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Nelson Stanley

Title(s)Professor In-Residence, Human Genetics
Phone(310) 794-5446
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    Other Positions
    Title(s)Director, DNA Microarray Technology

    Title(s)Co-Director, Center for Duchenne Muscular Dystrophy


    Collapse Research 
    Collapse Research Activities and Funding
    UCLA clinical site for the investigation of undiagnosed disorders
    NIH/NHGRI U01HG007703Jul 1, 2014 - Jun 30, 2022
    Role: Principal Investigator
    Rapid Phenotyping for Rare Variant Discovery in Autism
    NIH/NINDS R01NS073871Sep 1, 2011 - Aug 31, 2016
    Role: Principal Investigator
    Identification of Enhancers of Therapeutic Exon Skipping for DMD
    NIH/NIAMS RC1AR058333Sep 25, 2009 - Aug 31, 2011
    Role: Co-Principal Investigator
    SNP studies in ADHD linked regions
    NIH/NIMH R01MH071852Feb 1, 2006 - Jan 31, 2012
    Role: Principal Investigator
    UCLA NINDS/NIMH Microarray Center
    NIH/NINDS U24NS052108Jul 15, 2005 - May 31, 2011
    Role: Principal Investigator
    UCLA NHLBI Shared Microarray Facilities
    NIH/NHLBI R01HL072367Sep 30, 2002 - Jul 31, 2006
    Role: Principal Investigator
    UCLA NINDS/NIMH Microarray Center
    NIH/NINDS U24NS043562Jun 1, 2002 - May 31, 2005
    Role: Principal Investigator
    GENE EXPRESSION BASED CLASSIFICATION OF GLIAL TUMORS
    NIH/NCI U01CA088127Aug 1, 2000 - Jan 31, 2006
    Role: Principal Investigator
    PROFILING PEDIATRIC MALIGNANCIES BY RDA AND MICROARRAY
    NIH/NCI R01CA077038Sep 30, 1997 - Sep 29, 2000
    Role: Principal Investigator
    ADAPTING GENOMIC MISMATCH SCANNING TO HUMAN GENE MAPPING
    NIH/NHGRI R29HG001141Sep 30, 1994 - Jul 31, 1999
    Role: Principal Investigator
    LOCALIZATION OF THE WILMS TUMOR SUSCEPTIBILITY GENE(S)
    NIH/NICHD K11HD000929May 1, 1991 - Apr 30, 1997
    Role: Principal Investigator
    UCLA Intercampus Medical Genetics Training Program
    NIH/NIGMS T32GM008243Jul 1, 1987 - Jun 30, 2020
    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.
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    1. Kang X, Zhao Y, Van Arsdell G, Nelson SF, Touma M. Ppp1r1b-LncRNA Inhibits PRC2 at Myogenic Regulatory Genes to Promote Cardiac and Skeletal Muscle Development in Mouse and Human. RNA. 2020 Jan 17. PMID: 31953255.
      View in: PubMed
    2. Shieh C, Jones N, Vanle B, Au M, Huang AY, Silva APG, Lee H, Douine ED, Otero MG, Choi A, Grand K, Taff IP, Delgado MR, Hajianpour MJ, Seeley A, Rohena L, Vernon H, Gripp KW, Vergano SA, Mahida S, Naidu S, Sousa AB, Wain KE, Challman TD, Beek G, Basel D, Ranells J, Smith R, Yusupov R, Freckmann ML, Ohden L, Davis-Keppen L, Chitayat D, Dowling JJ, Finkel R, Dauber A, Spillmann R, Pena LDM, Metcalfe K, Splitt M, Lachlan K, McKee SA, Hurst J, Fitzpatrick DR, Morton JEV, Cox H, Venkateswaran S, Young JI, Marsh ED, Nelson SF, Martinez JA, Graham JM, Kini U, Mackay JP, Pierson TM. GATAD2B-associated neurodevelopmental disorder (GAND): clinical and molecular insights into a NuRD-related disorder. Genet Med. 2020 Jan 17. PMID: 31949314.
      View in: PubMed
    3. Zhao Y, Kang X, Gao F, Guzman A, Lau RP, Biniwale R, Wadehra M, Reemtsen B, Garg M, Halnon N, Quintero-Rivera F, Van Arsdell G, Coppola G, Nelson SF, Touma M. Gene-environment regulatory circuits of right ventricular pathology in tetralogy of fallot. J Mol Med (Berl). 2019 Dec; 97(12):1711-1722. PMID: 31834445.
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    4. Ngo KJ, Rexach JE, Lee H, Petty LE, Perlman S, Valera JM, Deignan JL, Mao Y, Aker M, Posey JE, Jhangiani SN, Coban-Akdemir ZH, Boerwinkle E, Muzny D, Nelson AB, Hassin-Baer S, Poke G, Neas K, Geschwind MD, Grody WW, Gibbs R, Geschwind DH, Lupski JR, Below JE, Nelson SF, Fogel BL. A diagnostic ceiling for exome sequencing in cerebellar ataxia and related neurological disorders. Hum Mutat. 2019 Nov 06. PMID: 31692161.
      View in: PubMed
    5. Lee H, Huang AY, Wang LK, Yoon AJ, Renteria G, Eskin A, Signer RH, Dorrani N, Nieves-Rodriguez S, Wan J, Douine ED, Woods JD, Dell'Angelica EC, Fogel BL, Martin MG, Butte MJ, Parker NH, Wang RT, Shieh PB, Wong DA, Gallant N, Singh KE, Tavyev Asher YJ, Sinsheimer JS, Krakow D, Loo SK, Allard P, Papp JC, Palmer CGS, Martinez-Agosto JA, Nelson SF. Diagnostic utility of transcriptome sequencing for rare Mendelian diseases. Genet Med. 2019 Oct 14. PMID: 31607746.
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    6. Barthélémy F, Wang RT, Hsu C, Douine ED, Marcantonio EE, Nelson SF, Miceli MC. Targeting RyR Activity Boosts Antisense Exon 44 and 45 Skipping in Human DMD Skeletal or Cardiac Muscle Culture Models. Mol Ther Nucleic Acids. 2019 Dec 06; 18:580-589. PMID: 31678734.
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    7. Gibbs EM, Barthélémy F, Douine ED, Hardiman NC, Shieh PB, Khanlou N, Crosbie RH, Nelson SF, Miceli MC. Large in-frame 5' deletions in DMD associated with mild Duchenne muscular dystrophy: Two case reports and a review of the literature. Neuromuscul Disord. 2019 Nov; 29(11):863-873. PMID: 31672265.
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    8. Ng BG, Sosicka P, Agadi S, Almannai M, Bacino CA, Barone R, Botto LD, Burton JE, Carlston C, Chung BH, Cohen JS, Coman D, Dipple KM, Dorrani N, Dobyns WB, Elias AF, Epstein L, Gahl WA, Garozzo D, Hammer TB, Haven J, Héron D, Herzog M, Hoganson GE, Hunter JM, Jain M, Juusola J, Lakhani S, Lee H, Lee J, Lewis K, Longo N, Lourenço CM, Mak CCY, McKnight D, Mendelsohn BA, Mignot C, Mirzaa G, Mitchell W, Muhle H, Nelson SF, Olczak M, Palmer CGS, Partikian A, Patterson MC, Pierson TM, Quinonez SC, Regan BM, Ross ME, Guillen Sacoto MJ, Scaglia F, Scheffer IE, Segal D, Singhal NS, Striano P, Sturiale L, Symonds JD, Tang S, Vilain E, Willis M, Wolfe LA, Yang H, Yano S, Powis Z, Suchy SF, Rosenfeld JA, Edmondson AC, Grunewald S, Freeze HH. SLC35A2-CDG: Functional characterization, expanded molecular, clinical, and biochemical phenotypes of 30 unreported Individuals. Hum Mutat. 2019 07; 40(7):908-925. PMID: 30817854.
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    9. Vo AH, Swaggart KA, Woo A, Gao QQ, Demonbreun AR, Fallon KS, Quattrocelli M, Hadhazy M, Page PGT, Chen Z, Eskin A, Squire K, Nelson SF, McNally EM. Dusp6 is a genetic modifier of growth through enhanced ERK activity. Hum Mol Genet. 2019 01 15; 28(2):279-289. PMID: 30289454.
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    10. Aartsma-Rus A, Hegde M, Ben-Omran T, Buccella F, Ferlini A, Gallano P, Howell RR, Leturcq F, Martin AS, Potulska-Chromik A, Saute JA, Schmidt WM, Sejersen T, Tuffery-Giraud S, Uyguner ZO, Witcomb LA, Yau S, Nelson SF. Evidence-Based Consensus and Systematic Review on Reducing the Time to Diagnosis of Duchenne Muscular Dystrophy. J Pediatr. 2019 01; 204:305-313.e14. PMID: 30579468.
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    11. Stephen J, Maddirevula S, Nampoothiri S, Burke JD, Herzog M, Shukla A, Steindl K, Eskin A, Patil SJ, Joset P, Lee H, Garrett LJ, Yokoyama T, Balanda N, Bodine SP, Tolman NJ, Zerfas PM, Zheng A, Ramantani G, Girisha KM, Rivas C, Suresh PV, Elkahloun A, Alsaif HS, Wakil SM, Mahmoud L, Ali R, Prochazkova M, Kulkarni AB, Ben-Omran T, Colak D, Morris HD, Rauch A, Martinez-Agosto JA, Nelson SF, Alkuraya FS, Gahl WA, Malicdan MCV. Bi-allelic TMEM94 Truncating Variants Are Associated with Neurodevelopmental Delay, Congenital Heart Defects, and Distinct Facial Dysmorphism. Am J Hum Genet. 2018 12 06; 103(6):948-967. PMID: 30526868.
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    12. Magrath P, Maforo N, Renella P, Nelson SF, Halnon N, Ennis DB. Cardiac MRI biomarkers for Duchenne muscular dystrophy. Biomark Med. 2018 11; 12(11):1271-1289. PMID: 30499689.
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    13. Splinter K, Adams DR, Bacino CA, Bellen HJ, Bernstein JA, Cheatle-Jarvela AM, Eng CM, Esteves C, Gahl WA, Hamid R, Jacob HJ, Kikani B, Koeller DM, Kohane IS, Lee BH, Loscalzo J, Luo X, McCray AT, Metz TO, Mulvihill JJ, Nelson SF, Palmer CGS, Phillips JA, Pick L, Postlethwait JH, Reuter C, Shashi V, Sweetser DA, Tifft CJ, Walley NM, Wangler MF, Westerfield M, Wheeler MT, Wise AL, Worthey EA, Yamamoto S, Ashley EA. Effect of Genetic Diagnosis on Patients with Previously Undiagnosed Disease. N Engl J Med. 2018 11 29; 379(22):2131-2139. PMID: 30304647.
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    14. Kennedy J, Goudie D, Blair E, Chandler K, Joss S, McKay V, Green A, Armstrong R, Lees M, Kamien B, Hopper B, Tan TY, Yap P, Stark Z, Okamoto N, Miyake N, Matsumoto N, Macnamara E, Murphy JL, McCormick E, Hakonarson H, Falk MJ, Li D, Blackburn P, Klee E, Babovic-Vuksanovic D, Schelley S, Hudgins L, Kant S, Isidor B, Cogne B, Bradbury K, Williams M, Patel C, Heussler H, Duff-Farrier C, Lakeman P, Scurr I, Kini U, Elting M, Reijnders M, Schuurs-Hoeijmakers J, Wafik M, Blomhoff A, Ruivenkamp CAL, Nibbeling E, Dingemans AJM, Douine ED, Nelson SF, Arboleda VA, Newbury-Ecob R. KAT6A Syndrome: genotype-phenotype correlation in 76 patients with pathogenic KAT6A variants. Genet Med. 2019 04; 21(4):850-860. PMID: 30245513.
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    15. Marcogliese PC, Shashi V, Spillmann RC, Stong N, Rosenfeld JA, Koenig MK, Martínez-Agosto JA, Herzog M, Chen AH, Dickson PI, Lin HJ, Vera MU, Salamon N, Graham JM, Ortiz D, Infante E, Steyaert W, Dermaut B, Poppe B, Chung HL, Zuo Z, Lee PT, Kanca O, Xia F, Yang Y, Smith EC, Jasien J, Kansagra S, Spiridigliozzi G, El-Dairi M, Lark R, Riley K, Koeberl DD, Golden-Grant K, Yamamoto S, Wangler MF, Mirzaa G, Hemelsoet D, Lee B, Nelson SF, Goldstein DB, Bellen HJ, Pena LDM. IRF2BPL Is Associated with Neurological Phenotypes. Am J Hum Genet. 2018 09 06; 103(3):456. PMID: 30193138.
