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Student Publications

Below is a list of publications by year of current students and recent graduates. Students' names are highlighted in bold. 
2021

 

  • Zhang D, Lam J, Blobel GA. Engineering three-dimensional genome folding. Nat Genet. 2021 May;53(5):602-611. doi: 10.1038/s41588-021-00860-9. Epub 2021 May 6. [Pubmed]
  • Miao Z, Balzer MS, Ma Z, Liu H, Wu J, Shrestha R, Aranyi T, Kwan A, Kondo A, Pontoglio M, Kim J, Li M, Kaestner KH, Susztak K. Single cell regulatory landscape of the mouse kidney highlights cellular differentiation programs and disease targets. Nat Commun. 2021 Apr 15;12(1):2277. doi: 10.1038/s41467-021-22266-1. [Pubmed]
  • Chen GM, Chen C, Das RK, Gao P, Chen CH, Bandyopadhyay S, Ding YY, Uzun Y, Yu W, Zhu Q, Myers RM, Grupp SA, Barrett DM, Tan K. Integrative bulk and single-cell profiling of pre-manufacture T-cell populations reveals factors mediating long-term persistence of CAR T-cell therapy. Cancer Discov. 2021 Apr 5:candisc.1677.2020. doi: 10.1158/2159-8290.CD-20-1677. [Pubmed]
  • Moore JH, Truong VQ, Robbins AB, Nicholson D, Williams-Devane CL. Ten important roles for academic leaders to promote equity, diversity, and inclusion in data science. BioData Min. 2021 Mar 30;14(1):22. doi: 10.1186/s13040-021-00256-9. [Pubmed]
  • Ahmadmehrabi S, Li B, Park J, Devkota B, Vujkovic M, Ko YA, Van Wagoner D, Tang WHW, Krantz I, Ritchie M; Regeneron Genetics Center, Brant J, Ruckenstein MJ, Epstein DJ, Rader DJ. Genome-first approach to rare EYA4 variants and cardio-auditory phenotypes in adults. Hum Genet. 2021 Mar 21. doi: 10.1007/s00439-021-02263-6. Epub ahead of print. PMID: 33745059. [Pubmed]
  • Gregg JT, Le TT, Moore JH. (2021). REGENS: an open source Python package for simulating realistic autosomal genotypes. Journal of Open Source Software, 6(59), 2743, https://doi.org/10.21105/joss.02743. [Link to paper]
  • Lee DSM, Park J, Kromer A, Baras A, Rader DJ, Ritchie MD, Ghanem LR, Barash Y. Disrupting upstream translation in mRNAs is associated with human disease. Nat Commun. 2021 Mar 9;12(1):1515. doi: 10.1038/s41467-021-21812-1. PMID: 33750777; PMCID: PMC7943595. [Pubmed]
  • Bone WP, Siewert KM, Jha A, Klarin D, Damrauer SM; VA Million Veteran Program, Chang KM, Tsao PS, Assimes TL, Ritchie MD, Voight BF. Multi-trait association studies discover pleiotropic loci between Alzheimer's disease and cardiometabolic traits. Alzheimers Res Ther. 2021 Feb 4;13(1):34. doi: 10.1186/s13195-021-00773-z. PMCID: PMC7860582. [Pubmed]

  • Gu X, Yang H, Sheng X, Ko YA, Qiu C, Park J, Huang S, Kember R, Judy RL, Park J, Damrauer SM, Nadkarni G, Loos RJF, My VTH, Chaudhary K, Bottinger EP, Paranjpe I, Saha A, Brown C, Akilesh S, Hung AM, Palmer M, Baras A, Overton JD, Reid J, Ritchie M, Rader DJ, Susztak K. Kidney disease genetic risk variants alter lysosomal beta-mannosidase (MANBA) expression and disease severity. Sci Transl Med. 2021 Jan 13;13(576):eaaz1458. doi: 10.1126/scitranslmed.aaz1458. [Pubmed]

