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. Complete genomes of two Variovorax endophytes isolated from surface-sterilized alfalfa nodules. Microbiol Resour Announc. 2024 Jul 05; e0033624. Hirsch AM, Humm E, Rubbi M, Del Vecchio G, Ha SM, Pellegrini M, Gunsalus RP. PMID: 38967468.
      View in: PubMed   Mentions:
    2. 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:    Fields:    
    3. 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
    4. 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:    Fields:    Translation:HumansAnimals
    5. 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
    6. 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: 1     Fields:    Translation:HumansCells
    7. 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: 2     Fields:    Translation:HumansCellsPHPublic Health
    8. 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:
    9. 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: 2     Fields:    Translation:HumansCells
    10. 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: 1     Fields:    
    11. 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
    12. 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:
    13. 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: 1     Fields:    Translation:HumansCells
    14. 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
    15. 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
    16. 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: 1     Fields:    Translation:Humans
    17. 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: Translation:AnimalsCells
    18. 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: 2     Fields:    Translation:HumansCells
    19. 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:
    20. 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  
    21. 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
    22. 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.
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    23. 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: 9     Fields:    Translation:AnimalsCells
    24. 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: 1  
    25. 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.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimalsCells
    26. Pan-primate studies of age and sex. Geroscience. 2023 Dec; 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: 2     Fields:    Translation:HumansAnimalsCells
    27. 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: 17     Fields:    Translation:HumansCells
    28. 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: 1  
    29. 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: 2     Fields:    Translation:AnimalsCells
    30. Conserved multi-tissue transcriptomic adaptations to exercise training in humans and mice. Cell Rep. 2023 05 30; 42(5):112499. Moore TM, Lee S, Olsen T, Morselli M, Strumwasser AR, Lin AJ, Zhou Z, Abrishami A, Garcia SM, Bribiesca J, Cory K, Whitney K, Ho T, Ho T, Lee JL, Rucker DH, Nguyen CQA, Anand ATS, Yackly A, Mendoza LQ, Leyva BK, Aliman C, Artiga DJ, Meng Y, Charugundla S, Pan C, Jedian V, Seldin MM, Ahn IS, Diamante G, Blencowe M, Yang X, Mouisel E, Pellegrini M, Turcotte LP, Birkeland KI, Norheim F, Drevon CA, Lusis AJ, Hevener AL. PMID: 37178122.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    31. Transcriptional drifts associated with environmental changes in endothelial cells. Elife. 2023 03 27; 12. Afshar Y, Ma F, Quach A, Jeong A, Sunshine HL, Freitas V, Jami-Alahmadi Y, Helaers R, Li X, Pellegrini M, Wohlschlegel JA, Romanoski CE, Vikkula M, Iruela-Arispe ML. PMID: 36971339; PMCID: PMC10168696.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    32. The X-linked epigenetic regulator UTX controls NK cell-intrinsic sex differences. Nat Immunol. 2023 05; 24(5):780-791. Cheng MI, Li JH, Riggan L, Chen B, Tafti RY, Chin S, Ma F, Pellegrini M, Hrncir H, Arnold AP, O'Sullivan TE, Su MA. PMID: 36928413.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansAnimalsCells
    33. Genetic variants of glucose metabolism and exposure to smoking in African American breast cancer. Endocr Relat Cancer. 2023 04 01; 30(4). Jung SY, Papp JC, Sobel EM, Pellegrini M, Yu H. PMID: 36705562; PMCID: PMC10095926.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    34. CD5 expression by dendritic cells directs T cell immunity and sustains immunotherapy responses. Science. 2023 02 17; 379(6633):eabg2752. He M, Roussak K, Ma F, Borcherding N, Garin V, White M, Schutt C, Jensen TI, Zhao Y, Iberg CA, Shah K, Bhatia H, Korenfeld D, Dinkel S, Gray J, Ulezko Antonova A, Ferris S, Donermeyer D, Lindestam Arlehamn C, Gubin MM, Luo J, Gorvel L, Pellegrini M, Sette A, Tung T, Bak R, Modlin RL, Fields RC, Schreiber RD, Allen PM, Klechevsky E. PMID: 36795805; PMCID: PMC10424698.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    35. DNA methylation in peripheral blood leukocytes for the association with glucose metabolism and invasive breast cancer. Clin Epigenetics. 2023 02 13; 15(1):23. Jung SY, Bhatti P, Pellegrini M. PMID: 36782224; PMCID: PMC9926571.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    36. Comparative transcriptomics reveals highly conserved regional programs between porcine and human colonic enteric nervous system. Commun Biol. 2023 01 24; 6(1):98. Li T, Morselli M, Su T, Million M, Larauche M, Pellegrini M, Taché Y, Yuan PQ. PMID: 36693960; PMCID: PMC9872754.