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    16. Marcogliese PC, Shashi V, Spillmann RC, Stong N, Rosenfeld JA, Koenig MK, Martínez-Agosto JA, Herzog M, Chen AH, Dickson PI, Lin HJ, Vera MU, Salamon N, Graham JM, Ortiz D, Infante E, Steyaert W, Dermaut B, Poppe B, Chung HL, Zuo Z, Lee PT, Kanca O, Xia F, Yang Y, Smith EC, Jasien J, Kansagra S, Spiridigliozzi G, El-Dairi M, Lark R, Riley K, Koeberl DD, Golden-Grant K, Yamamoto S, Wangler MF, Mirzaa G, Hemelsoet D, Lee B, Nelson SF, Goldstein DB, Bellen HJ, Pena LDM. IRF2BPL Is Associated with Neurological Phenotypes. Am J Hum Genet. 2018 08 02; 103(2):245-260. PMID: 30057031.
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    17. Wang RT, Barthelemy F, Martin AS, Douine ED, Eskin A, Lucas A, Lavigne J, Peay H, Khanlou N, Sweeney L, Cantor RM, Miceli MC, Nelson SF. DMD genotype correlations from the Duchenne Registry: Endogenous exon skipping is a factor in prolonged ambulation for individuals with a defined mutation subtype. Hum Mutat. 2018 09; 39(9):1193-1202. PMID: 29907980.
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    18. Rao AR, Nelson SF. Calculating the statistical significance of rare variants causal for Mendelian and complex disorders. BMC Med Genomics. 2018 Jun 13; 11(1):53. PMID: 29898714.
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    19. Chia PH, Zhong FL, Niwa S, Bonnard C, Utami KH, Zeng R, Lee H, Eskin A, Nelson SF, Xie WH, Al-Tawalbeh S, El-Khateeb M, Shboul M, Pouladi MA, Al-Raqad M, Reversade B. A homozygous loss-of-function CAMK2A mutation causes growth delay, frequent seizures and severe intellectual disability. Elife. 2018 05 22; 7. PMID: 29784083.
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    20. Clark MJ, Homer N, O'Connor BD, Chen Z, Eskin A, Lee H, Merriman B, Nelson SF. Correction: U87MG Decoded: The Genomic Sequence of a Cytogenetically Aberrant Human Cancer Cell Line. PLoS Genet. 2018 05; 14(5):e1007392. PMID: 29768410.
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    21. Kramerova I, Torres JA, Eskin A, Nelson SF, Spencer MJ. Calpain 3 and CaMKIIß signaling are required to induce HSP70 necessary for adaptive muscle growth after atrophy. Hum Mol Genet. 2018 05 01; 27(9):1642-1653. PMID: 29528394.
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    22. Takeuchi H, Wong D, Schneider M, Freeze HH, Takeuchi M, Berardinelli SJ, Ito A, Lee H, Nelson SF, Haltiwanger RS. Variant in human POFUT1 reduces enzymatic activity and likely causes a recessive microcephaly, global developmental delay with cardiac and vascular features. Glycobiology. 2018 05 01; 28(5):276-283. PMID: 29452367.
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    23. Wang DW, Mokhonova EI, Kendall GC, Becerra D, Naeini YB, Cantor RM, Spencer MJ, Nelson SF, Miceli MC. Repurposing Dantrolene for Long-Term Combination Therapy to Potentiate Antisense-Mediated DMD Exon Skipping in the mdx Mouse. Mol Ther Nucleic Acids. 2018 Jun 01; 11:180-191. PMID: 29858053.
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    24. Barseghyan H, Symon A, Zadikyan M, Almalvez M, Segura EE, Eskin A, Bramble MS, Arboleda VA, Baxter R, Nelson SF, Délot EC, Harley V, Vilain E. Identification of novel candidate genes for 46,XY disorders of sex development (DSD) using a C57BL/6J-Y POS mouse model. Biol Sex Differ. 2018 01 30; 9(1):8. PMID: 29378665.
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    25. Barthelemy F, Wang D, Nelson SF, Miceli MC. Validation and Detection of Exon Skipping Boosters in DMD Patient Cell Models and mdx Mouse. Methods Mol Biol. 2018; 1828:309-326. PMID: 30171550.
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    26. Hicks MR, Hiserodt J, Paras K, Fujiwara W, Eskin A, Jan M, Xi H, Young CS, Evseenko D, Nelson SF, Spencer MJ, Handel BV, Pyle AD. ERBB3 and NGFR mark a distinct skeletal muscle progenitor cell in human development and hPSCs. Nat Cell Biol. 2018 01; 20(1):46-57. PMID: 29255171.
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    27. Palmer N, Beam A, Agniel D, Eran A, Manrai A, Spettell C, Steinberg G, Mandl K, Fox K, Nelson SF, Kohane I. Association of Sex With Recurrence of Autism Spectrum Disorder Among Siblings. JAMA Pediatr. 2017 11 01; 171(11):1107-1112. PMID: 28973142.
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    28. Barseghyan H, Tang W, Wang RT, Almalvez M, Segura E, Bramble MS, Lipson A, Douine ED, Lee H, Délot EC, Nelson SF, Vilain E. Next-generation mapping: a novel approach for detection of pathogenic structural variants with a potential utility in clinical diagnosis. Genome Med. 2017 10 25; 9(1):90. PMID: 29070057.
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    29. Touma M, Reemtsen B, Halnon N, Alejos J, Finn JP, Nelson SF, Wang Y. A Path to Implement Precision Child Health Cardiovascular Medicine. Front Cardiovasc Med. 2017; 4:36. PMID: 28620608.
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    30. Nelson SF, Miceli MC. FDA Approval of Eteplirsen for Muscular Dystrophy. JAMA. 2017 04 11; 317(14):1480. PMID: 28399245.
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    31. Rosti RO, Sotak BN, Bielas SL, Bhat G, Silhavy JL, Aslanger AD, Altunoglu U, Bilge I, Tasdemir M, Yzaguirrem AD, Musaev D, Infante S, Thuong W, Marin-Valencia I, Nelson SF, Kayserili H, Gleeson JG. Homozygous mutation in NUP107 leads to microcephaly with steroid-resistant nephrotic condition similar to Galloway-Mowat syndrome. J Med Genet. 2017 06; 54(6):399-403. PMID: 28280135.
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    32. Schoch K, Meng L, Szelinger S, Bearden DR, Stray-Pedersen A, Busk OL, Stong N, Liston E, Cohn RD, Scaglia F, Rosenfeld JA, Tarpinian J, Skraban CM, Deardorff MA, Friedman JN, Akdemir ZC, Walley N, Mikati MA, Kranz PG, Jasien J, McConkie-Rosell A, McDonald M, Wechsler SB, Freemark M, Kansagra S, Freedman S, Bali D, Millan F, Bale S, Nelson SF, Lee H, Dorrani N, Goldstein DB, Xiao R, Yang Y, Posey JE, Martinez-Agosto JA, Lupski JR, Wangler MF, Shashi V. A Recurrent De Novo Variant in NACC1 Causes a Syndrome Characterized by Infantile Epilepsy, Cataracts, and Profound Developmental Delay. Am J Hum Genet. 2017 Feb 02; 100(2):343-351. PMID: 28132692.
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    33. Yoon WH, Sandoval H, Nagarkar-Jaiswal S, Jaiswal M, Yamamoto S, Haelterman NA, Putluri N, Putluri V, Sreekumar A, Tos T, Aksoy A, Donti T, Graham BH, Ohno M, Nishi E, Hunter J, Muzny DM, Carmichael J, Shen J, Arboleda VA, Nelson SF, Wangler MF, Karaca E, Lupski JR, Bellen HJ. Loss of Nardilysin, a Mitochondrial Co-chaperone for a-Ketoglutarate Dehydrogenase, Promotes mTORC1 Activation and Neurodegeneration. Neuron. 2017 Jan 04; 93(1):115-131. PMID: 28017472.
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    34. Wan J, Steffen J, Yourshaw M, Mamsa H, Andersen E, Rudnik-Schöneborn S, Pope K, Howell KB, McLean CA, Kornberg AJ, Joseph J, Lockhart PJ, Zerres K, Ryan MM, Nelson SF, Koehler CM, Jen JC. Loss of function of SLC25A46 causes lethal congenital pontocerebellar hypoplasia. Brain. 2016 11 01; 139(11):2877-2890. PMID: 27543974.
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    35. Ge X, Gong H, Dumas K, Litwin J, Phillips JJ, Waisfisz Q, Weiss MM, Hendriks Y, Stuurman KE, Nelson SF, Grody WW, Lee H, Kwok PY, Shieh JT. Missense-depleted regions in population exomes implicate ras superfamily nucleotide-binding protein alteration in patients with brain malformation. NPJ Genom Med. 2016; 1. PMID: 28868155.
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    36. Klein S, Goldman A, Lee H, Ghahremani S, Bhakta V, Nelson SF, Martinez-Agosto JA. Truncating mutations in APP cause a distinct neurological phenotype. Ann Neurol. 2016 Sep; 80(3):456-60. PMID: 27422356.
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    37. Monte E, Rosa-Garrido M, Karbassi E, Chen H, Lopez R, Rau CD, Wang J, Nelson SF, Wu Y, Stefani E, Lusis AJ, Wang Y, Kurdistani SK, Franklin S, Vondriska TM. Reciprocal Regulation of the Cardiac Epigenome by Chromatin Structural Proteins Hmgb and Ctcf: IMPLICATIONS FOR TRANSCRIPTIONAL REGULATION. J Biol Chem. 2016 07 22; 291(30):15428-46. PMID: 27226577.
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    38. Praissman JL, Willer T, Sheikh MO, Toi A, Chitayat D, Lin YY, Lee H, Stalnaker SH, Wang S, Prabhakar PK, Nelson SF, Stemple DL, Moore SA, Moremen KW, Campbell KP, Wells L. The functional O-mannose glycan on a-dystroglycan contains a phospho-ribitol primed for matriglycan addition. Elife. 2016 04 29; 5. PMID: 27130732.
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    39. Miceli MC, Nelson SF. The case for eteplirsen: Paving the way for precision medicine. Mol Genet Metab. 2016 06; 118(2):70-1. PMID: 27102846.
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    40. Oud MM, Bonnard C, Mans DA, Altunoglu U, Tohari S, Ng AYJ, Eskin A, Lee H, Rupar CA, de Wagenaar NP, Wu KM, Lahiry P, Pazour GJ, Nelson SF, Hegele RA, Roepman R, Kayserili H, Venkatesh B, Siu VM, Reversade B, Arts HH. A novel ICK mutation causes ciliary disruption and lethal endocrine-cerebro-osteodysplasia syndrome. Cilia. 2016; 5:8. PMID: 27069622.
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    41. Kramerova I, Ermolova N, Eskin A, Hevener A, Quehenberger O, Armando AM, Haller R, Romain N, Nelson SF, Spencer MJ. Failure to up-regulate transcription of genes necessary for muscle adaptation underlies limb girdle muscular dystrophy 2A (calpainopathy). Hum Mol Genet. 2016 06 01; 25(11):2194-2207. PMID: 27005420.
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    42. Freedman AH, Schweizer RM, Ortega-Del Vecchyo D, Han E, Davis BW, Gronau I, Silva PM, Galaverni M, Fan Z, Marx P, Lorente-Galdos B, Ramirez O, Hormozdiari F, Alkan C, Vilà C, Squire K, Geffen E, Kusak J, Boyko AR, Parker HG, Lee C, Tadigotla V, Siepel A, Bustamante CD, Harkins TT, Nelson SF, Marques-Bonet T, Ostrander EA, Wayne RK, Novembre J. Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs. PLoS Genet. 2016 Mar; 12(3):e1005851. PMID: 26943675.
