2011 - 2012

  1. Extensivegenetic variation in somatic human tissues
    O'Huallachain M, Karczewski KJ, Weissman SM, Urban AE, Snyder MP. Proc Natl Acad Sci U S A. 2012 Oct30;109(44):18018-23. doi: 10.1073/pnas.1213736109. Epub 2012 Oct 5. PubMed PMID: 23043118

  2. SWI/SNF chromatin-remodeling factors:multiscale analyses and diverse functions
    Euskirchen G, Auerbach RK, Snyder M. J Biol Chem. 2012 Sep7;287(37):30897-905. doi: 10.1074/jbc.R111.309302. Epub 2012 Sep 5. Review.PubMed PMID: 22952240;

  3. ChIP-seq guidelinesand practices of the ENCODE and modENCODE consortia
    Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S,Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C,Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM,Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L,Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE,Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, TolstorukovMY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M. Genome Res. 2012Sep;22(9):1813-31. doi: 10.1101/gr.136184.111. PubMed PMID: 22955991; PubMedCentral PMCID: PMC3431496.

  4. Annotation of functionalvariation in personal genomes using RegulomeDB
    Boyle AP, Hong EL, Hariharan M, Cheng Y, Schaub MA, Kasowski M, KarczewskiKJ, Park J, Hitz BC, Weng S, Cherry JM, Snyder M. Genome Res. 2012Sep;22(9):1790-7. doi: 10.1101/gr.137323.112. PubMed PMID: 22955989; PubMedCentral PMCID: PMC3431494.

  5. Linking diseaseassociations with regulatory information in the human genome.
    Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M. Genome Res. 2012Sep;22(9):1748-59. doi: 10.1101/gr.136127.111. PubMed PMID: 22955986; PubMedCentral PMCID: PMC3431491.

  6. Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements.
    Kundaje A, Kyriazopoulou-Panagiotopoulou S, Libbrecht M, Smith CL, Raha D,Winters EE, Johnson SM, Snyder M, Batzoglou S, Sidow A. Genome Res.2012 Sep;22(9):1735-47. doi: 10.1101/gr.136366.111. PubMed PMID: 22955985;

  7. Correlation of Global MicroRNA Expression With Basal Cell Carcinoma Subtype.
    Heffelfinger C, Ouyang Z, Engberg A, Leffell DJ, Hanlon AM, Gordon PB, Zheng W, Zhao H, Snyder MP, Bale AE. G3 (Bethesda). 2012;2(2):279-86. PMCID: PMC3284335.

  8. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation.
    Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, Poh HM, Goh Y, Lim J, Zhang J, Sim HS, Peh SQ, Mulawadi FH, Ong CT, Orlov YL, Hong S, Zhang Z, Landt S, Raha D, Euskirchen G, Wei CL, Ge W, Wang H, Davis C, Fisher-Aylor KI, Mortazavi A, Gerstein M, Gingeras T, Wold B, Sun Y, Fullwood MJ, Cheung E, Liu E, Sung WK, Snyder M, Ruan Y. Cell. 2012;148(1-2):84-98. PMCID: PMC3339270.

  9. Systems biology: personalized medicine for the future?
    Chen R, Snyder M. CurrOpin Pharmacol. 2012 Oct;12(5):623-8. doi: 10.1016/j.coph.2012.07.011. Epub 2012 Jul 31. Review. PubMed PMID: 22858243.

  10. Characterization of Enhancer Function from Genome-Wide Analyses.
    Maston GA, Landt SG, Snyder M, Green MR. Annu Rev Genomics Hum Genet. 2012.

  11. A computational framework to functionally annotate variants in personal genomes within a cloud-computing environment.
    Habegger L, Balasubramanian S, Chen DZ, Khurana E, Sboner A, Harmanci A, Rozowsky J, Clarke D, Snyder M, Gerstein M. VAT: Bioinformatics. 2012.

