Graduate Group in Genomics and Computational Biology

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Publications of current students and recent graduates

Aggarwala V, Voight BF. An expanded sequence context model broadly explains variability in polymorphism levels across the human genome. Nat Genet. 2016
Apr;48(4):349-55. [Pubmed]

Leung YY, Kuksa PP, Amlie-Wolf A, Valladares O, Ungar LH, Kannan S, Gregory BD, Wang LS. DASHR: database of small human noncoding RNAs. Nucleic Acids Res. 2016 Jan 4;44(D1):D216-22. [Pubmed]

Amlie-Wolf A, Ryvkin P, Tong R, Dragomir I, Suh E, Xu Y, Van Deerlin VM, Gregory BD, Kwong LK, Trojanowski JQ, Lee VM, Wang LS, Lee EB. Transcriptomic Changes Due to Cytoplasmic TDP-43 Expression Reveal Dysregulation of Histone Transcripts and Nuclear Chromatin. PLoS One. 2015 Oct 28;10(10):e0141836. [Pubmed]

Beaulieu-Jones BK, Moore JH. Missing Data Imputation in the Electronic Health Record using Deeply Learned Autoencoders. Pac Symp Biocomput. 2016;22:207-218. PMCID: PMC5144587. [Pubmed]

Beaulieu-Jones BK, Greene CS; Pooled Resource Open-Access ALS Clinical Trials Consortium. Semi-supervised learning of the electronic health record for phenotype stratification. J Biomed Inform. 2016 Dec;64:168-178. doi: 10.1016/j.jbi.2016.10.007. [Pubmed]

Silverman IM, Berkowitz ND, Gosai SJ, Gregory BD. Genome-Wide Approaches for RNA Structure Probing. Adv Exp Med Biol. 2016;907:29-59. doi: 10.1007/978-3-319-29073-7_2. [Pubmed]

Berkowitz ND, Silverman IM, Childress DM, Kazan H, Wang LS, Gregory BD. A comprehensive database of high-throughput sequencing-based RNA secondary structure probing data (Structure Surfer). BMC Bioinformatics. 2016 May 17;17(1):215. doi: 10.1186/s12859-016-1071-0. PMCID: PMC4869249. [Pubmed]

Willmann MR, Berkowitz ND, Gregory BD. Improved genome-wide mapping of uncapped and cleaved transcripts in eukaryotes--GMUCT 2.0. Methods. 2014 May 1;67(1):64-73. [Pubmed]

Burdick J, Walton T, Preston E, Zacharias A, Raj A, Murray JI. Overlapping cell population expression profiling and regulatory inference in C. elegans. BMC Genomics. 2016 Feb 29;17(1):159. doi: 10.1186/s12864-016-2482-z. PMCID: PMC4772325. [Pubmed]

Burdick JT, Murray JI. Deconvolution of gene expression from cell populations across the C. elegans lineage. BMC Bioinformatics. 2013 Jun 22;14:204. doi:10.1186/1471-2105-14-204. PMCID:PMC3704917. [Pubmed]

Richards JL, Zacharias AL, Walton T, Burdick JT, Murray JI. A quantitative model of normal Caenorhabditis elegans embryogenesis and its disruption after stress. Dev Biol. 2013 Feb 1;374(1):12-23. doi: 10.1016/j.ydbio.2012.11.034. Epub 2012 Dec 7. PMCID: PMC3548946. [Pubmed]

Cheung VG, Bruzel A, Burdick JT, Morley M, Devlin JL, Spielman RS. Monozygotic twins reveal germline contribution to allelic expression differences. Am J Hum Genet. 2008 Jun;82(6):1357-60. doi: 10.1016/j.ajhg.2008.05.003. PMCID: PMC2427304. [Pubmed]

Wu GD, Compher C, Chen EZ, Smith SA, Shah RD, Bittinger K, Chehoud C, Albenberg LG, Nessel L, Gilroy E, Star J, Weljie AM, Flint HJ, Metz DC, Bennett MJ, Li H, Bushman FD, Lewis JD. Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production. Gut. 2016 Jan;65(1):63-72. PMCID: PMC4583329. [Pubmed]

Lee D, Baldassano RN, Otley AR, Albenberg L, Griffiths AM, Compher C, Chen EZ, Li H, Gilroy E, Nessel L, Grant A, Chehoud C, Bushman FD, Wu GD, Lewis JD. Comparative Effectiveness of Nutritional and Biological Therapy in North American Children with Active Crohn's Disease. Inflamm Bowel Dis. 2015 Aug;21(8):1786-93. [Pubmed]