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    43. Xue Y, Schoser B, Rao AR, Quadrelli R, Vaglio A, Rupp V, Beichler C, Nelson SF, Schapacher-Tilp G, Windpassinger C, Wilcox WR. Exome Sequencing Identified a Splice Site Mutation in FHL1 that Causes Uruguay Syndrome, an X-Linked Disorder With Skeletal Muscle Hypertrophy and Premature Cardiac Death. Circ Cardiovasc Genet. 2016 Apr; 9(2):130-5. PMID: 26933038.
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    44. Panosyan EH, Lasky JL, Lin HJ, Lai A, Hai Y, Guo X, Quinn M, Nelson SF, Cloughesy TF, Nghiemphu PL. Clinical aggressiveness of malignant gliomas is linked to augmented metabolism of amino acids. J Neurooncol. 2016 05; 128(1):57-66. PMID: 26922345.
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    45. Young CS, Hicks MR, Ermolova NV, Nakano H, Jan M, Younesi S, Karumbayaram S, Kumagai-Cresse C, Wang D, Zack JA, Kohn DB, Nakano A, Nelson SF, Miceli MC, Spencer MJ, Pyle AD. A Single CRISPR-Cas9 Deletion Strategy that Targets the Majority of DMD Patients Restores Dystrophin Function in hiPSC-Derived Muscle Cells. Cell Stem Cell. 2016 Apr 07; 18(4):533-40. PMID: 26877224.
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    46. Wang X, Pandey AK, Mulligan MK, Williams EG, Mozhui K, Li Z, Jovaisaite V, Quarles LD, Xiao Z, Huang J, Capra JA, Chen Z, Taylor WL, Bastarache L, Niu X, Pollard KS, Ciobanu DC, Reznik AO, Tishkov AV, Zhulin IB, Peng J, Nelson SF, Denny JC, Auwerx J, Lu L, Williams RW. Joint mouse-human phenome-wide association to test gene function and disease risk. Nat Commun. 2016 Feb 02; 7:10464. PMID: 26833085.
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    47. Tafakhori A, Yu Jin Ng A, Tohari S, Venkatesh B, Lee H, Eskin A, Nelson SF, Bonnard C, Reversade B, Kariminejad A. Mutation in TWINKLE in a Large Iranian Family with Progressive External Ophthalmoplegia, Myopathy, Dysphagia and Dysphonia, and Behavior Change. Arch Iran Med. 2016 Feb; 19(2):87-91. PMID: 26838077.
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    48. Tso JL, Yang S, Menjivar JC, Yamada K, Zhang Y, Hong I, Bui Y, Stream A, McBride WH, Liau LM, Nelson SF, Cloughesy TF, Yong WH, Lai A, Tso CL. Bone morphogenetic protein 7 sensitizes O6-methylguanine methyltransferase expressing-glioblastoma stem cells to clinically relevant dose of temozolomide. Mol Cancer. 2015 Nov 06; 14:189. PMID: 26546412.
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    49. Yong WH, Shabihkhani M, Telesca D, Yang S, Tso JL, Menjivar JC, Wei B, Lucey GM, Mareninov S, Chen Z, Liau LM, Lai A, Nelson SF, Cloughesy TF, Tso CL. Ribosomal Proteins RPS11 and RPS20, Two Stress-Response Markers of Glioblastoma Stem Cells, Are Novel Predictors of Poor Prognosis in Glioblastoma Patients. PLoS One. 2015; 10(10):e0141334. PMID: 26506620.
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    50. Eyre HA, Eskin A, Nelson SF, St Cyr NM, Siddarth P, Baune BT, Lavretsky H. Genomic predictors of remission to antidepressant treatment in geriatric depression using genome-wide expression analyses: a pilot study. Int J Geriatr Psychiatry. 2016 May; 31(5):510-7. PMID: 26471432.
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    51. Wang RT, Nelson SF. What can Duchenne Connect teach us about treating Duchenne muscular dystrophy? Curr Opin Neurol. 2015 Oct; 28(5):535-41. PMID: 26356412.
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    52. Fogel BL, Lee H, Strom SP, Deignan JL, Nelson SF. Clinical exome sequencing in neurogenetic and neuropsychiatric disorders. Ann N Y Acad Sci. 2016 02; 1366(1):49-60. PMID: 26250888.
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    53. Taylor SP, Dantas TJ, Duran I, Wu S, Lachman RS, Nelson SF, Cohn DH, Vallee RB, Krakow D. Mutations in DYNC2LI1 disrupt cilia function and cause short rib polydactyly syndrome. Nat Commun. 2015 Jun 16; 6:7092. PMID: 26077881.
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    54. Ji J, Lee H, Argiropoulos B, Dorrani N, Mann J, Martinez-Agosto JA, Gomez-Ospina N, Gallant N, Bernstein JA, Hudgins L, Slattery L, Isidor B, Le Caignec C, David A, Obersztyn E, Wisniowiecka-Kowalnik B, Fox M, Deignan JL, Vilain E, Hendricks E, Horton Harr M, Noon SE, Jackson JR, Wilkens A, Mirzaa G, Salamon N, Abramson J, Zackai EH, Krantz I, Innes AM, Nelson SF, Grody WW, Quintero-Rivera F. DYRK1A haploinsufficiency causes a new recognizable syndrome with microcephaly, intellectual disability, speech impairment, and distinct facies. Eur J Hum Genet. 2015 Nov; 23(11):1473-81. PMID: 25944381.
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    55. Brown R, Lee H, Eskin A, Kichaev G, Lohmueller KE, Reversade B, Nelson SF, Pasaniuc B. Leveraging ancestry to improve causal variant identification in exome sequencing for monogenic disorders. Eur J Hum Genet. 2016 Jan; 24(1):113-9. PMID: 25898925.
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    56. Bandsma RH, van Goor H, Yourshaw M, Horlings RK, Jonkman MF, Schölvinck EH, Karrenbeld A, Scheenstra R, Kömhoff M, Rump P, Koopman-Keemink Y, Nelson SF, Escher JC, Cutz E, Martín MG. Loss of ADAM17 is associated with severe multiorgan dysfunction. Hum Pathol. 2015 Jun; 46(6):923-8. PMID: 25804906.
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    57. Arboleda VA, Lee H, Dorrani N, Zadeh N, Willis M, Macmurdo CF, Manning MA, Kwan A, Hudgins L, Barthelemy F, Miceli MC, Quintero-Rivera F, Kantarci S, Strom SP, Deignan JL, Grody WW, Vilain E, Nelson SF. De novo nonsense mutations in KAT6A, a lysine acetyl-transferase gene, cause a syndrome including microcephaly and global developmental delay. Am J Hum Genet. 2015 Mar 05; 96(3):498-506. PMID: 25728775.
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    58. Ng CK, Shboul M, Taverniti V, Bonnard C, Lee H, Eskin A, Nelson SF, Al-Raqad M, Altawalbeh S, Séraphin B, Reversade B. Loss of the scavenger mRNA decapping enzyme DCPS causes syndromic intellectual disability with neuromuscular defects. Hum Mol Genet. 2015 Jun 01; 24(11):3163-71. PMID: 25712129.
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    59. Lee H, Deignan JL, Dorrani N, Strom SP, Kantarci S, Quintero-Rivera F, Das K, Toy T, Harry B, Yourshaw M, Fox M, Fogel BL, Martinez-Agosto JA, Wong DA, Chang VY, Shieh PB, Palmer CG, Dipple KM, Grody WW, Vilain E, Nelson SF. Clinical exome sequencing for genetic identification of rare Mendelian disorders. JAMA. 2014 Nov 12; 312(18):1880-7. PMID: 25326637.
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    60. Baxter RM, Arboleda VA, Lee H, Barseghyan H, Adam MP, Fechner PY, Bargman R, Keegan C, Travers S, Schelley S, Hudgins L, Mathew RP, Stalker HJ, Zori R, Gordon OK, Ramos-Platt L, Pawlikowska-Haddal A, Eskin A, Nelson SF, Délot E, Vilain E. Exome sequencing for the diagnosis of 46,XY disorders of sex development. J Clin Endocrinol Metab. 2015 Feb; 100(2):E333-44. PMID: 25383892.
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    61. Paganini I, Chang VY, Capone GL, Vitte J, Benelli M, Barbetti L, Sestini R, Trevisson E, Hulsebos TJ, Giovannini M, Nelson SF, Papi L. Expanding the mutational spectrum of LZTR1 in schwannomatosis. Eur J Hum Genet. 2015 Jul; 23(7):963-8. PMID: 25335493.
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    62. Wang RT, Silverstein Fadlon CA, Ulm JW, Jankovic I, Eskin A, Lu A, Rangel Miller V, Cantor RM, Li N, Elashoff R, Martin AS, Peay HL, Halnon N, Nelson SF. Online self-report data for duchenne muscular dystrophy confirms natural history and can be used to assess for therapeutic benefits. PLoS Curr. 2014 Oct 17; 6. PMID: 25635234.
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    63. Fogel BL, Lee H, Deignan JL, Strom SP, Kantarci S, Wang X, Quintero-Rivera F, Vilain E, Grody WW, Perlman S, Geschwind DH, Nelson SF. Exome sequencing in the clinical diagnosis of sporadic or familial cerebellar ataxia. JAMA Neurol. 2014 Oct; 71(10):1237-46. PMID: 25133958.
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    64. Grody WW, Vilain E, Nelson SF. Interpreting whole-genome sequencing. JAMA. 2014 Jul 16; 312(3):296. PMID: 25027151.
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    65. Wu NC, Young AP, Al-Mawsawi LQ, Olson CA, Feng J, Qi H, Chen SH, Lu IH, Lin CY, Chin RG, Luan HH, Nguyen N, Nelson SF, Li X, Wu TT, Sun R. High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution. Sci Rep. 2014 May 13; 4:4942. PMID: 24820965.
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    66. Nelson MD, Rader F, Tang X, Tavyev J, Nelson SF, Miceli MC, Elashoff RM, Sweeney HL, Victor RG. PDE5 inhibition alleviates functional muscle ischemia in boys with Duchenne muscular dystrophy. Neurology. 2014 Jun 10; 82(23):2085-91. PMID: 24808022.
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    67. Strom SP, Lozano R, Lee H, Dorrani N, Mann J, O'Lague PF, Mans N, Deignan JL, Vilain E, Nelson SF, Grody WW, Quintero-Rivera F. De Novo variants in the KMT2A (MLL) gene causing atypical Wiedemann-Steiner syndrome in two unrelated individuals identified by clinical exome sequencing. BMC Med Genet. 2014 May 01; 15:49. PMID: 24886118.
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    68. Swaggart KA, Demonbreun AR, Vo AH, Swanson KE, Kim EY, Fahrenbach JP, Holley-Cuthrell J, Eskin A, Chen Z, Squire K, Heydemann A, Palmer AA, Nelson SF, McNally EM. Annexin A6 modifies muscular dystrophy by mediating sarcolemmal repair. Proc Natl Acad Sci U S A. 2014 Apr 22; 111(16):6004-9. PMID: 24717843.
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    69. Klein S, Lee H, Ghahremani S, Kempert P, Ischander M, Teitell MA, Nelson SF, Martinez-Agosto JA. Expanding the phenotype of mutations in DICER1: mosaic missense mutations in the RNase IIIb domain of DICER1 cause GLOW syndrome. J Med Genet. 2014 May; 51(5):294-302. PMID: 24676357.
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    70. Yourshaw M, Taylor SP, Rao AR, Martín MG, Nelson SF. Rich annotation of DNA sequencing variants by leveraging the Ensembl Variant Effect Predictor with plugins. Brief Bioinform. 2015 Mar; 16(2):255-64. PMID: 24626529.
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    71. Lee H, Lin MC, Kornblum HI, Papazian DM, Nelson SF. Exome sequencing identifies de novo gain of function missense mutation in KCND2 in identical twins with autism and seizures that slows potassium channel inactivation. Hum Mol Genet. 2014 Jul 01; 23(13):3481-9. PMID: 24501278.
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    72. Ortube MC, Strom SP, Nelson SF, Nusinowitz S, Martinez A, Gorin MB. Whole exome sequencing detects homozygosity for ABCA4 p.Arg602Trp missense mutation in a pediatric patient with rapidly progressive retinal dystrophy. BMC Med Genet. 2014 Jan 20; 15:11. PMID: 24444108.