  12. Investigating metabolite-protein interactions: anoverview of available techniques.
    Yang GX, Li X, Snyder M. IMethods. 2012 Aug;57(4):459-66. doi:10.1016/j.ymeth.2012.06.013. Epub 2012 Jun 28. Review. PubMed PMID: 22750303;PubMed Central PMCID: PMC3448827.

  13. The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome.
    Paik YK, Jeong SK, Omenn GS, Uhlen M, Hanash S, Cho SY, Lee HJ, Na K, Choi EY, Yan F, Zhang F, Zhang Y, Snyder M, Cheng Y, Chen R, Marko-Varga G, Deutsch EW, Kim H, Kwon JY, Aebersold R, Bairoch A, Taylor AD, Kim KY, Lee EY, Hochstrasser D, Legrain P, Hancock WS. Nat Biotechnol. 2012;30(3):221-3.

  14. Tcf7 is an important regulator of the switch of self-renewal and differentiation in a multipotential hematopoietic cell line.
    Wu JQ, Seay M, Schulz VP, Hariharan M, Tuck D, Lian J, Du J, Shi M, Ye Z, Gerstein M, Snyder MP, Weissman S. PLoS Genet. 2012;8(3):e1002565. PMCID: PMC3297581.

  15. A core erythroid transcriptional network is repressed by a master regulator of myelo-lymphoid differentiation.
    Wontakal SN, Guo X, Smith C, MacCarthy T, Bresnick EH, Bergman A, Snyder MP, Weissman SM, Zheng D, Skoultchi AI. Proc Natl Acad Sci U S A. 2012;109(10):3832-7. PMCID: PMC3309740.

  16. Q & A: the Snyderome.

    Snyder M. (2012). Genome Biol 13, 147.

  17. Personal omics profiling reveals dynamic molecular and medical phenotypes.
    Chen R, Mias GI, Li-Pook-Than J, Jiang L, Lam HY, Miriami E, Karczewski KJ, Hariharan M, Dewey FE, Cheng Y, Clark MJ, Im H, Habegger L, Balasubramanian S, O'Huallachain M, Dudley JT, Hillenmeyer S, Haraksingh R, Sharon D, Euskirchen G, Lacroute P, Bettinger K, Boyle AP, Kasowski M, Grubert F, Seki S, Garcia M, Whirl-Carrillo M, Gallardo M, Blasco MA, Greenberg PL, Snyder P, Klein TE, Altman RB, Butte AJ, Ashley EA, Gerstein M, Nadeau KC, Tang H, Snyder M. Cell. 2012;148(6):1293-307. PMCID: PMC3341616.

  18. Tcf7 is an important regulator of the switch of self-renewal and differentiation in a multipotential hematopoietic cell line.
    Wu, J.Q., Seay, M., Schulz, V.P., Hariharan, M., Tuck, D., Lian, J., Du, J., Shi, M., Ye, Z., Gerstein, M., Snyder M.P., and Weissman, S. (2012). PLoS Genet 8, e1002565.

  19. Detecting and annotating genetic variations using the HugeSeq pipeline.
    Lam HY, Pan C, Clark MJ, Lacroute P, Chen R, Haraksingh R, O'Huallachain M, Gerstein MB, Kidd JM, Bustamante CD, Snyder M. Nat Biotechnol. 2012;30(3):226-9.

  20. Interpretome: a freely available, modular, and secure personal genome interpretation engine.
    Karczewski KJ, Tirrell RP, Cordero P, Tatonetti NP, Dudley JT, Salari K, Snyder M, Altman RB, Kim SK.Pac Symp Biocomput. 2012:339-50.

  21. Phosphorylation of yeast transcription factors correlates with the evolution of novel sequence and function.
    Kaganovich M, Snyder M. J Proteome Res. 2012;11(1):261-8.

  22. Performance comparison of whole-genome sequencing platforms.
    Lam HY, Clark MJ, Chen R, Natsoulis G, O'Huallachain M, Dewey FE, Habegger L, Ashley EA, Gerstein MB, Butte AJ, Ji HP, Snyder M. Nat Biotechnol. 2012;30(1):78-82.