Lewis JD, Chen EZ, Baldassano RN, Otley AR, Griffiths AM, Lee D, Bittinger K, Bailey A, Friedman ES, Hoffmann C, Albenberg L, Sinha R, Compher C, Gilroy E, Nessel L, Grant A, Chehoud C, Li H, Wu GD, Bushman FD. Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease. Cell Host Microbe. 2015 Oct 14;18(4):489-500. PMCID: PMC4633303. [Pubmed]

Kameswaran V, Bramswig NC, McKenna LB, Penn M, Schug J, Hand NJ, Chen Y, Choi I, Vourekas A, Won KJ, Liu C, Vivek K, Naji A, Friedman JR, Kaestner KH. Epigenetic regulation of the DLK1-MEG3 microRNA cluster in human type 2 diabetic islets. Cell Metab. 2014 Jan 7;19(1):135-45. [Pubmed]

Vandivier L, Li F, Zheng Q, Willmann M, Chen Y, Gregory B. Arabidopsis mRNA secondary structure correlates with protein function and domains. Plant Signal Behav. 2013 Jun;8(6):e24301. [Pubmed]

Li F, Zheng Q, Vandivier LE, Willmann MR, Chen Y, Gregory BD. Regulatory Impact of RNA Secondary Structure across the Arabidopsis Transcriptome. Plant Cell. 2012 Nov;24(11):4346-59. [Pubmed]

Zhang Y, Liu J, Jia C, Li T, Wu R, Wang J, Chen Y, Zou X, Chen R, Wang XJ, Zhu D. Systematic identification and evolutionary features of rhesus monkey small nucleolar RNAs. BMC Genomics. 2010 Jan 25;11:61. [Pubmed]

Zheng Q, Zhang Y, Chen Y, Yang N, Wang XJ, Zhu D. Systematic identification of genes involved in divergent skeletal muscle growth rates of broiler and layer chickens. BMC Genomics. 2009 Feb 22;10:87. [Pubmed]

Clarke EL
, Lauder AP, Hofstaedter CE, Hwang Y, Fitzgerald AS, Imai I, Biernat W, Rękawiecki B, Majewska H, Dubaniewicz A, Litzky LA, Feldman MD, Bittinger K, Rossman MD, Patterson KC, Bushman FD, Collman RG. Microbial Lineages in Sarcoidosis: A Metagenomic Analysis Tailored for Low Microbial Content Samples. Am J Respir Crit Care Med. 2017 Aug 28. doi: 10.1164/rccm.201705-0891OC. [Pubmed]

Clarke EL, Sundararaman SA, Seifert SN, Bushman FD, Hahn BH, Brisson D. swga: A primer design toolkit for selective whole genome amplification. Bioinformatics. 2017 Feb 27. doi: 10.1093/bioinformatics/btx118. [Pubmed]

Brauer PM, Pessach IM, Clarke E, Rowe JH, Ott de Bruin L, Lee YN, Dominguez-Brauer C, Comeau AM, Awong G, Felgentreff K, Zhang YH, Bredemeyer A, Al-Herz W, Du L, Ververs F, Kennedy M, Giliani S, Keller G, Sleckman BP, Schatz DG, Bushman FD, Notarangelo LD, Zúñiga-Pflücker JC. Modeling altered T-cell development with induced pluripotent stem cells from patients with RAG1-dependent immune deficiencies. Blood. 2016 Aug 11;128(6):783-93. PMCID: PMC4982452. [Pubmed]

Dueck H, Eberwine J, Kim J. Variation is function: Are single cell differences functionally important?: Testing the hypothesis that single cell variation is required for aggregate function. Bioessays. 2016 Feb;38(2):172-80. doi: 10.1002/bies.201500124. PMCID: PMC4738397. [Pubmed]

Spaethling JM, Sanchez-Alavez M, Lee J, Xia FC, Dueck H, Wang W, Fisher SA, Sul JY, Seale P, Kim J, Bartfai T, Eberwine J. Single-cell transcriptomics and functional target validation of brown adipocytes show their complex roles in metabolic homeostasis. FASEB J. 2016 Jan;30(1):81-92. [Pubmed]