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    73. Freedman AH, Gronau I, Schweizer RM, Ortega-Del Vecchyo D, Han E, Silva PM, Galaverni M, Fan Z, Marx P, Lorente-Galdos B, Beale H, Ramirez O, Hormozdiari F, Alkan C, Vilà C, Squire K, Geffen E, Kusak J, Boyko AR, Parker HG, Lee C, Tadigotla V, Wilton A, Siepel A, Bustamante CD, Harkins TT, Nelson SF, Ostrander EA, Marques-Bonet T, Wayne RK, Novembre J. Genome sequencing highlights the dynamic early history of dogs. PLoS Genet. 2014 Jan; 10(1):e1004016. PMID: 24453982.
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    74. Strom SP, Lee H, Das K, Vilain E, Nelson SF, Grody WW, Deignan JL. Assessing the necessity of confirmatory testing for exome-sequencing results in a clinical molecular diagnostic laboratory. Genet Med. 2014 Jul; 16(7):510-5. PMID: 24406459.
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    75. Bissar-Tadmouri N, Donahue WL, Al-Gazali L, Nelson SF, Bayrak-Toydemir P, Kantarci S. X chromosome exome sequencing reveals a novel ALG13 mutation in a nonsyndromic intellectual disability family with multiple affected male siblings. Am J Med Genet A. 2014 Jan; 164A(1):164-9. PMID: 24501762.
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    76. Nathanson DA, Gini B, Mottahedeh J, Visnyei K, Koga T, Gomez G, Eskin A, Hwang K, Wang J, Masui K, Paucar A, Yang H, Ohashi M, Zhu S, Wykosky J, Reed R, Nelson SF, Cloughesy TF, James CD, Rao PN, Kornblum HI, Heath JR, Cavenee WK, Furnari FB, Mischel PS. Targeted therapy resistance mediated by dynamic regulation of extrachromosomal mutant EGFR DNA. Science. 2014 Jan 03; 343(6166):72-6. PMID: 24310612.
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    77. Yourshaw M, Solorzano-Vargas RS, Pickett LA, Lindberg I, Wang J, Cortina G, Pawlikowska-Haddal A, Baron H, Venick RS, Nelson SF, Martín MG. Exome sequencing finds a novel PCSK1 mutation in a child with generalized malabsorptive diarrhea and diabetes insipidus. J Pediatr Gastroenterol Nutr. 2013 Dec; 57(6):759-67. PMID: 24280991.
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    78. Kerner B, Rao AR, Christensen B, Dandekar S, Yourshaw M, Nelson SF. Rare Genomic Variants Link Bipolar Disorder with Anxiety Disorders to CREB-Regulated Intracellular Signaling Pathways. Front Psychiatry. 2013; 4:154. PMID: 24348429.
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    79. Ye F, Zhang Y, Liu Y, Yamada K, Tso JL, Menjivar JC, Tian JY, Yong WH, Schaue D, Mischel PS, Cloughesy TF, Nelson SF, Liau LM, McBride W, Tso CL. Protective properties of radio-chemoresistant glioblastoma stem cell clones are associated with metabolic adaptation to reduced glucose dependence. PLoS One. 2013; 8(11):e80397. PMID: 24260384.
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    80. Yoshida-Moriguchi T, Willer T, Anderson ME, Venzke D, Whyte T, Muntoni F, Lee H, Nelson SF, Yu L, Campbell KP. SGK196 is a glycosylation-specific O-mannose kinase required for dystroglycan function. Science. 2013 Aug 23; 341(6148):896-9. PMID: 23929950.
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    81. Tanaka K, Eskin A, Chareyre F, Jessen WJ, Manent J, Niwa-Kawakita M, Chen R, White CH, Vitte J, Jaffer ZM, Nelson SF, Rubenstein AE, Giovannini M. Therapeutic potential of HSP90 inhibition for neurofibromatosis type 2. Clin Cancer Res. 2013 Jul 15; 19(14):3856-70. PMID: 23714726.
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    82. Babic I, Anderson ES, Tanaka K, Guo D, Masui K, Li B, Zhu S, Gu Y, Villa GR, Akhavan D, Nathanson D, Gini B, Mareninov S, Li R, Camacho CE, Kurdistani SK, Eskin A, Nelson SF, Yong WH, Cavenee WK, Cloughesy TF, Christofk HR, Black DL, Mischel PS. EGFR mutation-induced alternative splicing of Max contributes to growth of glycolytic tumors in brain cancer. Cell Metab. 2013 Jun 04; 17(6):1000-8. PMID: 23707073.
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    83. Chang VY, Basso G, Sakamoto KM, Nelson SF. Identification of somatic and germline mutations using whole exome sequencing of congenital acute lymphoblastic leukemia. BMC Cancer. 2013 Feb 04; 13:55. PMID: 23379653.
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    84. Pickett LA, Yourshaw M, Albornoz V, Chen Z, Solorzano-Vargas RS, Nelson SF, Martín MG, Lindberg I. Functional consequences of a novel variant of PCSK1. PLoS One. 2013; 8(1):e55065. PMID: 23383060.
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    85. Rudnik-Schöneborn S, Senderek J, Jen JC, Houge G, Seeman P, Puchmajerová A, Graul-Neumann L, Seidel U, Korinthenberg R, Kirschner J, Seeger J, Ryan MM, Muntoni F, Steinlin M, Sztriha L, Colomer J, Hübner C, Brockmann K, Van Maldergem L, Schiff M, Holzinger A, Barth P, Reardon W, Yourshaw M, Nelson SF, Eggermann T, Zerres K. Pontocerebellar hypoplasia type 1: clinical spectrum and relevance of EXOSC3 mutations. Neurology. 2013 Jan 29; 80(5):438-46. PMID: 23284067.
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    86. Kendall GC, Mokhonova EI, Moran M, Sejbuk NE, Wang DW, Silva O, Wang RT, Martinez L, Lu QL, Damoiseaux R, Spencer MJ, Nelson SF, Miceli MC. Dantrolene enhances antisense-mediated exon skipping in human and mouse models of Duchenne muscular dystrophy. Sci Transl Med. 2012 Dec 12; 4(164):164ra160. PMID: 23241744.
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    87. Lee H, Nelson SF. Rethinking clinical practice: clinical implementation of exome sequencing. Per Med. 2012 Nov; 9(8):785-787. PMID: 29776228.
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    88. Chang VY, Federman N, Martinez-Agosto J, Tatishchev SF, Nelson SF. Whole exome sequencing of pediatric gastric adenocarcinoma reveals an atypical presentation of Li-Fraumeni syndrome. Pediatr Blood Cancer. 2013 Apr; 60(4):570-4. PMID: 23015295.
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    89. Chou AP, Chowdhury R, Li S, Chen W, Kim AJ, Piccioni DE, Selfridge JM, Mody RR, Chang S, Lalezari S, Lin J, Sanchez DE, Wilson RW, Garrett MC, Harry B, Mottahedeh J, Nghiemphu PL, Kornblum HI, Mischel PS, Prins RM, Yong WH, Cloughesy T, Nelson SF, Liau LM, Lai A. Identification of retinol binding protein 1 promoter hypermethylation in isocitrate dehydrogenase 1 and 2 mutant gliomas. J Natl Cancer Inst. 2012 Oct 03; 104(19):1458-69. PMID: 22945948.
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    90. Strom SP, Gao YQ, Martinez A, Ortube C, Chen Z, Nelson SF, Nusinowitz S, Farber DB, Gorin MB. Molecular diagnosis of putative Stargardt Disease probands by exome sequencing. BMC Med Genet. 2012 Aug 03; 13:67. PMID: 22863181.
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    91. Nyman ES, Loukola A, Varilo T, Taanila A, Hurtig T, Moilanen I, Loo S, McGough JJ, Järvelin MR, Smalley SL, Nelson SF, Peltonen L. Sex-specific influence of DRD2 on ADHD-type temperament in a large population-based birth cohort. Psychiatr Genet. 2012 Aug; 22(4):197-201. PMID: 22531292.
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    92. Anney R, Klei L, Pinto D, Almeida J, Bacchelli E, Baird G, Bolshakova N, Bölte S, Bolton PF, Bourgeron T, Brennan S, Brian J, Casey J, Conroy J, Correia C, Corsello C, Crawford EL, de Jonge M, Delorme R, Duketis E, Duque F, Estes A, Farrar P, Fernandez BA, Folstein SE, Fombonne E, Gilbert J, Gillberg C, Glessner JT, Green A, Green J, Guter SJ, Heron EA, Holt R, Howe JL, Hughes G, Hus V, Igliozzi R, Jacob S, Kenny GP, Kim C, Kolevzon A, Kustanovich V, Lajonchere CM, Lamb JA, Law-Smith M, Leboyer M, Le Couteur A, Leventhal BL, Liu XQ, Lombard F, Lord C, Lotspeich L, Lund SC, Magalhaes TR, Mantoulan C, McDougle CJ, Melhem NM, Merikangas A, Minshew NJ, Mirza GK, Munson J, Noakes C, Nygren G, Papanikolaou K, Pagnamenta AT, Parrini B, Paton T, Pickles A, Posey DJ, Poustka F, Ragoussis J, Regan R, Roberts W, Roeder K, Roge B, Rutter ML, Schlitt S, Shah N, Sheffield VC, Soorya L, Sousa I, Stoppioni V, Sykes N, Tancredi R, Thompson AP, Thomson S, Tryfon A, Tsiantis J, Van Engeland H, Vincent JB, Volkmar F, Vorstman JA, Wallace S, Wing K, Wittemeyer K, Wood S, Zurawiecki D, Zwaigenbaum L, Bailey AJ, Battaglia A, Cantor RM, Coon H, Cuccaro ML, Dawson G, Ennis S, Freitag CM, Geschwind DH, Haines JL, Klauck SM, McMahon WM, Maestrini E, Miller J, Monaco AP, Nelson SF, Nurnberger JI, Oliveira G, Parr JR, Pericak-Vance MA, Piven J, Schellenberg GD, Scherer SW, Vicente AM, Wassink TH, Wijsman EM, Betancur C, Buxbaum JD, Cook EH, Gallagher L, Gill M, Hallmayer J, Paterson AD, Sutcliffe JS, Szatmari P, Vieland VJ, Hakonarson H, Devlin B. Individual common variants exert weak effects on the risk for autism spectrum disorders. Hum Mol Genet. 2012 Nov 01; 21(21):4781-92. PMID: 22843504.
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    93. Arboleda VA, Lee H, Parnaik R, Fleming A, Banerjee A, Ferraz-de-Souza B, Délot EC, Rodriguez-Fernandez IA, Braslavsky D, Bergadá I, Dell'Angelica EC, Nelson SF, Martinez-Agosto JA, Achermann JC, Vilain E. Mutations in the PCNA-binding domain of CDKN1C cause IMAGe syndrome. Nat Genet. 2012 May 27; 44(7):788-92. PMID: 22634751.
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    94. Bonnard C, Strobl AC, Shboul M, Lee H, Merriman B, Nelson SF, Ababneh OH, Uz E, Güran T, Kayserili H, Hamamy H, Reversade B. Mutations in IRX5 impair craniofacial development and germ cell migration via SDF1. Nat Genet. 2012 May 13; 44(6):709-13. PMID: 22581230.
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    95. Cabrera PV, Pang M, Marshall JL, Kung R, Nelson SF, Stalnaker SH, Wells L, Crosbie-Watson RH, Baum LG. High throughput screening for compounds that alter muscle cell glycosylation identifies new role for N-glycans in regulating sarcolemmal protein abundance and laminin binding. J Biol Chem. 2012 Jun 29; 287(27):22759-70. PMID: 22570487.
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    96. Willer T, Lee H, Lommel M, Yoshida-Moriguchi T, de Bernabe DB, Venzke D, Cirak S, Schachter H, Vajsar J, Voit T, Muntoni F, Loder AS, Dobyns WB, Winder TL, Strahl S, Mathews KD, Nelson SF, Moore SA, Campbell KP. ISPD loss-of-function mutations disrupt dystroglycan O-mannosylation and cause Walker-Warburg syndrome. Nat Genet. 2012 May; 44(5):575-80. PMID: 22522420.
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    97. Wan J, Yourshaw M, Mamsa H, Rudnik-Schöneborn S, Menezes MP, Hong JE, Leong DW, Senderek J, Salman MS, Chitayat D, Seeman P, von Moers A, Graul-Neumann L, Kornberg AJ, Castro-Gago M, Sobrido MJ, Sanefuji M, Shieh PB, Salamon N, Kim RC, Vinters HV, Chen Z, Zerres K, Ryan MM, Nelson SF, Jen JC. Mutations in the RNA exosome component gene EXOSC3 cause pontocerebellar hypoplasia and spinal motor neuron degeneration. Nat Genet. 2012 Apr 29; 44(6):704-8. PMID: 22544365.