  • Park J, Lucas AM, Zhang X, Chaudhary K, Cho JH, Nadkarni G, Dobbyn A, Chittoor G, Josyula NS, Katz N, Breeyear JH, Ahmadmehrabi S, Drivas TG, Chavali VRM, Fasolino M, Sawada H, Daugherty A, Li Y, Zhang C, Bradford Y, Weaver J, Verma A, Judy RL, Kember RL, Overton JD, Reid JG, Ferreira MAR, Li AH, Baras A, LeMaire SA, Shen YH, Naji A, Kaestner KH, Vahedi G, Edwards TL, Chen J, Damrauer SM, Justice AE, Do R, Ritchie MD, Rader DJ. Exome-wide evaluation of rare coding variants using electronic health records identifies new gene-phenotype associations. Nat Med. 2021 Jan;27(1):66-72. doi: 10.1038/s41591-020-1133-8. Epub 2021 Jan 11. [Pubmed]

2020

  • Sanford EM, Emert BL, Coté A, Raj A. Gene regulation gravitates toward either addition or multiplication when combining the effects of two signals. Elife. 2020 Dec 7;9:e59388. doi: 10.7554/eLife.59388. PMCID: PMC7771960. [Pubmed]

  • Hippen AA, Greene CS. Expanding and Remixing the Metadata Landscape. Trends Cancer. 2021 Apr;7(4):276-278. doi: 10.1016/j.trecan.2020.10.011. Epub 2020 Nov 20. [Pubmed]

  • Lee AJ, Park Y, Doing G, Hogan DA, Greene CS. Correcting for experiment-specific variability in expression compendia can remove underlying signals. Gigascience. 2020 Nov 3;9(11):giaa117. doi: 10.1093/gigascience/giaa117. PMCID: PMC7607552. [Pubmed]

  • Pan H, Xue C, Auerbach BJ, Fan J, Bashore AC, Cui J, Yang DY, Trignano SB, Liu W, Shi J, Ihuegbu CO, Bush EC, Worley J, Vlahos L, Laise P, Solomon RA, Connolly ES, Califano A, Sims PA, Zhang H, Li M, Reilly MP. Single-Cell Genomics Reveals a Novel Cell State During Smooth Muscle Cell Phenotypic Switching and Potential Therapeutic Targets for Atherosclerosis in Mouse and Human. Circulation. 2020 Sep 23. doi: 10.1161/CIRCULATIONAHA.120.048378. Epub ahead of print. [Pubmed]

  • Wu X, Niculite CM, Preda MB, Rossi A, Tebaldi T, Butoi E, White MK, Tudoran OM, Petrusca DN, Jannasch AS, Bone WP, Zong X, Fang F, Burlacu A, Paulsen MT, Hancock BA, Sandusky GE, Mitra S, Fishel ML, Buechlein A, Ivan C, Oikonomopoulos S, Gorospe M, Mosley A, Radovich M, Davé UP, Ragoussis J, Nephew KP, Mari B, McIntyre A, Konig H, Ljungman M, Cousminer DL, Macchi P, Ivan M. Regulation of cellular sterol homeostasis by the oxygen responsive noncoding RNA lincNORS. Nat Commun. 2020 Sep 21;11(1):4755. doi: 10.1038/s41467-020-18411-x. [Pubmed]

  • He B, Gao P, Ding YY, Chen CH, Chen G, Chen C, Kim H, Tasian SK, Hunger SP, Tan K. Diverse noncoding mutations contribute to deregulation of cis-regulatory landscape in pediatric cancers. Sci Adv. 2020 Jul 24;6(30):eaba3064. doi: 10.1126/sciadv.aba3064. PMCID: PMC7439310.  [Pubmed]
  • Paul MR, Pan TC, Pant DK, Shih NN, Chen Y, Harvey KL, Solomon A, Lieberman D, Morrissette JJD, Soucier-Ernst D, Goodman NG, Stavropoulos SW, Maxwell KN, Clark C, Belka GK, Feldman M, DeMichele A and Chodosh LA. Genomic landscape of metastatic breast cancer identifies preferentially dysregulated pathways and targets [published online ahead of print, 2020 Jul 13]. J Clin Invest. 2020;129941. doi:10.1172/JCI129941. [Pubmed]

  • Jha A, K Aicher J, R Gazzara M, Singh D, Barash Y. Enhanced Integrated Gradients: improving interpretability of deep learning models using splicing codes as a case study. Genome Biol. 2020 Jun 19;21(1):149. doi: 10.1186/s13059-020-02055-7. PMCID: PMC7305616. [Pubmed]