  23. Dissecting phosphorylation networks: lessons learned from yeast.
    Mok J, Zhu X, Snyder M. Expert Rev Proteomics. 2011;8(6):775-86. PMCID: PMC3262144.

  24. Genome-wide mapping of copy number variation in humans: comparative analysis of high resolution array platforms.
    Haraksingh RR, Abyzov A, Gerstein M, Urban AE, Snyder M. PLoS One. 2011;6(11):e27859. PMCID: PMC3227574.

  25. Performance comparison of exome DNA sequencing technologies.
    Clark MJ, Chen R, Lam HY, Karczewski KJ, Euskirchen G, Butte AJ, Snyder M. Nat Biotechnol. 2011;29(10):908-14.

  26. AlleleSeq: analysis of allele-specific expression and binding in a network framework.
    Rozowsky J, Abyzov A, Wang J, Alves P, Raha D, Harmanci A, Leng J, Bjornson R, Kong Y, Kitabayashi N, Bhardwaj N, Rubin M, Snyder M, Gerstein M.Mol Syst Biol. 2011;7:522.

  27. Measuring the evolutionary rewiring of biological networks.
    Shou C, Bhardwaj N, Lam HY, Yan KK, Kim PM, Snyder M, Gerstein MB. PLoS Comput Biol. 2011;7(1):e1001050.

  28. Identification of genomic indels and structural variations using split reads.
    Zhang ZD, Du J, Lam H, Abyzov A, Urban AE, Snyder M, Gerstein M. BMC Genomics. 2011;12:375. PMCID: PMC3161018.

  29. A user's guide to the encyclopedia of DNA elements (ENCODE).
    Consortium EP, Myers RM, Stamatoyannopoulos J, Snyder M, Dunham I, Hardison RC, Bernstein BE, Gingeras TR, Kent WJ, Birney E, Wold B, Crawford GE. PLoS Biol. 2011;9(4):e1001046. PMCID: PMC3079585.

  30. Diverse protein kinase interactions identified by protein microarrays reveal novel connections between cellular processes.
    Fasolo J, Sboner A, Sun MG, Yu H, Chen R, Sharon D, Kim PM, Gerstein M, Snyder M. Genes Dev. 2011;25(7):767-78.

  31. CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.
    Abyzov A, Urban AE, Snyder M, Gerstein M. Genome Res. 2011.

  32. Metabolites as global regulators: A new view of protein regulation: Systematic investigation of metabolite-protein interactions may help bridge the gap between genome-wide association studies and small molecule screening studies.
    Li X, Snyder M. Bioessays. 2011.

  33. A comprehensive map of mobile element insertion polymorphisms in humans.
    Stewart C, Kural D, Stromberg MP, Walker JA, Konkel MK, Stutz AM, Urban AE, Grubert F, Lam HY, Lee WP, Busby M, Indap AR, Garrison E, Huff C, Xing J, Snyder MP, Jorde LB, Batzer MA, Korbel JO, Marth GT, Genomes P. PLoS Genet. 2011;7(8):e1002236. PMCID: PMC3158055.

  34. Cooperative transcription factor associations discovered using regulatory variation
    Karczewski KJ, Tatonetti NP, Landt SG, Yang X, Slifer T, Altman RB, Snyder M. . Proc Natl Acad Sci U S A. 2011;108(32):13353-8. PMCID: PMC3156166.

  35. Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans.
    Niu W, Lu ZJ, Zhong M, Sarov M, Murray JI, Brdlik CM, Janette J, Chen C, Alves P, Preston E, Slightham C, Jiang L, Hyman AA, Kim SK, Waterston RH, Gerstein M, Snyder M, Reinke V. Genome Res. 2011;21(2):245-54.

  36. Mapping copy number variation by population-scale genome sequencing.
    Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stutz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO, Genomes P. Nature. 2011;470(7332):59-65.

  37. Genome-wide chromatin occupancy analysis reveals a role for ASH2 in transcriptional pausing.<>
    Perez-Lluch S, Blanco E, Carbonell A, Raha D, Snyder M, Serras F, Corominas M. Nucleic Acids Res. 2011.