Dueck H, Khaladkar M, Kim TK, Spaethling JM, Francis C, Suresh S, Fisher SA, Seale P, Beck SG, Bartfai T, Kuhn B, Eberwine J, Kim J. Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation. Genome Biol.  2015 Jun 9;16:122. [Pubmed]

Lahens NF, Kavakli IH, Zhang R, Hayer K, Black MB, Dueck H, Pizarro A, Kim J, Irizarry R, Thomas RS, Grant GR, Hogenesch JB. IVT-seq reveals extreme bias in RNA sequencing. Genome Biol. 2014 Jun 30;15(6):R86. doi: 10.1186/gb-2014-15-6-r86. PMCID: PMC4197826. [Pubmed]

Hwang YC, Lin CF, Valladares O, Malamon J, Kuksa PP, Zheng Q, Gregory BD, Wang LS. HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements. Bioinformatics. 2015 Apr 15;31(8):1290-2. doi: 10.1093/bioinformatics/btu801. Epub 2014 Dec 4. PMCID: PMC4393516. [Pubmed]

Cao K, Ryvkin P, Hwang YC, Johnson FB, Wang LS. Analysis of nonlinear gene expression progression reveals extensive pathway and age-specific transitions in aging human brains. PLoS One. 2013 Oct 3;8(10):e74578. doi: 10.1371/journal.pone.0074578. PMCID: PMC3789733. [Pubmed]

Lin CF, Valladares O, Childress DM, Klevak E, Geller ET, Hwang YC, Tsai EA, Schellenberg GD, Wang LS. DRAW+SneakPeek: analysis workflow and quality metric management for DNA-seq experiments. Bioinformatics. 2013 Oct 1;29(19):2498-500. doi: 10.1093/bioinformatics/btt422. Epub 2013 Aug 13. PMCID: PMC3777113. [Pubmed]

Hwang YC, Zheng Q, Gregory BD, Wang LS. High-throughput identification of long-range regulatory elements and their target promoters in the human genome. Nucleic Acids Res. 2013 May;41(9):4835-46. doi: 10.1093/nar/gkt188. Epub 2013 Mar 21. PMCID: PMC3643598. [Pubmed]

Olarerin-George AO, Anton L, Hwang YC, Elovitz MA, Hogenesch JB. A functional genomics screen for microRNA regulators of NF-kappaB signaling. BMC Biol. 2013 Feb 28;11:19. doi: 10.1186/1741-7007-11-19. PMCID: PMC3621838. [Pubmed]

Ji X, Kember RL, Brown CD, Bućan M. Increased burden of deleterious variants in essential genes in autism spectrum disorder. Proc Natl Acad Sci U S A. 2016 Dec 27;113(52):15054-15059. doi: 10.1073/pnas.1613195113. PMCID: PMC5206557. [Pubmed]

Dickinson ME*, Flenniken AM*, Ji X*, Teboul L*, Wong MD*, et al. High-throughput discovery of novel developmental phenotypes. Nature. 2016 Sep14;537(7621):508-514. *contributed equally [Pubmed]

Jiang Y, Qiu Y, Minn AJ, Zhang NR. Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencing. Proc Natl Acad Sci U S A. 2016 Sep 13;113(37):E5528-37. [Pubmed]

Jiang Y, Oldridge DA, Diskin SJ, Zhang NR. CODEX: a normalization and copy number variation detection method for whole exome sequencing. Nucleic Acids Res. 2015 Mar 31;43(6):e39. [Pubmed]

Kelly DE, Vatsa AK, Mayham WG, Hearne LB, Kazic T. Extracting complex lesion phenotypes in Zea mays. Machine Vision and Applications. 2016. 27(1):145-156. [link to paper]

Kelly DE, Hansen M, Tishkoff SA. Global variation in gene expression and the value of diverse sampling. Current Opinion in Systems Biology, 1 (2017), pp. 102-108. [link to paper]

Xiao J, Jin R, Yu X, Shen M, Wagner JD, Pai A, Song C, Zhuang M, Klasfeld S, He C, Santos AM, Helliwell C, Pruneda-Paz JL, Kay SA, Lin X, Cui S, Garcia MF, Clarenz O, Goodrich J, Zhang X, Austin RS, Bonasio R, Wagner D. Cis and trans determinants of epigenetic silencing by Polycomb repressive complex 2 in Arabidopsis. Nat Genet. 2017 Aug 21. doi: 10.1038/ng.3937. [Pubmed]