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    98. Lee H, Graham JM, Rimoin DL, Lachman RS, Krejci P, Tompson SW, Nelson SF, Krakow D, Cohn DH. Exome sequencing identifies PDE4D mutations in acrodysostosis. Am J Hum Genet. 2012 Apr 06; 90(4):746-51. PMID: 22464252.
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    99. Li G, Bahn JH, Lee JH, Peng G, Chen Z, Nelson SF, Xiao X. Identification of allele-specific alternative mRNA processing via transcriptome sequencing. Nucleic Acids Res. 2012 Jul; 40(13):e104. PMID: 22467206.
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    100. Shi H, Moriceau G, Kong X, Lee MK, Lee H, Koya RC, Ng C, Chodon T, Scolyer RA, Dahlman KB, Sosman JA, Kefford RF, Long GV, Nelson SF, Ribas A, Lo RS. Melanoma whole-exome sequencing identifies (V600E)B-RAF amplification-mediated acquired B-RAF inhibitor resistance. Nat Commun. 2012 Mar 06; 3:724. PMID: 22395615.
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    101. Loo SK, Shtir C, Doyle AE, Mick E, McGough JJ, McCracken J, Biederman J, Smalley SL, Cantor RM, Faraone SV, Nelson SF. Genome-wide association study of intelligence: additive effects of novel brain expressed genes. J Am Acad Child Adolesc Psychiatry. 2012 Apr; 51(4):432-440.e2. PMID: 22449649.
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    102. Palomaki GE, Deciu C, Kloza EM, Lambert-Messerlian GM, Haddow JE, Neveux LM, Ehrich M, van den Boom D, Bombard AT, Grody WW, Nelson SF, Canick JA. DNA sequencing of maternal plasma reliably identifies trisomy 18 and trisomy 13 as well as Down syndrome: an international collaborative study. Genet Med. 2012 Mar; 14(3):296-305. PMID: 22281937.
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    103. Lee JE, Silhavy JL, Zaki MS, Schroth J, Bielas SL, Marsh SE, Olvera J, Brancati F, Iannicelli M, Ikegami K, Schlossman AM, Merriman B, Attié-Bitach T, Logan CV, Glass IA, Cluckey A, Louie CM, Lee JH, Raynes HR, Rapin I, Castroviejo IP, Setou M, Barbot C, Boltshauser E, Nelson SF, Hildebrandt F, Johnson CA, Doherty DA, Valente EM, Gleeson JG. CEP41 is mutated in Joubert syndrome and is required for tubulin glutamylation at the cilium. Nat Genet. 2012 Jan 15; 44(2):193-9. PMID: 22246503.
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    104. Ombrello MJ, Remmers EF, Sun G, Freeman AF, Datta S, Torabi-Parizi P, Subramanian N, Bunney TD, Baxendale RW, Martins MS, Romberg N, Komarow H, Aksentijevich I, Kim HS, Ho J, Cruse G, Jung MY, Gilfillan AM, Metcalfe DD, Nelson C, O'Brien M, Wisch L, Stone K, Douek DC, Gandhi C, Wanderer AA, Lee H, Nelson SF, Shianna KV, Cirulli ET, Goldstein DB, Long EO, Moir S, Meffre E, Holland SM, Kastner DL, Katan M, Hoffman HM, Milner JD. Cold urticaria, immunodeficiency, and autoimmunity related to PLCG2 deletions. N Engl J Med. 2012 Jan 26; 366(4):330-8. PMID: 22236196.
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    105. Elia J, Glessner JT, Wang K, Takahashi N, Shtir CJ, Hadley D, Sleiman PM, Zhang H, Kim CE, Robison R, Lyon GJ, Flory JH, Bradfield JP, Imielinski M, Hou C, Frackelton EC, Chiavacci RM, Sakurai T, Rabin C, Middleton FA, Thomas KA, Garris M, Mentch F, Freitag CM, Steinhausen HC, Todorov AA, Reif A, Rothenberger A, Franke B, Mick EO, Roeyers H, Buitelaar J, Lesch KP, Banaschewski T, Ebstein RP, Mulas F, Oades RD, Sergeant J, Sonuga-Barke E, Renner TJ, Romanos M, Romanos J, Warnke A, Walitza S, Meyer J, Pálmason H, Seitz C, Loo SK, Smalley SL, Biederman J, Kent L, Asherson P, Anney RJ, Gaynor JW, Shaw P, Devoto M, White PS, Grant SF, Buxbaum JD, Rapoport JL, Williams NM, Nelson SF, Faraone SV, Hakonarson H. Genome-wide copy number variation study associates metabotropic glutamate receptor gene networks with attention deficit hyperactivity disorder. Nat Genet. 2011 Dec 04; 44(1):78-84. PMID: 22138692.
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    106. Kyriakides T, Pegoraro E, Hoffman EP, Piva L, Cagnin S, Lanfranchi G, Griggs RC, Nelson SF. SPP1 genotype is a determinant of disease severity in Duchenne muscular dystrophy: predicting the severity of Duchenne muscular dystrophy: implications for treatment. Neurology. 2011 Nov 15; 77(20):1858; author reply 1858-9. PMID: 22084278.
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    107. Palomaki GE, Kloza EM, Lambert-Messerlian GM, Haddow JE, Neveux LM, Ehrich M, van den Boom D, Bombard AT, Deciu C, Grody WW, Nelson SF, Canick JA. DNA sequencing of maternal plasma to detect Down syndrome: an international clinical validation study. Genet Med. 2011 Nov; 13(11):913-20. PMID: 22005709.
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    108. Liu Y, Ye F, Yamada K, Tso JL, Zhang Y, Nguyen DH, Dong Q, Soto H, Choe J, Dembo A, Wheeler H, Eskin A, Schmid I, Yong WH, Mischel PS, Cloughesy TF, Kornblum HI, Nelson SF, Liau LM, Tso CL. Autocrine endothelin-3/endothelin receptor B signaling maintains cellular and molecular properties of glioblastoma stem cells. Mol Cancer Res. 2011 Dec; 9(12):1668-85. PMID: 22013079.
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    109. Casey JP, Magalhaes T, Conroy JM, Regan R, Shah N, Anney R, Shields DC, Abrahams BS, Almeida J, Bacchelli E, Bailey AJ, Baird G, Battaglia A, Berney T, Bolshakova N, Bolton PF, Bourgeron T, Brennan S, Cali P, Correia C, Corsello C, Coutanche M, Dawson G, de Jonge M, Delorme R, Duketis E, Duque F, Estes A, Farrar P, Fernandez BA, Folstein SE, Foley S, Fombonne E, Freitag CM, Gilbert J, Gillberg C, Glessner JT, Green J, Guter SJ, Hakonarson H, Holt R, Hughes G, Hus V, Igliozzi R, Kim C, Klauck SM, Kolevzon A, Lamb JA, Leboyer M, Le Couteur A, Leventhal BL, Lord C, Lund SC, Maestrini E, Mantoulan C, Marshall CR, McConachie H, McDougle CJ, McGrath J, McMahon WM, Merikangas A, Miller J, Minopoli F, Mirza GK, Munson J, Nelson SF, Nygren G, Oliveira G, Pagnamenta AT, Papanikolaou K, Parr JR, Parrini B, Pickles A, Pinto D, Piven J, Posey DJ, Poustka A, Poustka F, Ragoussis J, Roge B, Rutter ML, Sequeira AF, Soorya L, Sousa I, Sykes N, Stoppioni V, Tancredi R, Tauber M, Thompson AP, Thomson S, Tsiantis J, Van Engeland H, Vincent JB, Volkmar F, Vorstman JA, Wallace S, Wang K, Wassink TH, White K, Wing K, Wittemeyer K, Yaspan BL, Zwaigenbaum L, Betancur C, Buxbaum JD, Cantor RM, Cook EH, Coon H, Cuccaro ML, Geschwind DH, Haines JL, Hallmayer J, Monaco AP, Nurnberger JI, Pericak-Vance MA, Schellenberg GD, Scherer SW, Sutcliffe JS, Szatmari P, Vieland VJ, Wijsman EM, Green A, Gill M, Gallagher L, Vicente A, Ennis S. A novel approach of homozygous haplotype sharing identifies candidate genes in autism spectrum disorder. Hum Genet. 2012 Apr; 131(4):565-79. PMID: 21996756.
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    110. Sathirapongsasuti JF, Lee H, Horst BA, Brunner G, Cochran AJ, Binder S, Quackenbush J, Nelson SF. Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV. Bioinformatics. 2011 Oct 01; 27(19):2648-54. PMID: 21828086.
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    111. McCannel TA, Burgess BL, Nelson SF, Eskin A, Straatsma BR. Genomic identification of significant targets in ciliochoroidal melanoma. Invest Ophthalmol Vis Sci. 2011 May 09; 52(6):3018-22. PMID: 20688739.
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    112. Goudie DR, D'Alessandro M, Merriman B, Lee H, Szeverényi I, Avery S, O'Connor BD, Nelson SF, Coats SE, Stewart A, Christie L, Pichert G, Friedel J, Hayes I, Burrows N, Whittaker S, Gerdes AM, Broesby-Olsen S, Ferguson-Smith MA, Verma C, Lunny DP, Reversade B, Lane EB. Multiple self-healing squamous epithelioma is caused by a disease-specific spectrum of mutations in TGFBR1. Nat Genet. 2011 Feb 27; 43(4):365-9. PMID: 21358634.
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    113. Burgess BL, Rao NP, Eskin A, Nelson SF, McCannel TA. Characterization of three cell lines derived from fine needle biopsy of choroidal melanoma with metastatic outcome. Mol Vis. 2011 Feb 25; 17:607-15. PMID: 21386926.
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    114. Harper MA, Chen Z, Toy T, Machado IM, Nelson SF, Liao JC, Lee CJ. Phenotype sequencing: identifying the genes that cause a phenotype directly from pooled sequencing of independent mutants. PLoS One. 2011 Feb 18; 6(2):e16517. PMID: 21364744.
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    115. Nelson SF, Griggs RC. Predicting the severity of Duchenne muscular dystrophy: implications for treatment. Neurology. 2011 Jan 18; 76(3):208-9. PMID: 21178098.
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    116. O'Connor BD, Merriman B, Nelson SF. SeqWare Query Engine: storing and searching sequence data in the cloud. BMC Bioinformatics. 2010 Dec 21; 11 Suppl 12:S2. PMID: 21210981.
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    117. Tian J, Ling L, Shboul M, Lee H, O'Connor B, Merriman B, Nelson SF, Cool S, Ababneh OH, Al-Hadidy A, Masri A, Hamamy H, Reversade B. Loss of CHSY1, a secreted FRINGE enzyme, causes syndromic brachydactyly in humans via increased NOTCH signaling. Am J Hum Genet. 2010 Dec 10; 87(6):768-78. PMID: 21129727.
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    118. Prins RM, Soto H, Konkankit V, Odesa SK, Eskin A, Yong WH, Nelson SF, Liau LM. Gene expression profile correlates with T-cell infiltration and relative survival in glioblastoma patients vaccinated with dendritic cell immunotherapy. Clin Cancer Res. 2011 Mar 15; 17(6):1603-15. PMID: 21135147.
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    119. Leuchter AF, Cook IA, Hamilton SP, Narr KL, Toga A, Hunter AM, Faull K, Whitelegge J, Andrews AM, Loo J, Way B, Nelson SF, Horvath S, Lebowitz BD. Biomarkers to predict antidepressant response. Curr Psychiatry Rep. 2010 Dec; 12(6):553-62. PMID: 20963521.
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    120. Nazarian R, Shi H, Wang Q, Kong X, Koya RC, Lee H, Chen Z, Lee MK, Attar N, Sazegar H, Chodon T, Nelson SF, McArthur G, Sosman JA, Ribas A, Lo RS. Melanomas acquire resistance to B-RAF(V600E) inhibition by RTK or N-RAS upregulation. Nature. 2010 Dec 16; 468(7326):973-7. PMID: 21107323.
