positioning and DNA methylation. Nature. 2010 Jul 15; 466(7304):388-92. Chodavarapu RK, Feng S, Bernatavichute YV, Chen PY, Stroud H, Yu Y, Hetzel JA, Kuo F, Kim J, Cokus SJ, Casero D, Bernal M, Huijser P, Clark AT, Krämer U, Merchant SS, Zhang X, Jacobsen SE, Pellegrini M. PMID: 20512117; PMCID: PMC2964354.
      View in: PubMed   Mentions: 351     Fields:    Translation:HumansAnimalsCells
    365. BS Seeker: precise mapping for bisulfite sequencing. BMC Bioinformatics. 2010 Apr 23; 11:203. Chen PY, Cokus SJ, Pellegrini M. PMID: 20416082; PMCID: PMC2871274.
      View in: PubMed   Mentions: 125     Fields:    Translation:HumansCells
    366. Evolution of an expanded sex-determining locus in Volvox. Science. 2010 Apr 16; 328(5976):351-4. Ferris P, Olson BJ, De Hoff PL, Douglass S, Casero D, Prochnik S, Geng S, Rai R, Grimwood J, Schmutz J, Nishii I, Hamaji T, Nozaki H, Pellegrini M, Umen JG. PMID: 20395508; PMCID: PMC2880461.
      View in: PubMed   Mentions: 76     Fields:    Translation:AnimalsCells
    367. Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci U S A. 2010 May 11; 107(19):8689-94. Feng S, Cokus SJ, Zhang X, Chen PY, Bostick M, Goll MG, Hetzel J, Jain J, Strauss SH, Halpern ME, Ukomadu C, Sadler KC, Pradhan S, Pellegrini M, Jacobsen SE. PMID: 20395551; PMCID: PMC2889301.
      View in: PubMed   Mentions: 586     Fields:    Translation:AnimalsCells
    368. Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature. 2010 Feb 25; 463(7284):1101-5. Popp C, Dean W, Feng S, Cokus SJ, Andrews S, Pellegrini M, Jacobsen SE, Reik W. PMID: 20098412; PMCID: PMC2965733.
      View in: PubMed   Mentions: 393     Fields:    Translation:AnimalsCells
    369. Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expression. BMC Syst Biol. 2009 Dec 14; 3:115. Sprinzak E, Cokus SJ, Yeates TO, Eisenberg D, Pellegrini M. PMID: 20003439; PMCID: PMC2804736.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    370. Nonsense-mediated mRNA decay mutes the splicing defects of spliceosome component mutations. RNA. 2009 Dec; 15(12):2236-47. Kawashima T, Pellegrini M, Chanfreau GF. PMID: 19850912; PMCID: PMC2779665.
      View in: PubMed   Mentions: 21     Fields:    Translation:AnimalsCells
    371. Copy number variation influences gene expression and metabolic traits in mice. Hum Mol Genet. 2009 Nov 01; 18(21):4118-29. Orozco LD, Cokus SJ, Ghazalpour A, Ingram-Drake L, Wang S, van Nas A, Che N, Araujo JA, Pellegrini M, Lusis AJ. PMID: 19648292; PMCID: PMC2758141.
      View in: PubMed   Mentions: 62     Fields:    Translation:AnimalsCells
    372. Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana. Genome Biol. 2009; 10(6):R62. Zhang X, Bernatavichute YV, Cokus S, Pellegrini M, Jacobsen SE. PMID: 19508735; PMCID: PMC2718496.
      View in: PubMed   Mentions: 277     Fields:    Translation:AnimalsCells
    373. ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure and gene silencing. Nat Struct Mol Biol. 2009 Jul; 16(7):763-8. Jacob Y, Feng S, LeBlanc CA, Bernatavichute YV, Stroud H, Cokus S, Johnson LM, Pellegrini M, Jacobsen SE, Michaels SD. PMID: 19503079; PMCID: PMC2754316.
      View in: PubMed   Mentions: 144     Fields:    Translation:AnimalsCells
    374. Determining the conservation of DNA methylation in Arabidopsis. Epigenetics. 2009 Feb 16; 4(2):119-24. Widman N, Jacobsen SE, Pellegrini M. PMID: 19384058.