Hannigan GD, Zheng Q, Meisel JS, Minot SS, Bushman FD, Grice EA. Evolutionary and functional implications of hypervariable loci within the skin virome. PeerJ. 2017 Feb 7;5:e2959. doi: 10.7717/peerj.2959. PMCID: PMC5299996. [Pubmed]

Meisel JS
and Grice EA, Chapter 4 - The Human Microbiome, In Genomic and Precision Medicine (Third Edition), edited by Geoffrey S. Ginsburg and Huntington F. Willard, Academic Press, Boston, 2017, Pages 63-77, ISBN 9780128006818, [link to chapter].

Meisel JS, Hannigan GD, Tyldsley AS, SanMiguel AJ, Hodkinson BP, Zheng Q, Grice EA. Skin Microbiome Surveys Are Strongly Influenced by Experimental Design. J Invest Dermatol. 2016 May;136(5):947-56. PMCID: PMC4842136. [Pubmed]

Hannigan GD, Meisel JS, Tyldsley AS, Zheng Q, Hodkinson BP, SanMiguel AJ, Minot S, Bushman FD, Grice EA. The human skin double-stranded DNA virome: topographical and temporal diversity, genetic enrichment, and dynamic associations with the host microbiome. MBio. 2015 Oct 20;6(5):e01578-15. [Pubmed]

Mellis IA, Gupte R, Raj A, Rouhanifard SH. Visualizing adenosine-to-inosine RNA editing in single mammalian cells. Nat Methods. 2017 Jun 12. doi: 10.1038/nmeth.4332. [Pubmed]

Berlyand Y, Weintraub D, Xie SX, Mellis IA, Doshi J, Rick J, McBride J, Davatzikos C, Shaw LM, Hurtig H, Trojanowski JQ, Chen-Plotkin AS. An Alzheimer's Disease-Derived Biomarker Signature Identifies Parkinson's Disease Patients with Dementia. PLoS One. 2016 Jan 26;11(1):e0147319. [Pubmed]

Mellis IA, Raj A. Half dozen of one, six billion of the other: What can small-and large-scale molecular systems biology learn from one another? Genome Res. 2015 Oct;25(10):1466-72. [Pubmed]

Economides AN, Frendewey D, Yang P, Dominguez MG, Dore AT, Lobov IB, Persaud T, Rojas J, McClain J, Lengyel P, Droguett G, Chernomorsky R, Stevens S, Auerbach W, Dechiara TM, Pouyemirou W, Cruz JM Jr, Feeley K, Mellis IA, Yasenchack J, Hatsell SJ, Xie L, Latres E, Huang L, Zhang Y, Pefanis E, Skokos D, Deckelbaum RA, Croll SD, Davis S, Valenzuela DM, Gale NW, Murphy AJ, Yancopoulos GD. Conditionals by inversion provide a universal method for the generation of conditional alleles. Proc Natl Acad Sci U S A. 2013 Aug 20;110(34):E3179-88. [Pubmed]

Middleton SA, Illuminati J, Kim J. Complete fold annotation of the human proteome using a novel structural feature space. Sci Rep. 2017 Apr 13;7:46321. doi: 10.1038/srep46321. PMCID: PMC5390313. [Pubmed]

Kim H, Walsh MC, Takegahara N, Middleton SA, Shin HI, Kim J, Choi Y. The purinergic receptor P2X5 regulates inflammasome activity and hyper-multinucleation of murine osteoclasts. Sci Rep. 2017 Mar 15;7(1):196. doi: 10.1038/s41598-017-00139-2. [Pubmed]

Middleton SA, Kim J. NoFold: RNA structure clustering without folding or alignment. RNA. 2014 Nov;20(11):1671-83. [Pubmed]

Mishra R, Chesi A, Cousminer DL, Hawa MI, Bradfield JP, Hodge KM, Guy VC, Hakonarson H; Bone Mineral Density in Childhood Study., Mauricio D, Schloot NC, Yderstræde KB, Voight BF, Schwartz S, Boehm BO, Leslie RD, Grant SFA. Relative contribution of type 1 and type 2 diabetes loci to the genetic etiology of adult-onset, non-insulin-requiring autoimmune diabetes. BMC Med. 2017 Apr 25;15(1):88. doi: 10.1186/s12916-017-0846-0. PMCID: PMC5404312. [Pubmed]