  38. Global analysis of cdc14 phosphatase reveals diverse roles in mitotic processes.
    Bloom J, Cristea IM, Procko AL, Lubkov V, Chait BT, Snyder M, Cross FR. J Biol Chem. 2011;286(7):5434-45. PMCID: PMC3037656.

  39. mTOR-mediated dedifferentiation of the retinal pigment epithelium initiates photoreceptor degeneration in mice.
    Zhao C, Yasumura D, Li X, Matthes M, Lloyd M, Nielsen G, Ahern K, Snyder M, Bok D, Dunaief JL, LaVail MM, Vollrath D. J Clin Invest. 2011;121(1):369-83. PMCID: 3007156.

  40. Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data.
    Lu ZJ, Yip KY, Wang G, Shou C, Hillier LW, Khurana E, Agarwal A, Auerbach R, Rozowsky J, Cheng C, Kato M, Miller DM, Slack F, Snyder M, Waterston RH, Reinke V, Gerstein MB. Genome Res. 2011.

  41. RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries.
    Habegger L, Sboner A, Gianoulis TA, Rozowsky J, Agarwal A, Snyder M, Gerstein M. Bioinformatics. 2011;27(2):281-3. PMCID: 3018817.

  42. The human proteome project: current state and future direction.
    Legrain P, Aebersold R, Archakov A, Bairoch A, Bala K, Beretta L, Bergeron J, Borchers CH, Corthals GL, Costello CE, Deutsch EW, Domon B, Hancock W, He F, Hochstrasser D, Marko-Varga G, Salekdeh GH, Sechi S, Snyder M, Srivastava S, Uhlen M, Wu CH, Yamamoto T, Paik YK, Omenn GS. Mol Cell Proteomics. 2011;10(7):M111 009993. PMCID: PMC3134076.

  43. A large gene network in immature erythroid cells is controlled by the myeloid and B cell transcriptional regulator PU.1.
    Wontakal SN, Guo X, Will B, Shi M, Raha D, Mahajan MC, Weissman S, Snyder M, Steidl U, Zheng D, Skoultchi AI. PLoS Genet. 2011;7(6):e1001392. PMCID: PMC3111485.

  44. Diverse Roles and Interactions of the SWI/SNF Chromatin Remodeling Complex Revealed Using Global Approaches.
    Euskirchen GM, Auerbach RK, Davidov E, Gianoulis TA, Zhong G, Rozowsky J, Bhardwaj N, Gerstein MB, Snyder M. PLoS Genet. 2011;7(3):e1002008. PMCID: PMC3048368.

  45. The CRIT framework for identifying cross patterns in systems biology and application to chemogenomics.
    Gianoulis TA, Agarwal A, Snyder M, Gerstein MB.Genome Biol. 2011;12(3):R32. PMCID: PMC3129682.

  46. Phased whole-genome genetic risk in a family quartet using a major allele reference sequence.
    Dewey FE, Chen R, Cordero SP, Ormond KE, Caleshu C, Karczewski KJ, Whirl-Carrillo M, Wheeler MT, Dudley JT, Byrnes JK, Cornejo OE, Knowles JW, Woon M, Sangkuhl K, Gong L, Thorn CF, Hebert JM, Capriotti E, David SP, Pavlovic A, West A, Thakuria JV, Ball MP, Zaranek AW, Rehm HL, Church GM, West JS, Bustamante CD, Snyder M, Altman RB, Klein TE, Butte AJ, Ashley EA. PLoS Genet. 2011;7(9):e1002280. PMCID: PMC3174201.

  47. Arabidopsis RTNLB1 and RTNLB2 Reticulon-Like Proteins Regulate Intracellular Trafficking and Activity of the FLS2 Immune Receptor.
    Lee HY, Bowen CH, Popescu GV, Kang HG, Kato N, Ma S, Dinesh-Kumar S, Snyder M, Popescu SC. Plant Cell. 2011.