  • Gao P, Chen C, Howell ED, Li Y, Tober J, Uzan Y, He B, Gao L, Zhu Q, Siekmann A, Speck N, Tan K. Transcriptional regulatory network controlling the ontogeny of hematopoietic stem cells [published online ahead of print, 2020 Jun 4]. Genes Dev. 2020;10.1101/gad.338202.120. doi:10.1101/gad.338202.120 [Pubmed]

  • Zhu, Q.*, Gao, P.*, Tober, J.*, Bennett, L., Chen, C., Uzun, Y., Li, Y., Mumau, M., Yu, W., He, B., Speck, N. & Tan K. (2020). Developmental trajectory of pre-hematopoietic stem cell formation from endothelium. Blood Journal. Blood-2020004801. [Pubmed]

  • Yu, W., Uzun, Y., Zhu, Q., Chen, C. and Tan, K., 2020. scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data. Genome biology. 21, pp.1-17. [Pubmed]

  • Aicher JK, Jewell P, Vaquero-Garcia J, Barash Y, Bhoj EJ. Mapping RNA splicing variations in clinically accessible and nonaccessible tissues to facilitate Mendelian disease diagnosis using RNA-seq. Genet Med. 2020 Mar 30. doi: 10.1038/s41436-020-0780-y. [Pubmed]

  • Bellissimo DC, Chen CH, Zhu Q, Bagga S, Lee CT, He B, Wertheim GB, Jordan M, Tan K, Worthen GS, Gilliland DG, Speck NA. Runx1 negatively regulates inflammatory cytokine production by neutrophils in response to Toll-like receptor signaling. Blood Adv. 2020 Mar 24;4(6):1145-1158. doi: 10.1182/bloodadvances.2019000785. [Pubmed]

  • Chen GM, Azzam A, Ding YY, Barrett DM, Grupp SA, Tan K. Dissecting the tumor-immune landscape in chimeric antigen receptor T-cell therapy: key challenges and opportunities for a systems immunology approach. Clin Cancer Res. 2020 Mar 3. pii: clincanres.3888.2019. doi: 10.1158/1078-0432.CCR-19-3888. [Pubmed]

  • Zhou Z, Ye C, Wang J, Zhang NR. Surface protein imputation from single cell transcriptomes by deep neural networks. Nat Commun. 2020 Jan 31;11(1):651. doi: 10.1038/s41467-020-14391-0. [Pubmed]
  • Clay M, Hammond J, Zhong F, Chen X, Kowalski C, Lee AJ, Porter M, Hampton T, Greene C, Pletneva E, Hogan D. (2020). Pseudomonas aeruginosa lasR mutant fitness in microoxia is supported by an Anr-regulated oxygen-binding hemerythrin. Proceedings of the National Academy of Sciences. 117. 201917576. 10.1073/pnas.1917576117. [Pubmed]

  • Zhou Z, Xu B, Minn A, Zhang NR. DENDRO: genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing. Genome Biol. 2020 Jan 14;21(1):10. doi: 10.1186/s13059-019-1922-x. PMCID: PMC6961311. [Pubmed]

2019

  • Benson KK, Hu W, Weller AH, Bennett AH, Chen ER, Khetarpal SA, Yoshino S, Bone WP, Wang L, Rabinowitz JD, Voight BF, Soccio RE. Natural human genetic variation determines basal and inducible expression of PM20D1, an obesity-associated gene. Proc Natl Acad Sci U S A. 2019 Nov 12;116(46):23232-23242. doi: 10.1073/pnas.1913199116. Epub 2019 Oct 28. PMCID: PMC6859347. [Pubmed]

  • Zhou N, Jiang Y, Bergquist TR, Lee AJ, et al. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biol. 2019 Nov 19;20(1):244. doi: 10.1186/s13059-019-1835-8. PMCID: PMC6864930. [Pubmed]

  • Ransick, A.*, Lindström, N. O.*, Liu, J.*, Zhu, Q., Guo, J. J., Alvarado, G. F., Kim, A. D., Black, H. G., Kim, J. & McMahon, A. P. (2019). Single-Cell Profiling Reveals Sex, Lineage, and Regional Diversity in the Mouse Kidney. Developmental cell. 51(3), pp.399-413. [Pubmed]

