Student Publications

Jensen M, Girirajan S. Mapping a shared genetic basis for neurodevelopmental disorders. Genome Med. 2017 Dec 14;9(1):109. doi: 10.1186/s13073-017-0503-4. PubMed

Li B, Verma SS, Veturi YC, Verma A, Bradford Y, Haas DW, Ritchie MD. Evaluation of PrediXcan for prioritizing GWAS associations and predicting gene expression. Pac Symp Biocomput. 2018;23:448-459. PubMed

Rangavittal S, Harris RS, Cechova M, Tomaszkiewicz M, Chikhi R, Makova KD, Medvedev P. RecoverY: K-mer based read classification for Y-chromosome specific sequencing and assembly. Bioinformatics. 2017 Nov 28. doi: 10.1093/bioinformatics/btx771. [Epub ahead of print] PubMed

Jensen M, Kooy RF, Simon TJ, Reyniers E, Girirajan S, Tassone F. A higher rare CNV burden in the genetic background potentially contributes to intellectual disability phenotypes in 22q11.2 deletion syndrome. Eur J Med Genet. 2017 Nov 28. pii: S1769-7212(17)30358-0. doi: 10.1016/j.ejmg.2017.11.016. [Epub ahead of print] PubMed

Hall MA, Wallace J, Lucas A, Kim D, Basile AO, Verma SS , McCarty CA, Brilliant MH, Peissig PL, Kitchner TE, 1: Hall MA, Wallace J, Lucas A, Kim D, Basile AO, Verma SS, McCarty CA, Brilliant MH, Peissig PL, Kitchner TE, Verma A , Pendergrass SA, Dudek SM, Moore JH, Ritchie MD. PLATO software provides analytic framework for investigating complexity beyond genome-wide association studies. Nat Commun. 2017 Oct 27;8(1):1167. doi:10.1038/s41467-017-00802-2. PubMed

Kakumanu A, Velasco S, Mazzoni E, Mahony S. Deconvolving sequence features that discriminate between overlapping regulatory annotations. PLOS Comput Biol. 2017 Oct 19;13(10):e1005795. doi: 10.1371/journal.pcbi.1005795. [Epub ahead of print] PubMed

Kim D, Volk H, Girirajan S, Pendergrass S, Hall MA, Verma SS, Schmidt RJ, Hansen RL, Ghosh D, Ludena-Rodriguez Y, Kim K, Ritchie MD, Hertz-Picciotto I, Selleck SB. The joint effect of air pollution exposure and copy number variation on risk for autism. Autism Res. 2017 Sep;10(9):1470-1480. doi: 10.1002/aur.1799. Epub 2017 Apr 27. PubMed

Yang T, Zhang F, Yardimci GG, Song F, Hardison RC, Noble WS, Yue F, Li Q. HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient. Genome Res. 2017 Aug 30. pii: gr.220640.117. doi:10.1101/gr.220640.117. [Epub ahead of print] PubMed

Coble JL, Sheldon KE, Yue F, Salameh TJ, Harris LR III, Deiling S, Ruggiero FM, Eshelman MA, Yochum GS, Koltun WA, Gerhard GS, Broach JR. Identification of a rare LAMB4 variant associated with familial diverticulitis through exome sequencing. Hum Mol Genet. 2017 Aug 15;26(16):3212-3220. doi: 10.1093/hmg/ddx204. PubMed

Holzinger ER, Verma SS , Moore CB, Hall M, De R, Gilbert-Diamond D, Lanktree MB, Pankratz N, Amuzu A, Burt A, Dale C, Dudek S, Furlong CE, Gaunt TR, Kim DS, Riess H, Sivapalaratnam S, Tragante V, van Iperen EPA, Brautbar A, Carrell DS, Crosslin DR, Jarvik GP, Kuivaniemi H, Kullo IJ, Larson EB, Rasmussen-Torvik LJ, Tromp G, Baumert J, Cruickshanks KJ, Farrall M, Hingorani AD, Hovingh GK, Kleber  ME, Klein BE, Klein R, Koenig W, Lange LA, Mӓrz W, North KE, Charlotte Onland-Moret N, Reiner AP, Talmud PJ, van der Schouw YT, Wilson JG, Kivimaki M, Kumari M, Moore JH, Drenos F, Asselbergs FW, Keating BJ, Ritchie MD. Discovery and replication of SNP-SNP interactions for quantitative lipid traits in over 60,000 individuals. BioData Min. 2017 Jul 24;10:25. doi: 10.1186/s13040-017-0145-5. eCollection 2017. PubMed PMID: 28770004. PubMed