      View in: PubMed   Mentions: 14     Fields:    Translation:AnimalsCells
    375. Mef2C is a lineage-restricted target of Scl/Tal1 and regulates megakaryopoiesis and B-cell homeostasis. Blood. 2009 Apr 09; 113(15):3461-71. Gekas C, Rhodes KE, Gereige LM, Helgadottir H, Ferrari R, Kurdistani SK, Montecino-Rodriguez E, Bassel-Duby R, Olson E, Krivtsov AV, Armstrong S, Orkin SH, Pellegrini M, Mikkola HK. PMID: 19211936; PMCID: PMC2945827.
      View in: PubMed   Mentions: 26     Fields:    Translation:AnimalsCells
    376. A primer on regression methods for decoding cis-regulatory logic. PLoS Comput Biol. 2009 Jan; 5(1):e1000269. Das D, Pellegrini M, Gray JW. PMID: 19180174; PMCID: PMC2607548.
      View in: PubMed   Mentions: 10     Fields:    
    377. Expression profile of CREB knockdown in myeloid leukemia cells. BMC Cancer. 2008 Sep 18; 8:264. Pellegrini M, Cheng JC, Voutila J, Judelson D, Taylor J, Nelson SF, Sakamoto KM. PMID: 18801183; PMCID: PMC2647550.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansCells
    378. Identifying cognate binding pairs among a large set of paralogs: the case of PE/PPE proteins of Mycobacterium tuberculosis. PLoS Comput Biol. 2008 Sep 12; 4(9):e1000174. Riley R, Pellegrini M, Eisenberg D. PMID: 18787688; PMCID: PMC2519833.
      View in: PubMed   Mentions: 23     Fields:    Translation:Cells
    379. Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana. PLoS One. 2008 Sep 08; 3(9):e3156. Bernatavichute YV, Zhang X, Cokus S, Pellegrini M, Jacobsen SE. PMID: 18776934; PMCID: PMC2522283.
      View in: PubMed   Mentions: 172     Fields:    Translation:AnimalsCells
    380. Epigenetic reprogramming by adenovirus e1a. Science. 2008 Aug 22; 321(5892):1086-8. Ferrari R, Pellegrini M, Horwitz GA, Xie W, Berk AJ, Kurdistani SK. PMID: 18719284; PMCID: PMC2693122.
      View in: PubMed   Mentions: 125     Fields:    Translation:HumansCells
    381. X-inactivation in female human embryonic stem cells is in a nonrandom pattern and prone to epigenetic alterations. Proc Natl Acad Sci U S A. 2008 Mar 25; 105(12):4709-14. Shen Y, Matsuno Y, Fouse SD, Rao N, Root S, Xu R, Pellegrini M, Riggs AD, Fan G. PMID: 18339804; PMCID: PMC2290804.
      View in: PubMed   Mentions: 106     Fields:    Translation:HumansCells
    382. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008 Mar 13; 452(7184):215-9. Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE. PMID: 18278030; PMCID: PMC2377394.
      View in: PubMed   Mentions: 1014     Fields:    Translation:AnimalsCells
    383. Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation. Cell Stem Cell. 2008 Feb 07; 2(2):160-9. Fouse SD, Shen Y, Pellegrini M, Cole S, Meissner A, Van Neste L, Jaenisch R, Fan G. PMID: 18371437; PMCID: PMC3070208.
      View in: PubMed   Mentions: 214     Fields:    Translation:AnimalsCells
    384. Modeling the regulatory network of histone acetylation in Saccharomyces cerevisiae. Mol Syst Biol. 2007; 3:153. Pham H, Ferrari R, Cokus SJ, Kurdistani SK, Pellegrini M. PMID: 18091724; PMCID: PMC2174627.