      View in: PubMed   Mentions: 3  Translation:HumansAnimalsCells
    37. Polyunsaturated Fatty Acids Mend Macrophage Transcriptome, Glycome, and Phenotype in the Patients with Neurodegenerative Diseases, Including Alzheimer's Disease. J Alzheimers Dis. 2023; 91(1):245-261. Dover M, Moseley T, Biskaduros A, Paulchakrabarti M, Hwang SH, Hammock B, Choudhury B, Kaczor-Urbanowicz KE, Urbanowicz A, Morselli M, Dang J, Pellegrini M, Paul K, Bentolila LA, Fiala M. PMID: 36373322; PMCID: PMC9881025.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    38. Single-cell RNA sequencing identifies a population of human liver-type ILC1s. Cell Rep. 2023 01 31; 42(1):111937. Krämer B, Nalin AP, Ma F, Eickhoff S, Lutz P, Leonardelli S, Goeser F, Finnemann C, Hack G, Raabe J, ToVinh M, Ahmad S, Hoffmeister C, Kaiser KM, Manekeller S, Branchi V, Bald T, Hölzel M, Hüneburg R, Nischalke HD, Semaan A, Langhans B, Kaczmarek DJ, Benner B, Lordo MR, Kowalski J, Gerhardt A, Timm J, Toma M, Mohr R, Türler A, Charpentier A, van Bremen T, Feldmann G, Sattler A, Kotsch K, Abdallah AT, Strassburg CP, Spengler U, Carson WE, Mundy-Bosse BL, Pellegrini M, O'Sullivan TE, Freud AG, Nattermann J. PMID: 36640314; PMCID: PMC9950534.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    39. Longitudinal profiling in patients undergoing cardiac surgery reveals postoperative changes in DNA methylation. Clin Epigenetics. 2022 12 30; 14(1):195. Fischer MA, Chapski DJ, Soehalim E, Montoya DJ, Grogan T, Pellegrini M, Cai H, Shemin RJ, Vondriska TM. PMID: 36585726; PMCID: PMC9805211.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    40. Association of DNA methylation with energy and fear-related behaviors in canines. Front Psychol. 2022; 13:1025494. Sanders AR, Bhongir N, vonHoldt B, Pellegrini M. PMID: 36591016; PMCID: PMC9794564.
      View in: PubMed   Mentions: 1  
    41. Targeting the EIF2AK1 Signaling Pathway Rescues Red Blood Cell Production in SF3B1-Mutant Myelodysplastic Syndromes With Ringed Sideroblasts. Blood Cancer Discov. 2022 11 02; 3(6):554-567. Adema V, Ma F, Kanagal-Shamanna R, Thongon N, Montalban-Bravo G, Yang H, Peslak SA, Wang F, Acha P, Sole F, Lockyer P, Cassari M, Maciejewski JP, Visconte V, Gañán-Gómez I, Song Y, Bueso-Ramos C, Pellegrini M, Tan TM, Bejar R, Carew JS, Halene S, Santini V, Al-Atrash G, Clise-Dwyer K, Garcia-Manero G, Blobel GA, Colla S. PMID: 35926182; PMCID: PMC9894566.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    42. On the role of cell surface associated, mucin-like glycoproteins in the pennate diatom Craspedostauros australis (Bacillariophyceae). J Phycol. 2023 02; 59(1):54-69. Poulsen N, Hennig H, Geyer VF, Diez S, Wetherbee R, Fitz-Gibbon S, Pellegrini M, Kröger N. PMID: 36199194.