Brzezinski JD, Modi A, Liu M, Roth MJ. Repression of the Chromatin-Tethering Domain of Murine Leukemia Virus p12. J Virol. 2016 Nov 28;90(24):11197-11207. Print 2016 Dec 15. PMC5126376. [Pubmed]

Brzezinski JD, Felkner R, Modi A, Liu M, Roth MJ. Phosphorylation Requirement of Murine Leukemia Virus p12. J Virol. 2016 Nov 28;90(24):11208-11219. Print 2016 Dec 15.
PMC5126377. [Pubmed]

Oldridge DA, Wood AC, Weichert-Leahey N, Crimmins I, Sussman R, Winter C, McDaniel LD, Diamond M, Hart LS, Zhu S, Durbin AD, Abraham BJ, Anders L, Tian L, Zhang S, Wei JS, Khan J, Bramlett K, Rahman N, Capasso M, Iolascon A, Gerhard DS, Guidry Auvil JM, Young RA, Hakonarson H, Diskin SJ, Look AT, Maris JM. Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism. Nature. 2015 Dec 17;528(7582):418-21. doi: 10.1038/nature15540. Epub 2015 Nov 11. PMCID: PMC4775078. [Pubmed]

Sotillo E, Barrett DM, Black KL, Bagashev A, Oldridge D, Wu G, Sussman R, Lanauze C, Ruella M, Gazzara MR, Martinez NM, Harrington CT, Chung EY, Perazzelli J, Hofmann TJ, Maude SL, Raman P, Barrera A, Gill S, Lacey SF, Melenhorst JJ, Allman D, Jacoby E, Fry T, Mackall C, Barash Y, Lynch KW, Maris JM, Grupp SA,Thomas-Tikhonenko A. Convergence of Acquired Mutations and Alternative Splicing of CD19 Enables Resistance to CART-19 Immunotherapy. Cancer Discov. 2015 Dec;5(12):1282-95. doi: 10.1158/2159-8290.CD-15-1020. Epub 2015 Oct 29. PMCID: PMC4670800. [Pubmed]

Schnepp RW, Khurana P, Attiyeh EF, Raman P, Chodosh SE, Oldridge DA, Gagliardi ME, Conkrite KL, Asgharzadeh S, Seeger RC, Madison BB, Rustgi AK, Maris JM, Diskin SJ. A LIN28B-RAN-AURKA Signaling Network Promotes Neuroblastoma Tumorigenesis. Cancer Cell. 2015 Nov 9;28(5):599-609. doi: 10.1016/j.ccell.2015.09.012. Epub 2015 Oct 17. PMCID: PMC4643330. [Pubmed]

Eleveld TF, Oldridge DA, Bernard V, Koster J, Daage LC, Diskin SJ, Schild L, Bentahar NB, Bellini A, Chicard M, Lapouble E, Combaret V, Legoix-Né P, Michon J, Pugh TJ, Hart LS, Rader J, Attiyeh EF, Wei JS, Zhang S, Naranjo A, Gastier-Foster JM, Hogarty MD, Asgharzadeh S, Smith MA, Guidry Auvil JM, Watkins TB, Zwijnenburg DA, Ebus ME, van Sluis P, Hakkert A, van Wezel E, van der Schoot CE, Westerhout EM, Schulte JH, Tytgat GA, Dolman ME, Janoueix-Lerosey I, Gerhard DS, Caron HN, Delattre O, Khan J, Versteeg R, Schleiermacher G, Molenaar JJ, Maris JM. Relapsed neuroblastomas show frequent RAS-MAPK pathway mutations. Nat Genet. 2015 Aug;47(8):864-71. doi: 10.1038/ng.3333. Epub 2015 Jun 29. PMCID: PMC4775079. [Pubmed]

Russell MR, Penikis A, Oldridge DA, Alvarez-Dominguez JR, McDaniel L, Diamond M, Padovan O, Raman P, Li Y, Wei JS, Zhang S, Gnanchandran J, Seeger R, Asgharzadeh S, Khan J, Diskin SJ, Maris JM, Cole KA. CASC15-S Is a Tumor Suppressor lncRNA at the 6p22 Neuroblastoma Susceptibility Locus. Cancer Res. 2015 Aug 1;75(15):3155-66. doi: 10.1158/0008-5472.CAN-14-3613. Epub 2015 Jun 22. PMCID: PMC4526355. [Pubmed]