      View in: PubMed   Mentions: 13     Fields:    Translation:AnimalsCells
    385. Genomewide clonal analysis of lethal mutations in the Drosophila melanogaster eye: comparison of the X chromosome and autosomes. Genetics. 2007 Oct; 177(2):689-97. Call GB, Olson JM, Chen J, Villarasa N, Ngo KT, Yabroff AM, Cokus S, Pellegrini M, Bibikova E, Bui C, Cespedes A, Chan C, Chan S, Cheema AK, Chhabra A, Chitsazzadeh V, Do MT, Fang QA, Folick A, Goodstein GL, Huang CR, Hung T, Kim E, Kim W, Kim Y, Kohan E, Kuoy E, Kwak R, Lee E, Lee J, Lin H, Liu HC, Moroz T, Prasad T, Prashad SL, Patananan AN, Rangel A, Rosselli D, Sidhu S, Sitz D, Taber CE, Tan J, Topp K, Tran P, Tran QM, Unkovic M, Wells M, Wickland J, Yackle K, Yavari A, Zaretsky JM, Allen CM, Alli L, An J, Anwar A, Arevalo S, Ayoub D, Badal SS, Baghdanian A, Baghdanian AH, Baumann SA, Becerra VN, Chan HJ, Chang AE, Cheng XA, Chin M, Chong F, Crisostomo C, Datta S, Delosreyes A, Diep F, Ekanayake P, Engeln M, Evers E, Farshidi F, Fischer K, Formanes AJ, Gong J, Gupta R, Haas BE, Hahm V, Hsieh M, Hui JZ, Iao ML, Jin SD, Kim AY, Kim LS, King M, Knudsen-Robbins C, Kohanchi D, Kovshilovskaya B, Ku A, Kung RW, Landig ME, Latterman SS, Lauw SS, Lee DS, Lee JS, Lei KC, Leung LL, Lerner R, Lin JY, Lin K, Lim BC, Lui CP, Liu TQ, Luong V, Makshanoff J, Mei AC, Meza M, Mikhaeil YA, Moarefi M, Nguyen LH, Pai SS, Pandya M, Patel AR, Picard PD, Safaee MM, Salame C, Sanchez C, Sanchez N, Seifert CC, Shah A, Shilgevorkyan OH, Singh I, Soma V, Song JJ, Srivastava N, StaAna JL, Sun C, Tan D, Teruya AS, Tikia R, Tran T, Travis EG, Trinh JD, Vo D, Walsh T, Wong RS, Wu K, Wu YW, Yang NX, Yeranosian M, Yu JS, Zhou JJ, Zhu RX, Abrams A, Abramson A, Amado L, Anderson J, Bashour K, Beyer E, Bookatz A, Brewer S, Buu N, Calvillo S, Cao J, Chan A, Chan J, Chang A, Chang D, Chang Y, Chen Y, Choi J, Chou J, Dang P, Datta S, Davarifar A, Deravanesian A, Desai P, Fabrikant J, Farnad S, Fu K, Garcia E, Garrone N, Gasparyan S, Gayda P, Go S, Goffstein C, Gonzalez C, Guirguis M, Hassid R, Hermogeno B, Hong J, Hong A, Hovestreydt L, Hu C, Huff D, Jamshidian F, Jen J, Kahen K, Kao L, Kelley M, Kho T, Kim Y, Kim S, Kirkpatrick B, Langenbacher A, Laxamana S, Lee J, Lee C, Lee SY, Lee TS, Lee T, Lewis G, Lezcano S, Lin P, Luu T, Luu J, Marrs W, Marsh E, Marshall J, Min S, Minasian T, Minye H, Misra A, Morimoto M, Moshfegh Y, Murray J, Nguyen K, Nguyen C, Nodado E, O'Donahue A, Onugha N, Orjiakor N, Padhiar B, Paul E, Pavel-Dinu M, Pavlenko A, Paz E, Phaklides S, Pham L, Poulose P, Powell R, Pusic A, Ramola D, Regalia K, Ribbens M, Rifai B, Saakyan M, Saarikoski P, Segura M, Shadpour F, Shemmassian A, Singh R, Singh V, Skinner E, Solomin D, Soneji K, Spivey K, Stageberg E, Stavchanskiy M, Tekchandani L, Thai L, Thiyanaratnam J, Tong M, Toor A, Tovar S, Trangsrud K, Tsang WY, Uemura M, Vollmer E, Weiss E, Wood D, Wu J, Wu S, Wu W, Xu Q, Yamauchi Y, Yarosh W, Yee L, Yen G, Banerjee U. PMID: 17720911; PMCID: PMC2034635.