  • Park J, Damrauer SM, Baras A, Reid JG, Overton JD, Gonzalez-Alegre P. Epidemiology of DYT1 dystonia: Estimating prevalence via genetic ascertainment. Neurol Genet. 2019 Sep 13;5(5):e358. doi: 10.1212/NXG.0000000000000358. eCollection 2019 Oct. PMCID: PMC6745720. [Pubmed]
  • *Packer JS, *Zhu Q, Huynh C, Sivaramakrishnan P, Preston E, Dueck H, Stefanik D, Tan K, Trapnell C, Kim J, Waterston RH, Murray JI. A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution. Science. 2019 Sep 5.pii: eaax1971. doi: 10.1126/science.aax1971. [Pubmed] *contributed equally

  • Wang J, Agarwal D, Huang M, Hu G, Zhou Z, Ye C, Zhang NR. Data denoising with transfer learning in single-cell transcriptomics. Nat Methods. 2019 Sep;16(9):875-878. doi: 10.1038/s41592-019-0537-1. Epub 2019 Aug 30. PubMed PMID:31471617. [Pubmed]

  • Benci JL, Johnson LR, Choa R, Xu Y, Qiu J, Zhou Z, Xu B, Ye D, Nathanson KL, June CH, Wherry EJ, Zhang NR, Ishwaran H, Hellmann MD, Wolchok JD, Kambayashi T,  Minn AJ. Opposing Functions of Interferon Coordinate Adaptive and Innate Immune Responses to Cancer Immune Checkpoint Blockade. Cell. 2019 Aug 8;178(4):933-948.e14. doi: 10.1016/j.cell.2019.07.019. PMCID: PMC6830508. [Pubmed]

  • Park J, Levin MG, Haggerty CM, Hartzel DN, Judy R, Kember RL, Reza N; Regeneron Genetics Center, Ritchie MD, Owens AT, Damrauer SM, Rader DJ. A genome-first approach to aggregating rare genetic variants in LMNA for association with electronic health record phenotypes. Genet Med. 2019 Aug 6. doi: 10.1038/s41436-019-0625-8. [Pubmed]

  • Peng T, Zhu Q, Yin P, Tan K. SCRABBLE: single-cell RNA-seq imputation constrained by bulk RNA-seq data. Genome Biol. 2019 May 6;20(1):88. doi: 10.1186/s13059-019-1681-8. PMCID: PMC6501316. [Pubmed]

  • Fan S, Kelly DE, Beltrame MH, Hansen MEB, Mallick S, Ranciaro A, Hirbo J, Thompson S, Beggs W, Nyambo T, Omar SA, Meskel DW, Belay G, Froment A, Patterson  N, Reich D, Tishkoff SA. African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations. Genome Biol. 2019 Apr 26;20(1):82. doi: 10.1186/s13059-019-1679-2. PMCID: PMC6485071. [Pubmed]

  • Shields EJ, Petracovici AF, Bonasio R. lncRedibly versatile: biochemical and biological functions of long noncoding RNAs. Biochem J. 2019 Apr 10;476(7):1083-1104. doi: 10.1042/BCJ20180440. Review. PMCID: PMC6745715. [Pubmed]

  • Zhang X, Basile AO, Pendergrass SA, Ritchie MD. Real world scenarios in rare variant association analysis: the impact of imbalance and sample size on the power in silico. BMC Bioinformatics. 2019 Jan 22;20(1):46. Doi: 10.1186/s12859-018-2591-6. PMCID: PMC6343276.  [Pubmed]

  • Zhang X, Veturi Y, Verma S, Bone W, Verma A, Lucas A, Hebbring S, Denny JC, Stanaway IB, Jarvik GP, Crosslin D, Larson EB, Rasmussen-Torvik L, Pendergrass SA, Smoller JW, Hakonarson H, Sleiman P, Weng C, Fasel D, Wei WQ, Kullo I, Schaid D, Chung WK, Ritchie MD. Detecting potential pleiotropy across cardiovascular and neurological diseases using univariate, bivariate, and multivariate methods on 43,870 individuals from the eMERGE network. Pac Symp Biocomput. 2019;24:272-283. PMCID: PMC6457436. [Pubmed]