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    121. Funari VA, Krakow D, Nevarez L, Chen Z, Funari TL, Vatanavicharn N, Wilcox WR, Rimoin DL, Nelson SF, Cohn DH. BMPER mutation in diaphanospondylodysostosis identified by ancestral autozygosity mapping and targeted high-throughput sequencing. Am J Hum Genet. 2010 Oct 08; 87(4):532-7. PMID: 20869035.
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    122. Homer N, Nelson SF. Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA. Genome Biol. 2010; 11(10):R99. PMID: 20932289.
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    123. Lee H, Marvin AR, Watson T, Piggot J, Law JK, Law PA, Constantino JN, Nelson SF. Accuracy of phenotyping of autistic children based on Internet implemented parent report. Am J Med Genet B Neuropsychiatr Genet. 2010 Sep; 153B(6):1119-26. PMID: 20552678.
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    124. McCannel TA, Burgess BL, Rao NP, Nelson SF, Straatsma BR. Identification of candidate tumor oncogenes by integrative molecular analysis of choroidal melanoma fine-needle aspiration biopsy specimens. Arch Ophthalmol. 2010 Sep; 128(9):1170-7. PMID: 20837802.
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    125. Anney R, Klei L, Pinto D, Regan R, Conroy J, Magalhaes TR, Correia C, Abrahams BS, Sykes N, Pagnamenta AT, Almeida J, Bacchelli E, Bailey AJ, Baird G, Battaglia A, Berney T, Bolshakova N, Bölte S, Bolton PF, Bourgeron T, Brennan S, Brian J, Carson AR, Casallo G, Casey J, Chu SH, Cochrane L, Corsello C, Crawford EL, Crossett A, Dawson G, de Jonge M, Delorme R, Drmic I, Duketis E, Duque F, Estes A, Farrar P, Fernandez BA, Folstein SE, Fombonne E, Freitag CM, Gilbert J, Gillberg C, Glessner JT, Goldberg J, Green J, Guter SJ, Hakonarson H, Heron EA, Hill M, Holt R, Howe JL, Hughes G, Hus V, Igliozzi R, Kim C, Klauck SM, Kolevzon A, Korvatska O, Kustanovich V, Lajonchere CM, Lamb JA, Laskawiec M, Leboyer M, Le Couteur A, Leventhal BL, Lionel AC, Liu XQ, Lord C, Lotspeich L, Lund SC, Maestrini E, Mahoney W, Mantoulan C, Marshall CR, McConachie H, McDougle CJ, McGrath J, McMahon WM, Melhem NM, Merikangas A, Migita O, Minshew NJ, Mirza GK, Munson J, Nelson SF, Noakes C, Noor A, Nygren G, Oliveira G, Papanikolaou K, Parr JR, Parrini B, Paton T, Pickles A, Piven J, Posey DJ, Poustka A, Poustka F, Prasad A, Ragoussis J, Renshaw K, Rickaby J, Roberts W, Roeder K, Roge B, Rutter ML, Bierut LJ, Rice JP, Salt J, Sansom K, Sato D, Segurado R, Senman L, Shah N, Sheffield VC, Soorya L, Sousa I, Stoppioni V, Strawbridge C, Tancredi R, Tansey K, Thiruvahindrapduram B, Thompson AP, Thomson S, Tryfon A, Tsiantis J, Van Engeland H, Vincent JB, Volkmar F, Wallace S, Wang K, Wang Z, Wassink TH, Wing K, Wittemeyer K, Wood S, Yaspan BL, Zurawiecki D, Zwaigenbaum L, Betancur C, Buxbaum JD, Cantor RM, Cook EH, Coon H, Cuccaro ML, Gallagher L, Geschwind DH, Gill M, Haines JL, Miller J, Monaco AP, Nurnberger JI, Paterson AD, Pericak-Vance MA, Schellenberg GD, Scherer SW, Sutcliffe JS, Szatmari P, Vicente AM, Vieland VJ, Wijsman EM, Devlin B, Ennis S, Hallmayer J. A genome-wide scan for common alleles affecting risk for autism. Hum Mol Genet. 2010 Oct 15; 19(20):4072-82. PMID: 20663923.
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    126. Homer N, Nelson SF, Merriman B. Local alignment of generalized k-base encoded DNA sequence. BMC Bioinformatics. 2010 Jun 24; 11:347. PMID: 20576157.
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    127. Pinto D, Pagnamenta AT, Klei L, Anney R, Merico D, Regan R, Conroy J, Magalhaes TR, Correia C, Abrahams BS, Almeida J, Bacchelli E, Bader GD, Bailey AJ, Baird G, Battaglia A, Berney T, Bolshakova N, Bölte S, Bolton PF, Bourgeron T, Brennan S, Brian J, Bryson SE, Carson AR, Casallo G, Casey J, Chung BH, Cochrane L, Corsello C, Crawford EL, Crossett A, Cytrynbaum C, Dawson G, de Jonge M, Delorme R, Drmic I, Duketis E, Duque F, Estes A, Farrar P, Fernandez BA, Folstein SE, Fombonne E, Freitag CM, Gilbert J, Gillberg C, Glessner JT, Goldberg J, Green A, Green J, Guter SJ, Hakonarson H, Heron EA, Hill M, Holt R, Howe JL, Hughes G, Hus V, Igliozzi R, Kim C, Klauck SM, Kolevzon A, Korvatska O, Kustanovich V, Lajonchere CM, Lamb JA, Laskawiec M, Leboyer M, Le Couteur A, Leventhal BL, Lionel AC, Liu XQ, Lord C, Lotspeich L, Lund SC, Maestrini E, Mahoney W, Mantoulan C, Marshall CR, McConachie H, McDougle CJ, McGrath J, McMahon WM, Merikangas A, Migita O, Minshew NJ, Mirza GK, Munson J, Nelson SF, Noakes C, Noor A, Nygren G, Oliveira G, Papanikolaou K, Parr JR, Parrini B, Paton T, Pickles A, Pilorge M, Piven J, Ponting CP, Posey DJ, Poustka A, Poustka F, Prasad A, Ragoussis J, Renshaw K, Rickaby J, Roberts W, Roeder K, Roge B, Rutter ML, Bierut LJ, Rice JP, Salt J, Sansom K, Sato D, Segurado R, Sequeira AF, Senman L, Shah N, Sheffield VC, Soorya L, Sousa I, Stein O, Sykes N, Stoppioni V, Strawbridge C, Tancredi R, Tansey K, Thiruvahindrapduram B, Thompson AP, Thomson S, Tryfon A, Tsiantis J, Van Engeland H, Vincent JB, Volkmar F, Wallace S, Wang K, Wang Z, Wassink TH, Webber C, Weksberg R, Wing K, Wittemeyer K, Wood S, Wu J, Yaspan BL, Zurawiecki D, Zwaigenbaum L, Buxbaum JD, Cantor RM, Cook EH, Coon H, Cuccaro ML, Devlin B, Ennis S, Gallagher L, Geschwind DH, Gill M, Haines JL, Hallmayer J, Miller J, Monaco AP, Nurnberger JI, Paterson AD, Pericak-Vance MA, Schellenberg GD, Szatmari P, Vicente AM, Vieland VJ, Wijsman EM, Scherer SW, Sutcliffe JS, Betancur C. Functional impact of global rare copy number variation in autism spectrum disorders. Nature. 2010 Jul 15; 466(7304):368-72. PMID: 20531469.
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    128. Mick E, Todorov A, Smalley S, Hu X, Loo S, Todd RD, Biederman J, Byrne D, Dechairo B, Guiney A, McCracken J, McGough J, Nelson SF, Reiersen AM, Wilens TE, Wozniak J, Neale BM, Faraone SV. Family-based genome-wide association scan of attention-deficit/hyperactivity disorder. J Am Acad Child Adolesc Psychiatry. 2010 Sep; 49(9):898-905.e3. PMID: 20732626.
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    129. Kim WK, Meliton V, Tetradis S, Weinmaster G, Hahn TJ, Carlson M, Nelson SF, Parhami F. Osteogenic oxysterol, 20(S)-hydroxycholesterol, induces notch target gene expression in bone marrow stromal cells. J Bone Miner Res. 2010 Apr; 25(4):782-95. PMID: 19839776.
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    130. Clark MJ, Homer N, O'Connor BD, Chen Z, Eskin A, Lee H, Merriman B, Nelson SF. U87MG decoded: the genomic sequence of a cytogenetically aberrant human cancer cell line. PLoS Genet. 2010 Jan 29; 6(1):e1000832. PMID: 20126413.
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    131. Smits P, Bolton AD, Funari V, Hong M, Boyden ED, Lu L, Manning DK, Dwyer ND, Moran JL, Prysak M, Merriman B, Nelson SF, Bonafé L, Superti-Furga A, Ikegawa S, Krakow D, Cohn DH, Kirchhausen T, Warman ML, Beier DR. Lethal skeletal dysplasia in mice and humans lacking the golgin GMAP-210. N Engl J Med. 2010 Jan 21; 362(3):206-16. PMID: 20089971.
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    132. Day A, Dong J, Funari VA, Harry B, Strom SP, Cohn DH, Nelson SF. Disease gene characterization through large-scale co-expression analysis. PLoS One. 2009 Dec 31; 4(12):e8491. PMID: 20046828.
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    133. Lee H, O'Connor BD, Merriman B, Funari VA, Homer N, Chen Z, Cohn DH, Nelson SF. Improving the efficiency of genomic loci capture using oligonucleotide arrays for high throughput resequencing. BMC Genomics. 2009 Dec 31; 10:646. PMID: 20043857.
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    134. Homer N, Merriman B, Nelson SF. BFAST: an alignment tool for large scale genome resequencing. PLoS One. 2009 Nov 11; 4(11):e7767. PMID: 19907642.
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    135. Nelson SF, Crosbie RH, Miceli MC, Spencer MJ. Emerging genetic therapies to treat Duchenne muscular dystrophy. Curr Opin Neurol. 2009 Oct; 22(5):532-8. PMID: 19745732.
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    136. Lu KV, Zhu S, Cvrljevic A, Huang TT, Sarkaria S, Ahkavan D, Dang J, Dinca EB, Plaisier SB, Oderberg I, Lee Y, Chen Z, Caldwell JS, Xie Y, Loo JA, Seligson D, Chakravari A, Lee FY, Weinmann R, Cloughesy TF, Nelson SF, Bergers G, Graeber T, Furnari FB, James CD, Cavenee WK, Johns TG, Mischel PS. Fyn and SRC are effectors of oncogenic epidermal growth factor receptor signaling in glioblastoma patients. Cancer Res. 2009 Sep 01; 69(17):6889-98. PMID: 19690143.
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    137. Kappadakunnel M, Eskin A, Dong J, Nelson SF, Mischel PS, Liau LM, Ngheimphu P, Lai A, Cloughesy TF, Goldin J, Pope WB. Stem cell associated gene expression in glioblastoma multiforme: relationship to survival and the subventricular zone. J Neurooncol. 2010 Feb; 96(3):359-67. PMID: 19655089.
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    138. Reversade B, Escande-Beillard N, Dimopoulou A, Fischer B, Chng SC, Li Y, Shboul M, Tham PY, Kayserili H, Al-Gazali L, Shahwan M, Brancati F, Lee H, O'Connor BD, Schmidt-von Kegler M, Merriman B, Nelson SF, Masri A, Alkazaleh F, Guerra D, Ferrari P, Nanda A, Rajab A, Markie D, Gray M, Nelson J, Grix A, Sommer A, Savarirayan R, Janecke AR, Steichen E, Sillence D, Hausser I, Budde B, Nürnberg G, Nürnberg P, Seemann P, Kunkel D, Zambruno G, Dallapiccola B, Schuelke M, Robertson S, Hamamy H, Wollnik B, Van Maldergem L, Mundlos S, Kornak U. Mutations in PYCR1 cause cutis laxa with progeroid features. Nat Genet. 2009 Sep; 41(9):1016-21. PMID: 19648921.
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    139. Homer N, Merriman B, Nelson SF. Local alignment of two-base encoded DNA sequence. BMC Bioinformatics. 2009 Jun 09; 10:175. PMID: 19508732.
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    140. Liu Q, Nguyen DH, Dong Q, Shitaku P, Chung K, Liu OY, Tso JL, Liu JY, Konkankit V, Cloughesy TF, Mischel PS, Lane TF, Liau LM, Nelson SF, Tso CL. Molecular properties of CD133+ glioblastoma stem cells derived from treatment-refractory recurrent brain tumors. J Neurooncol. 2009 Aug; 94(1):1-19. PMID: 19468690.