      View in: PubMed   Mentions: 24     Fields:    Translation:AnimalsCells
    386. An improved method for identifying functionally linked proteins using phylogenetic profiles. BMC Bioinformatics. 2007 May 22; 8 Suppl 4:S7. Cokus S, Mizutani S, Pellegrini M. PMID: 17570150; PMCID: PMC1892086.
      View in: PubMed   Mentions: 29     Fields:    
    387. Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol. 2007 May; 5(5):e129. Zhang X, Clarenz O, Cokus S, Bernatavichute YV, Pellegrini M, Goodrich J, Jacobsen SE. PMID: 17439305; PMCID: PMC1852588.
      View in: PubMed   Mentions: 336     Fields:    Translation:AnimalsCells
    388. Pathway and gene-set activation measurement from mRNA expression data: the tissue distribution of human pathways. Genome Biol. 2006; 7(10):R93. Levine DM, Haynor DR, Castle JC, Stepaniants SB, Pellegrini M, Mao M, Johnson JM. PMID: 17044931; PMCID: PMC1794557.
      View in: PubMed   Mentions: 61     Fields:    Translation:HumansCells
    389. Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell. 2006 Sep 22; 126(6):1189-201. Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW, Chen H, Henderson IR, Shinn P, Pellegrini M, Jacobsen SE, Ecker JR. PMID: 16949657.
      View in: PubMed   Mentions: 802     Fields:    Translation:AnimalsCells
    390. Modelling the network of cell cycle transcription factors in the yeast Saccharomyces cerevisiae. BMC Bioinformatics. 2006 Aug 16; 7:381. Cokus S, Rose S, Haynor D, Grønbech-Jensen N, Pellegrini M. PMID: 16914048; PMCID: PMC1570153.
      View in: PubMed   Mentions: 20     Fields:    Translation:AnimalsCells
    391. Bioinformatic challenges for the next decade(s). Philos Trans R Soc Lond B Biol Sci. 2006 Mar 29; 361(1467):525-7. Eisenberg D, Marcotte E, McLachlan AD, Pellegrini M. PMID: 16524841; PMCID: PMC1609334.
      View in: PubMed   Mentions: 4     Fields:    
    392. Detection of parallel functional modules by comparative analysis of genome sequences. Nat Biotechnol. 2005 Feb; 23(2):253-60. Li H, Pellegrini M, Eisenberg D. PMID: 15696156.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    393. Protein interaction networks. Expert Rev Proteomics. 2004 Aug; 1(2):239-49. Pellegrini M, Haynor D, Johnson JM. PMID: 15966818.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansAnimals
    394. Prolinks: a database of protein functional linkages derived from coevolution. Genome Biol. 2004; 5(5):R35. Bowers PM, Pellegrini M, Thompson MJ, Fierro J, Yeates TO, Eisenberg D. PMID: 15128449; PMCID: PMC416471.
      View in: PubMed   Mentions: 119     Fields:    Translation:Animals
    395. Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps. Nucleic Acids Res. 2003 Dec 15; 31(24):7099-109. Strong M, Graeber TG, Beeby M, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D. PMID: 14654685; PMCID: PMC291866.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    396. Inferring protein interactions from phylogenetic distance matrices. Bioinformatics. 2003 Nov 01; 19(16):2039-45. Gertz J, Elfond G, Shustrova A, Weisinger M, Pellegrini M, Cokus S, Rothschild B. PMID: 14594708.
      View in: PubMed   Mentions: 32     Fields:    Translation:Cells
    397. Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach. Genome Biol. 2003; 4(9):R59. Strong M, Mallick P, Pellegrini M, Thompson MJ, Eisenberg D. PMID: 12952538; PMCID: PMC193659.
      View in: PubMed   Mentions: 38     Fields:    Translation:Cells
    398. Defining interacting partners for drug discovery. Expert Opin Ther Targets. 2003 Apr; 7(2):287-97. Pellegrini M. PMID: 12667104.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
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