  • Shan M, Anderson ZD, Gregory BD. Computationally Characterizing Protein-Bound Long Noncoding RNAs and Their Secondary Structure Using Protein Interaction Profile Sequencing (PIP-Seq) in Plants. Methods Mol Biol. 2019;1933:363-380. doi:10.1007/978-1-4939-9045-0_22. [Pubmed]

2018
  • Siewert KM, Voight BF. Bivariate Genome-Wide Association Scan Identifies 6 Novel Loci Associated With Lipid Levels and Coronary Artery Disease. Circ Genom Precis Med. 2018 Dec;11(12):e002239. doi: 10.1161/CIRCGEN.118.002239. PMCID: PMC6291836. [Pubmed]
  • Rouhanifard SH, Mellis IA, Dunagin M, Bayatpour S, Jiang CL, Dardani I, Symmons O, Emert B, Torre E, Cote A, Sullivan A, Stamatoyannopoulos JA, Raj A. ClampFISH detects individual nucleic acid molecules using click chemistry-based amplification. Nat Biotechnol. 2018 Nov 12. doi: 10.1038/nbt.4286. PMCID: PMC6511493. [Pubmed]

  • Lin N, Shay JES, Xie H, Lee DSM, Skuli N, Tang Q, Zhou Z, Azzam A, Meng H, Wang H, FitzGerald GA, Simon MC. Myeloid Cell Hypoxia-Inducible Factors Promote Resolution of Inflammation in Experimental Colitis. Front Immunol. 2018 Nov 5;9:2565. doi: 10.3389/fimmu.2018.02565. eCollection 2018. PMCID: PMC6230677. [Pubmed]

  • Mishra R*, Hodge KM*, Cousminer DL, Leslie RD, Grant SFA. A Global Perspective of Latent Autoimmune Diabetes in Adults. Trends Endocrinol Metab. 2018 Sep;29(9):638-650. doi: 10.1016/j.tem.2018.07.001. Epub 2018 Jul 23. Review. [Pubmed]

  • Sun JH, Zhou L, Emerson DJ, Phyo SA, Titus KR, Gong W, Gilgenast TG, Beagan JA, Davidson BL, Tassone F, Phillips-Cremins JE. Disease-Associated Short Tandem  Repeats Co-localize with Chromatin Domain Boundaries. Cell. 2018 Sep 20;175(1):224-238.e15. doi: 10.1016/j.cell.2018.08.005. Epub 2018 Aug 30. PMCID: PMC6175607. [Pubmed]

  • Sun JH, Zhou L, Emerson DJ, Phyo SA, Titus KR, Gong W, Gilgenast TG, Beagan JA, Davidson BL, Tassone F, Phillips-Cremins JE. Disease-Associated Short Tandem  Repeats Co-localize with Chromatin Domain Boundaries. Cell. 2018 Sep 20;175(1):224-238.e15. doi: 10.1016/j.cell.2018.08.005. Epub 2018 Aug 30. PMCID: PMC6175607. [Pubmed]

  • Amlie-Wolf A, Tang M, Mlynarski EE, Kuksa PP, Valladares O, Katanic Z, Tsuang D, Brown CD, Schellenberg GD, Wang LS. INFERNO: inferring the molecular mechanisms of noncoding genetic variants. Nucleic Acids Res. 2018 Aug 3. doi: 10.1093/nar/gky686. [Pubmed]

  • Mishra R*, Hodge KM*, Cousminer DL, Leslie RD, Grant SFA. A Global Perspective of Latent Autoimmune Diabetes in Adults. Trends Endocrinol Metab. 2018 Sep;29(9):638-650. doi: 10.1016/j.tem.2018.07.001. Epub 2018 Jul 23. Review. [Pubmed]

  • Weiner AK, Sidoli S, Diskin SJ, Garcia BA. Graphical Interpretation and Analysis of Proteins and their Ontologies (GiaPronto): A One-Click Graph Visualization Software for Proteomics Data Sets. Mol Cell Proteomics. 2018 Jul;17(7):1426-1431. doi: 10.1074/mcp.TIR117.000438 PMCID: PMC6030729. [Pubmed]