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    141. Saghizadeh M, Akhmedov NB, Yamashita CK, Gribanova Y, Theendakara V, Mendoza E, Nelson SF, Ljubimov AV, Farber DB. ZBED4, a BED-type zinc-finger protein in the cones of the human retina. Invest Ophthalmol Vis Sci. 2009 Aug; 50(8):3580-8. PMID: 19369242.
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    142. Merrill AE, Merriman B, Farrington-Rock C, Camacho N, Sebald ET, Funari VA, Schibler MJ, Firestein MH, Cohn ZA, Priore MA, Thompson AK, Rimoin DL, Nelson SF, Cohn DH, Krakow D. Ciliary abnormalities due to defects in the retrograde transport protein DYNC2H1 in short-rib polydactyly syndrome. Am J Hum Genet. 2009 Apr; 84(4):542-9. PMID: 19361615.
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    143. Tompson SW, Merriman B, Funari VA, Fresquet M, Lachman RS, Rimoin DL, Nelson SF, Briggs MD, Cohn DH, Krakow D. A recessive skeletal dysplasia, SEMD aggrecan type, results from a missense mutation affecting the C-type lectin domain of aggrecan. Am J Hum Genet. 2009 Jan; 84(1):72-9. PMID: 19110214.
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    144. Zhou K, Dempfle A, Arcos-Burgos M, Bakker SC, Banaschewski T, Biederman J, Buitelaar J, Castellanos FX, Doyle A, Ebstein RP, Ekholm J, Forabosco P, Franke B, Freitag C, Friedel S, Gill M, Hebebrand J, Hinney A, Jacob C, Lesch KP, Loo SK, Lopera F, McCracken JT, McGough JJ, Meyer J, Mick E, Miranda A, Muenke M, Mulas F, Nelson SF, Nguyen TT, Oades RD, Ogdie MN, Palacio JD, Pineda D, Reif A, Renner TJ, Roeyers H, Romanos M, Rothenberger A, Schäfer H, Sergeant J, Sinke RJ, Smalley SL, Sonuga-Barke E, Steinhausen HC, van der Meulen E, Walitza S, Warnke A, Lewis CM, Faraone SV, Asherson P. Meta-analysis of genome-wide linkage scans of attention deficit hyperactivity disorder. Am J Med Genet B Neuropsychiatr Genet. 2008 Dec 05; 147B(8):1392-8. PMID: 18988193.
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    145. Lu AT, Ogdie MN, Järvelin MR, Moilanen IK, Loo SK, McCracken JT, McGough JJ, Yang MH, Peltonen L, Nelson SF, Cantor RM, Smalley SL. Association of the cannabinoid receptor gene (CNR1) with ADHD and post-traumatic stress disorder. Am J Med Genet B Neuropsychiatr Genet. 2008 Dec 05; 147B(8):1488-94. PMID: 18213623.
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    146. Lee Y, Scheck AC, Cloughesy TF, Lai A, Dong J, Farooqi HK, Liau LM, Horvath S, Mischel PS, Nelson SF. Gene expression analysis of glioblastomas identifies the major molecular basis for the prognostic benefit of younger age. BMC Med Genomics. 2008 Oct 21; 1:52. PMID: 18940004.
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    147. Potikyan G, France KA, Carlson MR, Dong J, Nelson SF, Denny CT. Genetically defined EWS/FLI1 model system suggests mesenchymal origin of Ewing's family tumors. Lab Invest. 2008 Dec; 88(12):1291-302. PMID: 18838963.
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    148. Pope WB, Chen JH, Dong J, Carlson MR, Perlina A, Cloughesy TF, Liau LM, Mischel PS, Nghiemphu P, Lai A, Nelson SF. Relationship between gene expression and enhancement in glioblastoma multiforme: exploratory DNA microarray analysis. Radiology. 2008 Oct; 249(1):268-77. PMID: 18796682.
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    149. McGough JJ, Loo SK, McCracken JT, Dang J, Clark S, Nelson SF, Smalley SL. CBCL pediatric bipolar disorder profile and ADHD: comorbidity and quantitative trait loci analysis. J Am Acad Child Adolesc Psychiatry. 2008 Oct; 47(10):1151-7. PMID: 18724256.
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    150. Pellegrini M, Cheng JC, Voutila J, Judelson D, Taylor J, Nelson SF, Sakamoto KM. Expression profile of CREB knockdown in myeloid leukemia cells. BMC Cancer. 2008 Sep 18; 8:264. PMID: 18801183.
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    151. Homer N, Szelinger S, Redman M, Duggan D, Tembe W, Muehling J, Pearson JV, Stephan DA, Nelson SF, Craig DW. Resolving individuals contributing trace amounts of DNA to highly complex mixtures using high-density SNP genotyping microarrays. PLoS Genet. 2008 Aug 29; 4(8):e1000167. PMID: 18769715.
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    152. Homer N, Tembe WD, Szelinger S, Redman M, Stephan DA, Pearson JV, Nelson SF, Craig D. Multimarker analysis and imputation of multiple platform pooling-based genome-wide association studies. Bioinformatics. 2008 Sep 01; 24(17):1896-902. PMID: 18617537.
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    153. Rock MJ, Prenen J, Funari VA, Funari TL, Merriman B, Nelson SF, Lachman RS, Wilcox WR, Reyno S, Quadrelli R, Vaglio A, Owsianik G, Janssens A, Voets T, Ikegawa S, Nagai T, Rimoin DL, Nilius B, Cohn DH. Gain-of-function mutations in TRPV4 cause autosomal dominant brachyolmia. Nat Genet. 2008 Aug; 40(8):999-1003. PMID: 18587396.
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    154. Sivagnanam M, Mueller JL, Lee H, Chen Z, Nelson SF, Turner D, Zlotkin SH, Pencharz PB, Ngan BY, Libiger O, Schork NJ, Lavine JE, Taylor S, Newbury RO, Kolodner RD, Hoffman HM. Identification of EpCAM as the gene for congenital tufting enteropathy. Gastroenterology. 2008 Aug; 135(2):429-37. PMID: 18572020.
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    155. Walsh T, McClellan JM, McCarthy SE, Addington AM, Pierce SB, Cooper GM, Nord AS, Kusenda M, Malhotra D, Bhandari A, Stray SM, Rippey CF, Roccanova P, Makarov V, Lakshmi B, Findling RL, Sikich L, Stromberg T, Merriman B, Gogtay N, Butler P, Eckstrand K, Noory L, Gochman P, Long R, Chen Z, Davis S, Baker C, Eichler EE, Meltzer PS, Nelson SF, Singleton AB, Lee MK, Rapoport JL, King MC, Sebat J. Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science. 2008 Apr 25; 320(5875):539-43. PMID: 18369103.
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    156. Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008 Mar 13; 452(7184):215-9. PMID: 18278030.
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    157. Alarcón M, Abrahams BS, Stone JL, Duvall JA, Perederiy JV, Bomar JM, Sebat J, Wigler M, Martin CL, Ledbetter DH, Nelson SF, Cantor RM, Geschwind DH. Linkage, association, and gene-expression analyses identify CNTNAP2 as an autism-susceptibility gene. Am J Hum Genet. 2008 Jan; 82(1):150-9. PMID: 18179893.
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    158. Stanczak CM, Chen Z, Nelson SF, Suchard M, McCabe ER, McGhee S. Representational oligonucleotide microarray analysis (ROMA) and comparison of binning and change-point methods of analysis: application to detection of del22q11.2 (DiGeorge) syndrome. Hum Mutat. 2008 Jan; 29(1):176-81. PMID: 17694540.
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    159. Nakano I, Masterman-Smith M, Saigusa K, Paucar AA, Horvath S, Shoemaker L, Watanabe M, Negro A, Bajpai R, Howes A, Lelievre V, Waschek JA, Lazareff JA, Freije WA, Liau LM, Gilbertson RJ, Cloughesy TF, Geschwind DH, Nelson SF, Mischel PS, Terskikh AV, Kornblum HI. Maternal embryonic leucine zipper kinase is a key regulator of the proliferation of malignant brain tumors, including brain tumor stem cells. J Neurosci Res. 2008 Jan; 86(1):48-60. PMID: 17722061.
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    160. Lee H, Jen JC, Cha YH, Nelson SF, Baloh RW. Phenotypic and genetic analysis of a large family with migraine-associated vertigo. Headache. 2008 Nov-Dec; 48(10):1460-7. PMID: 18081823.
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    161. Smalley SL, McGough JJ, Moilanen IK, Loo SK, Taanila A, Ebeling H, Hurtig T, Kaakinen M, Humphrey LA, McCracken JT, Varilo T, Yang MH, Nelson SF, Peltonen L, Järvelin MR. Prevalence and psychiatric comorbidity of attention-deficit/hyperactivity disorder in an adolescent Finnish population. J Am Acad Child Adolesc Psychiatry. 2007 Dec; 46(12):1575-83. PMID: 18030079.
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    162. Nyman ES, Ogdie MN, Loukola A, Varilo T, Taanila A, Hurtig T, Moilanen IK, Loo SK, McGough JJ, Järvelin MR, Smalley SL, Nelson SF, Peltonen L. ADHD candidate gene study in a population-based birth cohort: association with DBH and DRD2. J Am Acad Child Adolesc Psychiatry. 2007 Dec; 46(12):1614-21. PMID: 18030083.
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    163. Liu T, Papagiannakopoulos T, Puskar K, Qi S, Santiago F, Clay W, Lao K, Lee Y, Nelson SF, Kornblum HI, Doyle F, Petzold L, Shraiman B, Kosik KS. Detection of a microRNA signal in an in vivo expression set of mRNAs. PLoS One. 2007 Aug 29; 2(8):e804. PMID: 17726534.
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    164. Richards A, van den Maagdenberg AM, Jen JC, Kavanagh D, Bertram P, Spitzer D, Liszewski MK, Barilla-Labarca ML, Terwindt GM, Kasai Y, McLellan M, Grand MG, Vanmolkot KR, de Vries B, Wan J, Kane MJ, Mamsa H, Schäfer R, Stam AH, Haan J, de Jong PT, Storimans CW, van Schooneveld MJ, Oosterhuis JA, Gschwendter A, Dichgans M, Kotschet KE, Hodgkinson S, Hardy TA, Delatycki MB, Hajj-Ali RA, Kothari PH, Nelson SF, Frants RR, Baloh RW, Ferrari MD, Atkinson JP. C-terminal truncations in human 3'-5' DNA exonuclease TREX1 cause autosomal dominant retinal vasculopathy with cerebral leukodystrophy. Nat Genet. 2007 Sep; 39(9):1068-70. PMID: 17660820.
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    165. Lee H, Sininger L, Jen JC, Cha YH, Baloh RW, Nelson SF. Association of progesterone receptor with migraine-associated vertigo. Neurogenetics. 2007 Aug; 8(3):195-200. PMID: 17609999.
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    166. Funari VA, Day A, Krakow D, Cohn ZA, Chen Z, Nelson SF, Cohn DH. Cartilage-selective genes identified in genome-scale analysis of non-cartilage and cartilage gene expression. BMC Genomics. 2007 Jun 12; 8:165. PMID: 17565682.
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    167. Carlson MR, Pope WB, Horvath S, Braunstein JG, Nghiemphu P, Tso CL, Mellinghoff I, Lai A, Liau LM, Mischel PS, Dong J, Nelson SF, Cloughesy TF. Relationship between survival and edema in malignant gliomas: role of vascular endothelial growth factor and neuronal pentraxin 2. Clin Cancer Res. 2007 May 01; 13(9):2592-8. PMID: 17473188.
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    168. Kerber KA, Jen JC, Lee H, Nelson SF, Baloh RW. A new episodic ataxia syndrome with linkage to chromosome 19q13. Arch Neurol. 2007 May; 64(5):749-52. PMID: 17502476.
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    169. Stone JL, Merriman B, Cantor RM, Geschwind DH, Nelson SF. High density SNP association study of a major autism linkage region on chromosome 17. Hum Mol Genet. 2007 Mar 15; 16(6):704-15. PMID: 17376794.
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    170. Stanczak CM, Chen Z, Zhang YH, Nelson SF, McCabe ER. Deletion mapping in Xp21 for patients with complex glycerol kinase deficiency using SNP mapping arrays. Hum Mutat. 2007 Mar; 28(3):235-42. PMID: 17089405.