Jiang Y, Oldridge DA, Diskin SJ, Zhang NR. CODEX: a normalization and copy number variation detection method for whole exome sequencing. Nucleic Acids Res. 2015 Mar 31;43(6):e39. doi: 10.1093/nar/gku1363. Epub 2015 Jan 23. PMCID: PMC4381046. [Pubmed]

Diskin SJ, Capasso M, Diamond M, Oldridge DA, Conkrite K, Bosse KR, Russell MR, Iolascon A, Hakonarson H, Devoto M, Maris JM. Rare variants in TP53 and susceptibility to neuroblastoma. J Natl Cancer Inst. 2014 Apr;106(4):dju047. doi: 10.1093/jnci/dju047. Epub 2014 Mar 14. PMCID: PMC3982892. [Pubmed]

Paul MR, Levitt NP, Moore DE, Watson PM, Wilson RC, Denlinger CE, Watson DK, Anderson PE. Multivariate models from RNA-Seq SNVs yield candidate molecular targets for biomarker discovery: SNV-DA. BMC Genomics. 2016 Mar 31;17(1):263. [Pubmed]

Sherrill-Mix S, Ocwieja KE, Bushman FD. Gene activity in primary T cells infected with HIV89.6: intron retention and induction of genomic repeats. Retrovirology. 2015 Sep 17;12:79. doi: 10.1186/s12977-015-0205-1. PMCID: PMC4574318. [Pubmed]

Bryson AL, Hwang Y, Sherrill-Mix S, Wu GD, Lewis JD, Black L, Clark TA, Bushman FD. Covalent Modification of Bacteriophage T4 DNA Inhibits CRISPR-Cas9. MBio. 2015 Jun 16;6(3):e00648. doi: 10.1128/mBio.00648-15. PMCID: PMC4471564. [Pubmed]

Kelly BJ, Gross R, Bittinger K, Sherrill-Mix S, Lewis JD, Collman RG, Bushman FD, Li H. Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA. Bioinformatics. 2015 Aug 1;31(15):2461-8. PMCID: PMC4514928. [Pubmed]

Ocwieja KE, Sherrill-Mix S, Liu C, Song J, Bau H, Bushman FD. A reverse transcription loop-mediated isothermal amplification assay optimized to detect multiple HIV subtypes. PLoS One. 2015 Feb 12;10(2):e0117852. doi: 10.1371/journal.pone.0117852. eCollection 2015. PMC4326360. [Pubmed]

Ocwieja KE, Fernando AN, Sherrill-Mix S, Sundararaman SA, Tennekoon RN, Tippalagama R, Krishnananthasivam S, Premawansa G, Premawansa S, De Silva AD. Phylogeography and molecular epidemiology of an epidemic strain of dengue virus type 1 in Sri Lanka. Am J Trop Med Hyg. 2014 Aug;91(2):225-34. doi: 10.4269/ajtmh.13-0523. Epub 2014 May 5. PMCID: PMC4125241. [Pubmed]

Sherrill-Mix S, Lewinski MK, Famiglietti M, Bosque A, Malani N, Ocwieja KE, Berry CC, Looney D, Shan L, Agosto LM, Pace MJ, Siliciano RF, O'Doherty U, Guatelli J, Planelles V, Bushman FD. HIV latency and integration site placement in five cell-based models. Retrovirology. 2013 Aug 16;10:90. doi: 10.1186/1742-4690-10-90. PMCID: PMC3765678. [Pubmed]

Sundararaman SA, Liu W, Keele BF, Learn GH, Bittinger K, Mouacha F, Ahuka-Mundeke S, Manske M, Sherrill-Mix S, Li Y, Malenke JA, Delaporte E, Laurent C, Mpoudi Ngole E, Kwiatkowski DP, Shaw GM, Rayner JC, Peeters M, Sharp PM, Bushman FD, Hahn BH. Plasmodium falciparum-like parasites infecting wild apes in southern Cameroon do not represent a recurrent source of human malaria. Proc Natl Acad Sci U S A. 2013 Apr 23;110(17):7020-5. doi: 10.1073/pnas.1305201110. PMCID: PMC3637760. [Pubmed]