  • Zhou Z, Wang W, Wang LS, Zhang NR. Integrative DNA copy number detection and genotyping from sequencing and array-based platforms. Bioinformatics. 2018 Jul 15;34(14):2349-2355. doi: 10.1093/bioinformatics/bty104. PMCID: PMC6041760 [Pubmed]

  • Zheng Q, Bartow-McKenney C, Meisel JS, Grice EA. HmmUFOtu: An HMM and phylogenetic placement based ultra-fast taxonomic assignment and OTU picking tool for microbiome amplicon sequencing studies. Genome Biol. 2018 Jun 27;19(1):82. doi: 10.1186/s13059-018-1450-0. [Pubmed]

  • Shields EJ, Sheng L, Weiner AK, Garcia BA, Bonasio R. High-Quality Genome Assemblies Reveal Long Non-coding RNAs Expressed in Ant Brains. Cell Rep. 2018 Jun 5;23(10):3078-3090. doi: 10.1016/j.celrep.2018.05.014. PMCID: PMC6023404. [Pubmed]

  • Hill DA, Lim HW, Kim YH, Ho WY, Foong YH, Nelson VL, Nguyen HCB, Chegireddy K, Kim J, Habertheuer A, Vallabhajosyula P, Kambayashi T, Won KJ, Lazar MA. Distinct macrophage populations direct inflammatory versus physiological changes in adipose tissue. Proc Natl Acad Sci U S A. 2018 May 29;115(22):E5096-E5105. doi: 10.1073/pnas.1802611115. PMC5984532. [Pubmed]

  • Bartow-McKenney C, Hannigan GD, Horwinski J, Hesketh P, Horan AD, Mehta S, Grice EA. The microbiota of traumatic, open fracture wounds is associated with mechanism of injury. Wound Repair Regen. 2018 May 26. doi: 10.1111/wrr.12642. [Pubmed]

  • Kuksa PP, Amlie-Wolf A, Katanic Ž, Valladares O, Wang LS, Leung YY. SPAR: small RNA-seq portal for analysis of sequencing experiments. Nucleic Acids Res. 2018 May 4. doi: 10.1093/nar/gky330. [Pubmed]

  • Nativio R, Donahue G, Berson A, Lan Y, Amlie-Wolf A, Tuzer F, Toledo JB, Gosai SJ, Gregory BD, Torres C, Trojanowski JQ, Wang LS, Johnson FB, Bonini NM, Berger SL. Dysregulation of the epigenetic landscape of normal aging in Alzheimer's disease. Nat Neurosci. 2018 Apr;21(4):497-505. doi: 10.1038/s41593-018-0101-9. Epub 2018 Mar 5. Erratum in: Nat Neurosci. 2018 Mar 19,. [Pubmed]

  • Verma SS, Lucas A, Zhang X, Veturi Y, Dudek S, Li B, Li R, Urbanowicz R, Moore JH, Kim D, Ritchie MD. Collective feature selection to identify crucial epistatic variants. BioData Min. 2018 Apr 19;11:5. doi: 10.1186/s13040-018-0168-6. eCollection 2018. PMCID: PMC5907720. [Pubmed]

  • Way GP, Sanchez-Vega F, La K, Armenia J, Chatila WK, Luna A, Sander C, Cherniack AD, Mina M, Ciriello G, Schultz N; Cancer Genome Atlas Research Network, Sanchez Y, Greene CS. Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas. Cell Rep. 2018 Apr 3;23(1):172-180.e3. doi: 10.1016/j.celrep.2018.03.046.PMCID: PMC5918694. [Pubmed]

  • Kuehn MH, Mishra R, Deonovic BE, Miller KN, McCormack SE, Liu GT, Kupersmith MJ, Wall M; NORDIC IIHTT Study Group. Genetic Survey of Adult-Onset Idiopathic Intracranial Hypertension. J Neuroophthalmol. 2018 Mar 30. doi: 10.1097/WNO.0000000000000648. [Pubmed]

  • Nativio R, Donahue G, Berson A, Lan Y, Amlie-Wolf A, Tuzer F, Toledo JB, Gosai SJ, Gregory BD, Torres C, Trojanowski JQ, Wang LS, Johnson FB, Bonini NM, Berger SL. Dysregulation of the epigenetic landscape of normal aging in Alzheimer's disease. Nat Neurosci. 2018 Apr;21(4):497-505. doi: 10.1038/s41593-018-0101-9. Epub 2018 Mar 5. Erratum in: Nat Neurosci. 2018 Mar 19,. [Pubmed]