      View in: PubMed   Mentions: 2     Fields:    Translation:Animals
    43. Single-Cell RNA-Seq Identifies Dynamic Cardiac Transition Program from ADCs Induced by Leukemia Inhibitory Factor. Stem Cells. 2022 10 21; 40(10):932-948. Yao J, Ma F, Zhang L, Zhu C, Jumabay M, Yao Z, Wang L, Cai X, Zhang D, Qiao X, Shivkumar K, Pellegrini M, Yao Y, Wu X, Boström KI. PMID: 35896368; PMCID: PMC9585902.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    44. A Hypertrophic Spinal Pachymeningitis Patient With Factor V Leiden (G1691A), MTHFR C677T, MTHFR A1298C, PAI-1 4G-5G, Glycoprotein IIIa L33P Gene Mutations. Cureus. 2022 Oct; 14(10):e29937. Civlan S, Harvey C, Herek D, Türkçüer I, Sabirli R, Pellegrini M, Koseler A. PMID: 36348907; PMCID: PMC9634853.
      View in: PubMed   Mentions:
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    101. 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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    102. 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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    103. 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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    104. 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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    105. 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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    106. 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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    107. 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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    108. 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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    109. 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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    110. 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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    111. 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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    112. 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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    113. 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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    114. 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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    115. 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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    116. 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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    117. 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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    118. 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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    119. 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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    120. 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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    121. 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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    122. 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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    123. 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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    124. 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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    125. 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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    126. 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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    127. 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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    128. 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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    129. 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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    130. 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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    131. 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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    132. 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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    133. 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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    134. 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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    135. 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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    136. 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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    137. 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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    138. 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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    139. 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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    140. 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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    141. 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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    142. 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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    143. 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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    144. 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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    145. 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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    146. 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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    147. 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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    148. 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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    149. 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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    150. 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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    151. 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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    152. 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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    153. 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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    154. 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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    155. 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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    156. 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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    157. 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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    159. 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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    160. 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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    161. 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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    162. 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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    164. 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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    165. 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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    167. 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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    168. 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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    170. 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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    171. 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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    172. 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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    177. 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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    218. 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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    219. 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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    221. 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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    222. 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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    223. 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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    224. 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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    225. 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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    226. 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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    227. 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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    228. 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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    229. 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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    231. 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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    232. 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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    233. 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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    234. 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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    236. 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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    239. 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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    249. 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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    341. 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.
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    342. 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.
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    343. 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.
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    344. 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.
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    345. BS Seeker: precise mapping for bisulfite sequencing. BMC Bioinformatics. 2010 Apr 23; 11:203. Chen PY, Cokus SJ, Pellegrini M. PMID: 20416082; PMCID: PMC2871274.
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    346. 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.
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    347. 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.
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    348. 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.
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    349. 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.
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    350. 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.
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    351. 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.
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    352. 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.
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    353. 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.
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    354. Determining the conservation of DNA methylation in Arabidopsis. Epigenetics. 2009 Feb 16; 4(2):119-24. Widman N, Jacobsen SE, Pellegrini M. PMID: 19384058.
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    355. 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.
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    356. 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.
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    357. 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.
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    358. 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.
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    359. 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.
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    360. 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.
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    361. 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.
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    362. 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.
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    363. 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.
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    364. 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.
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    365. 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.
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    366. 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.
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    367. 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.
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    368. 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.
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    369. 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.
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    370. 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.
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    371. 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.
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    372. 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.
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    373. Protein interaction networks. Expert Rev Proteomics. 2004 Aug; 1(2):239-49. Pellegrini M, Haynor D, Johnson JM. PMID: 15966818.
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    374. 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.
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    375. 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.
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    376. 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.
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    377. 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.
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    378. Defining interacting partners for drug discovery. Expert Opin Ther Targets. 2003 Apr; 7(2):287-97. Pellegrini M. PMID: 12667104.
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