Ocwieja KE, Sherrill-Mix S, Mukherjee R, Custers-Allen R, David P, Brown M, Wang S, Link DR, Olson J, Travers K, Schadt E, Bushman FD. Dynamic regulation of  HIV-1 mRNA populations analyzed by single-molecule enrichment and long-read sequencing. Nucleic Acids Res. 2012 Nov 1;40(20):10345-55. doi:10.1093/nar/gks753. Epub 2012 Aug 25. PMCID: PMC3488221. [Pubmed]

Berg MG, Singh LN, Younis I, Liu Q, Pinto AM, Kaida D, Zhang Z, Cho S, Sherrill-Mix S, Wan L, Dreyfuss G. U1 snRNP determines mRNA length and regulates  isoform expression. Cell. 2012 Jul 6;150(1):53-64. doi:10.1016/j.cell.2012.05.029. PMCID: PMC3412174. [Pubmed]

Dollive S, Peterfreund GL, Sherrill-Mix S, Bittinger K, Sinha R, Hoffmann C, Nabel CS, Hill DA, Artis D, Bachman MA, Custers-Allen R, Grunberg S, Wu GD, Lewis JD, Bushman FD. A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples. Genome Biol. 2012 Jul 3;13(7):R60. doi: 10.1186/gb-2012-13-7-r60. PMCID: PMC4053730. [Pubmed]

Gospocic J, Shields EJ, Glastad KM, Lin Y, Penick CA, Yan H, Mikheyev AS, Linksvayer TA, Garcia BA, Berger SL, Liebig J, Reinberg D, Bonasio R. The Neuropeptide Corazonin Controls Social Behavior and Caste Identity in Ants. Cell. 2017 Aug 10;170(4):748-759.e12. doi: 10.1016/j.cell.2017.07.014. PMCID: PMC5564227. [Pubmed]

Yin P, Anttila V, Siewert KM, Palotie A, Davey Smith G, Voight BF. Serum calcium and risk of migraine: a Mendelian randomization study. Hum Mol Genet. 2016 Dec 26. pii: ddw416. doi: 10.1093/hmg/ddw416. [Epub ahead of print] [Pubmed]

Way GP, Youngstrom DW, Hankenson KD, Greene CS, Grant SF. Implicating candidate genes at GWAS signals by leveraging topologically associating domains. Eur J Hum Genet. 2017 Aug 9. doi: 10.1038/ejhg.2017.108. [Pubmed]

Way GP, Allaway RJ, Bouley SJ, Fadul CE, Sanchez Y, Greene CS. A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma. BMC Genomics. 2017 Feb 6;18(1):127. doi: 10.1186/s12864-017-3519-7. PMCID: PMC5292791. [Pubmed]

Way GP, Rudd J, Wang C, Hamidi H, Fridley BL, Konecny GE, Goode EL, Greene CS, Doherty JA. Comprehensive Cross-Population Analysis of High-Grade Serous Ovarian Cancer Supports No More Than Three Subtypes. G3 (Bethesda). 2016 Dec 7;6(12):4097-4103. PMCID: PMC5144978 [Pubmed]

Zhang R, Podtelezhnikov AA, Hogenesch JB, Anafi RC. Discovering Biology in Periodic Data through Phase Set Enrichment Analysis (PSEA). J Biol Rhythms. 2016 Mar 8. [Pubmed]

Zhang R, Lahens NF, Ballance HI, Hughes ME, Hogenesch JB. A circadian gene expression atlas in mammals: implications for biology and medicine. Proc Natl Acad Sci U S A. 2014 Nov 11;111(45):16219-24. doi: 10.1073/pnas.1408886111. Epub 2014 Oct 27. PMCID: PMC4234565. [Pubmed]

Lahens NF, Kavakli IH, Zhang R, Hayer K, Black MB, Dueck H, Pizarro A, Kim J, Irizarry R, Thomas RS, Grant GR, Hogenesch JB. IVT-seq reveals extreme bias in  RNA sequencing. Genome Biol. 2014 Jun 30;15(6):R86. doi: 10.1186/gb-2014-15-6-r86. PMCID:  PMC4197826. [Pubmed]

Gao F, Chang D, Biddanda A, Ma L, Guo Y, Zhou Z, Keinan A. XWAS: A Software Toolset for Genetic Data Analysis and Association Studies of the X Chromosome. J Hered. 2015 Sep-Oct;106(5):666-71. [Pubmed]