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    171. Dwyer JR, Sever N, Carlson M, Nelson SF, Beachy PA, Parhami F. Oxysterols are novel activators of the hedgehog signaling pathway in pluripotent mesenchymal cells. J Biol Chem. 2007 Mar 23; 282(12):8959-68. PMID: 17200122.
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    172. Day A, Carlson MR, Dong J, O'Connor BD, Nelson SF. Celsius: a community resource for Affymetrix microarray data. Genome Biol. 2007; 8(6):R112. PMID: 17570842.
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    173. Lee JC, Vivanco I, Beroukhim R, Huang JH, Feng WL, DeBiasi RM, Yoshimoto K, King JC, Nghiemphu P, Yuza Y, Xu Q, Greulich H, Thomas RK, Paez JG, Peck TC, Linhart DJ, Glatt KA, Getz G, Onofrio R, Ziaugra L, Levine RL, Gabriel S, Kawaguchi T, O'Neill K, Khan H, Liau LM, Nelson SF, Rao PN, Mischel P, Pieper RO, Cloughesy T, Leahy DJ, Sellers WR, Sawyers CL, Meyerson M, Mellinghoff IK. Epidermal growth factor receptor activation in glioblastoma through novel missense mutations in the extracellular domain. PLoS Med. 2006 Dec; 3(12):e485. PMID: 17177598.
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    174. Tso CL, Shintaku P, Chen J, Liu Q, Liu J, Chen Z, Yoshimoto K, Mischel PS, Cloughesy TF, Liau LM, Nelson SF. Primary glioblastomas express mesenchymal stem-like properties. Mol Cancer Res. 2006 Sep; 4(9):607-19. PMID: 16966431.
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    175. Gargalovic PS, Imura M, Zhang B, Gharavi NM, Clark MJ, Pagnon J, Yang WP, He A, Truong A, Patel S, Nelson SF, Horvath S, Berliner JA, Kirchgessner TG, Lusis AJ. Identification of inflammatory gene modules based on variations of human endothelial cell responses to oxidized lipids. Proc Natl Acad Sci U S A. 2006 Aug 22; 103(34):12741-6. PMID: 16912112.
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    176. Lacombe A, Lee H, Zahed L, Choucair M, Muller JM, Nelson SF, Salameh W, Vilain E. Disruption of POF1B binding to nonmuscle actin filaments is associated with premature ovarian failure. Am J Hum Genet. 2006 Jul; 79(1):113-9. PMID: 16773570.
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    177. Carlson MR, Zhang B, Fang Z, Mischel PS, Horvath S, Nelson SF. Gene connectivity, function, and sequence conservation: predictions from modular yeast co-expression networks. BMC Genomics. 2006 Mar 03; 7:40. PMID: 16515682.
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    178. Tso CL, Freije WA, Day A, Chen Z, Merriman B, Perlina A, Lee Y, Dia EQ, Yoshimoto K, Mischel PS, Liau LM, Cloughesy TF, Nelson SF. Distinct transcription profiles of primary and secondary glioblastoma subgroups. Cancer Res. 2006 Jan 01; 66(1):159-67. PMID: 16397228.
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    179. Mitchell S, Ota A, Foster W, Zhang B, Fang Z, Patel S, Nelson SF, Horvath S, Wang Y. Distinct gene expression profiles in adult mouse heart following targeted MAP kinase activation. Physiol Genomics. 2006 Mar 13; 25(1):50-9. PMID: 16368875.
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    180. Lee H, Jen JC, Wang H, Chen Z, Mamsa H, Sabatti C, Baloh RW, Nelson SF. A genome-wide linkage scan of familial benign recurrent vertigo: linkage to 22q12 with evidence of heterogeneity. Hum Mol Genet. 2006 Jan 15; 15(2):251-8. PMID: 16330481.
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    181. Lee H, Zhang Y, Lee FY, Nelson SF, Gonzalez FJ, Edwards PA. FXR regulates organic solute transporters alpha and beta in the adrenal gland, kidney, and intestine. J Lipid Res. 2006 Jan; 47(1):201-14. PMID: 16251721.
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    182. Todd RD, Huang H, Smalley SL, Nelson SF, Willcutt EG, Pennington BF, Smith SD, Faraone SV, Neuman RJ. Collaborative analysis of DRD4 and DAT genotypes in population-defined ADHD subtypes. J Child Psychol Psychiatry. 2005 Oct; 46(10):1067-73. PMID: 16178930.
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    183. Saghizadeh M, Kramerov AA, Tajbakhsh J, Aoki AM, Wang C, Chai NN, Ljubimova JY, Sasaki T, Sosne G, Carlson MR, Nelson SF, Ljubimov AV. Proteinase and growth factor alterations revealed by gene microarray analysis of human diabetic corneas. Invest Ophthalmol Vis Sci. 2005 Oct; 46(10):3604-15. PMID: 16186340.
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    184. Nakano I, Paucar AA, Bajpai R, Dougherty JD, Zewail A, Kelly TK, Kim KJ, Ou J, Groszer M, Imura T, Freije WA, Nelson SF, Sofroniew MV, Wu H, Liu X, Terskikh AV, Geschwind DH, Kornblum HI. Maternal embryonic leucine zipper kinase (MELK) regulates multipotent neural progenitor proliferation. J Cell Biol. 2005 Aug 01; 170(3):413-27. PMID: 16061694.
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    185. Mehrian Shai R, Reichardt JK, Ya-Hsuan H, Kremen TJ, Liau LM, Cloughesy TF, Mischel PS, Nelson SF. Robustness of gene expression profiling in glioma specimen samplings and derived cell lines. Brain Res Mol Brain Res. 2005 May 20; 136(1-2):99-103. PMID: 15893592.
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    186. Lu KV, Jong KA, Kim GY, Singh J, Dia EQ, Yoshimoto K, Wang MY, Cloughesy TF, Nelson SF, Mischel PS. Differential induction of glioblastoma migration and growth by two forms of pleiotrophin. J Biol Chem. 2005 Jul 22; 280(29):26953-64. PMID: 15908427.
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    187. Lynn DE, Lubke G, Yang M, McCracken JT, McGough JJ, Ishii J, Loo SK, Nelson SF, Smalley SL. Temperament and character profiles and the dopamine D4 receptor gene in ADHD. Am J Psychiatry. 2005 May; 162(5):906-13. PMID: 15863792.
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    188. Cantor RM, Kono N, Duvall JA, Alvarez-Retuerto A, Stone JL, Alarcón M, Nelson SF, Geschwind DH. Replication of autism linkage: fine-mapping peak at 17q21. Am J Hum Genet. 2005 Jun; 76(6):1050-6. PMID: 15877280.
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    189. Shen D, Chang HR, Chen Z, He J, Lonsberry V, Elshimali Y, Chia D, Seligson D, Goodglick L, Nelson SF, Gornbein JA. Loss of annexin A1 expression in human breast cancer detected by multiple high-throughput analyses. Biochem Biophys Res Commun. 2005 Jan 07; 326(1):218-27. PMID: 15567174.
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    190. Le K, Mitsouras K, Roy M, Wang Q, Xu Q, Nelson SF, Lee C. Detecting tissue-specific regulation of alternative splicing as a qualitative change in microarray data. Nucleic Acids Res. 2004 Dec 14; 32(22):e180. PMID: 15598820.
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    191. Lee H, Wang H, Jen JC, Sabatti C, Baloh RW, Nelson SF. A novel mutation in KCNA1 causes episodic ataxia without myokymia. Hum Mutat. 2004 Dec; 24(6):536. PMID: 15532032.
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    192. Stone JL, Merriman B, Cantor RM, Yonan AL, Gilliam TC, Geschwind DH, Nelson SF. Evidence for sex-specific risk alleles in autism spectrum disorder. Am J Hum Genet. 2004 Dec; 75(6):1117-23. PMID: 15467983.
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    193. Mischel PS, Cloughesy TF, Nelson SF. DNA-microarray analysis of brain cancer: molecular classification for therapy. Nat Rev Neurosci. 2004 Oct; 5(10):782-92. PMID: 15378038.
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    194. Freije WA, Castro-Vargas FE, Fang Z, Horvath S, Cloughesy T, Liau LM, Mischel PS, Nelson SF. Gene expression profiling of gliomas strongly predicts survival. Cancer Res. 2004 Sep 15; 64(18):6503-10. PMID: 15374961.
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    195. Ogdie MN, Fisher SE, Yang M, Ishii J, Francks C, Loo SK, Cantor RM, McCracken JT, McGough JJ, Smalley SL, Nelson SF. Attention deficit hyperactivity disorder: fine mapping supports linkage to 5p13, 6q12, 16p13, and 17p11. Am J Hum Genet. 2004 Oct; 75(4):661-8. PMID: 15297934.
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    196. Jen JC, Chan WM, Bosley TM, Wan J, Carr JR, Rüb U, Shattuck D, Salamon G, Kudo LC, Ou J, Lin DD, Salih MA, Kansu T, Al Dhalaan H, Al Zayed Z, MacDonald DB, Stigsby B, Plaitakis A, Dretakis EK, Gottlob I, Pieh C, Traboulsi EI, Wang Q, Wang L, Andrews C, Yamada K, Demer JL, Karim S, Alger JR, Geschwind DH, Deller T, Sicotte NL, Nelson SF, Baloh RW, Engle EC. Mutations in a human ROBO gene disrupt hindbrain axon pathway crossing and morphogenesis. Science. 2004 Jun 04; 304(5676):1509-13. PMID: 15105459.
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    197. Shai R, Shi T, Kremen TJ, Horvath S, Liau LM, Cloughesy TF, Mischel PS, Nelson SF. Gene expression profiling identifies molecular subtypes of gliomas. Oncogene. 2003 Jul 31; 22(31):4918-23. PMID: 12894235.
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    198. Mischel PS, Nelson SF, Cloughesy TF. Molecular analysis of glioblastoma: pathway profiling and its implications for patient therapy. Cancer Biol Ther. 2003 May-Jun; 2(3):242-7. PMID: 12878856.
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    199. Mischel PS, Shai R, Shi T, Horvath S, Lu KV, Choe G, Seligson D, Kremen TJ, Palotie A, Liau LM, Cloughesy TF, Nelson SF. Identification of molecular subtypes of glioblastoma by gene expression profiling. Oncogene. 2003 Apr 17; 22(15):2361-73. PMID: 12700671.
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    200. Ogdie MN, Macphie IL, Minassian SL, Yang M, Fisher SE, Francks C, Cantor RM, McCracken JT, McGough JJ, Nelson SF, Monaco AP, Smalley SL. A genomewide scan for attention-deficit/hyperactivity disorder in an extended sample: suggestive linkage on 17p11. Am J Hum Genet. 2003 May; 72(5):1268-79. PMID: 12687500.
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    201. Saghizadeh M, Brown DJ, Tajbakhsh J, Chen Z, Kenney MC, Farber DB, Nelson SF. Evaluation of techniques using amplified nucleic acid probes for gene expression profiling. Biomol Eng. 2003 Mar; 20(3):97-106. PMID: 12684071.
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    202. Smalley SL, Kustanovich V, Minassian SL, Stone JL, Ogdie MN, McGough JJ, McCracken JT, MacPhie IL, Francks C, Fisher SE, Cantor RM, Monaco AP, Nelson SF. Genetic linkage of attention-deficit/hyperactivity disorder on chromosome 16p13, in a region implicated in autism. Am J Hum Genet. 2002 Oct; 71(4):959-63. PMID: 12187510.
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    203. Fisher SE, Francks C, McCracken JT, McGough JJ, Marlow AJ, MacPhie IL, Newbury DF, Crawford LR, Palmer CG, Woodward JA, Del'Homme M, Cantwell DP, Nelson SF, Monaco AP, Smalley SL. A genomewide scan for loci involved in attention-deficit/hyperactivity disorder. Am J Hum Genet. 2002 May; 70(5):1183-96. PMID: 11923911.
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    204. Nishitani J, Chen Z, Qin M, Liu F, Chen H, Nelson SF, Liu X. Identification of genes required for immortalization in human papillomavirus-infected human oral keratinocytes. Cell Mol Biol (Noisy-le-grand). 2002; 48 Online Pub:OL331-41. PMID: 12643451.
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