  • Urrutia E, Chen H, Zhou Z, Zhang NR, Jiang Y. Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny. Bioinformatics. 2018 Feb 5. doi: 10.1093/bioinformatics/bty057. [Pubmed]

  • Zhu Q, Fisher SA, Dueck H, Middleton S, Khaladkar M, Kim J. PIVOT: platform for interactive analysis and visualization of transcriptomics data. BMC Bioinformatics. 2018 Jan 5;19(1):6. doi: 10.1186/s12859-017-1994-0. PMCID: PMC5756333. [Pubmed]

2017
  • Norton S, Vaquero-Garcia J, Lahens NF, Grant GR, Barash Y. Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates. Bioinformatics. 2017 Dec 11. doi: 10.1093/bioinformatics/btx790. [Pubmed]

  • Agarwal D, Nowak C, Zhang NR, Pusztai L, Hatzis C. Functional germline variants as potential co-oncogenes. NPJ Breast Cancer. 2017 Nov 22;3:46. doi: 10.1038/s41523-017-0051-5. eCollection 2017. Review. PMCID: PMC5700137. [Pubmed]

  • Crawford NG, Kelly DE, Hansen MEB, Beltrame MH, Fan S, Bowman SL, Jewett E, Ranciaro A, Thompson S, Lo Y, Pfeifer SP, Jensen JD, Campbell MC, Beggs W, Hormozdiari F, Mpoloka SW, Mokone GG, Nyambo T, Meskel DW, Belay G, Haut J; NISC Comparative Sequencing Program, Rothschild H, Zon L, Zhou Y, Kovacs MA, Xu M, Zhang T, Bishop K, Sinclair J, Rivas C, Elliot E, Choi J, Li SA, Hicks B, Burgess S, Abnet C, Watkins-Chow DE, Oceana E, Song YS, Eskin E, Brown KM, Marks MS, Loftus SK, Pavan WJ, Yeager M, Chanock S, Tishkoff SA. Loci associated with skin pigmentation identified in African populations. Science. 2017 Nov 17;358(6365). pii: eaan8433. doi: 10.1126/science.aan8433. PMCID: PMC5759959. [Pubmed]

  • Jia C, Hu Y, Kelly D, Kim J, Li M, Zhang NR. Accounting for technical noise in differential expression analysis of single-cell RNA sequencing data. Nucleic Acids Res. 2017 Nov 2;45(19):10978-10988. doi: 10.1093/nar/gkx754. PMCID: PMC5737676. [Pubmed]

  • Titus AJ, Way GP, Johnson KC, Christensen BC. Deconvolution of DNA methylation identifies differentially methylated gene regions on 1p36 across breast cancer subtypes. Sci Rep. 2017 Sep 14;7(1):11594. doi: 10.1038/s41598-017-10199-z. PMC5599639. [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]

  • 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]

  • 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]

  • 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]

  • Beagan JA, Duong MT, Titus KR, Zhou L, Cao Z, Ma J, Lachanski CV, Gillis DR, Phillips-Cremins JE. YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment. Genome Res. 2017 Jul;27(7):1139-1152. doi: 10.1101/gr.215160.116. PMCID: PMC5495066. [Pubmed]

  • Siewert KM, Voight BF. Detecting Long-Term Balancing Selection Using Allele Frequency Correlation. Mol Biol Evol. 2017 Jul 21. doi: 10.1093/molbev/msx209. [Epub ahead of print] [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]

  • 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]

  • 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]

  • 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]

  • 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]

  • 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]

  • 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]

  • 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]

  • Beaulieu-Jones BK, Moore JH. Missing Data Imputation in the Electronic Health Record using Deeply Learned Autoencoders. Pac Symp Biocomput. 2017;22:207-218. PMCID: PMC5144587. [Pubmed]

2016
  •  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]
  • 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, 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]

  • 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]

  • 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]

  • 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]

  • 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]

  • 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]

  •  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]

  • 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]

  • 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]

  • 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]

  • 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]

2015
  • 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]

  • 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]

  • 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]

  • 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]

  • 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]