Rieber L, Mahony S. miniMDS: 3D structural inference from high-resolution Hi-C data. Bioinformatics. 2017 Jul 15;33(14):i261-i266. doi: 10.1093/bioinformatics/btx271. PubMed

Döring K, Ahmed N, Riemer T, Suresh HG, Vainshtein Y, Habich M, Riemer J,Mayer MP, O'Brien EP, Kramer G, Bukau B. Profiling Ssb-Nascent Chain Interactions Reveals Principles of Hsp70-Assisted Folding. Cell. 2017 Jul 13;170(2):298-311.e20. doi: 10.1016/j.cell.2017.06.038. PubMed

Li R, Kim D, Ritchie MD. Methods to analyze big data in pharmacogenomics research. Pharmacogenomics. 2017 Jun;18(8):807-820. doi: 10.2217/pgs-2016-0152.Epub 2017 Jun 14. PubMed

Ritchey LE, Su Z, Tang Y, Tack DC, Assmann SM, Bevilacqua PC. Structure-seq2: sensitive and accurate genome-wide profiling of RNA structure in vivo. Nucleic Acids Res. 2017 Jun 16. doi: 10.1093/nar/gkx533. [Epub ahead of print] PubMed

Coble JL, Sheldon K, Yue F, Salameh T, Harris L, Deiling S, Ruggiero F, Eshelman M, Yochum GS, Koltun WA, Gerhard GS, Broach JR. Identification of a rare LAMB4 variant associated with familial diverticulitis through exome sequencing. Hum Mol Genet. 2017 Jun 8. doi: 10.1093/hmg/ddx204. [Epub ahead of print] PubMed

Shan Y, Tromp G, Kuivaniemi H, Smelser DT, Verma SS, Ritchie MD, Elmore JR, Carey DJ, Conley YP, Gorin MB, Weeks DE. Genetic risk models: Influence of model size on risk estimates and precision. Genet Epidemiol. 2017 May;41(4):282-296. doi: 10.1002/gepi.22035. Epub 2017 Feb 15. PubMed

Kim D, Volk H, Girirajan S, Pendergrass S, Hall MA, Verma SS, Schmidt RJ, Hansen RL, Ghosh D, Ludena-Rodriguez Y, Kim K, Ritchie MD, Hertz-Picciotto I, Selleck SB. The joint effect of air pollution exposure and copy number variation on risk for autism. Autism Res. 2017 Apr 27. doi: 10.1002/aur.1799. [Epub ahead of print] PubMed

Wang Q, Shashikant CS, Jensen M, Altman NS, Girirajan S. Novel metrics to measure coverage in whole exome sequencing datasets reveal local and global non-uniformity. Sci Rep. 2017 Apr 13;7(1):885. doi: 10.1038/s41598-017-01005-x. PubMed

Velasco S*, Ibrahim MM*, Kakumanu A*, Garipler G, Aydin B, Al-Sayegh MA, Hirsekorn A, Abdul-Rahman F, Satija R, Ohler U, Mahony S, Mazzoni EO. A multi-step transcriptional and chromatin state cascade underlies motor neuron programming from embryonic stem cells. Cell Stem Cell. 2017 Feb 2;20(2):205-217.e8. doi: 10.1016/j.stem.2016.11.006. PubMed

Shan Y, Tromp G, Kuivaniemi H, Smelser DT, Verma SS, Ritchie MD, Elmore JR, Carey DJ, Conley YP, Gorin MB, Weeks DE. Genetic risk models: Influence of model size on risk estimates and precision. Genet Epidemiol. 2017 Feb 15. doi:10.1002/gepi.22035. [Epub ahead of print] PubMed

Verma A, Bradford Y, Verma SS, Pendergrass SA, Daar ES, Venuto C, Morse GD, Ritchie MD, Haas DW. Multiphenotype association study of patients randomized to initiate antiretroviral regimens in AIDS Clinical Trials Group protocol A5202. Pharmacogenet Genomics. 2017 Mar;27(3):101-111. doi:10.1097/FPC.0000000000000263. PubMed

Kim D, Li R, Lucas A, Verma SS, Dudek SM, Ritchie MD. Using knowledge-driven genomic interactions for multi-omics data analysis: metadimensional models for predicting clinical outcomes in ovarian carcinoma. J Am Med Inform Assoc. 2016 Dec 31. pii: ocw165. doi: 10.1093/jamia/ocw165. [Epub ahead of print] PubMed

Jones GT, Tromp G, Kuivaniemi H, Gretarsdottir S, Baas AF, Giusti B, Strauss E, Van't Hof FN, Webb TR, Erdman R, Ritchie MD, Elmore JR, Verma A, Pendergrass S, Kullo IJ, Ye Z, Peissig PL, Gottesman O, Verma SS, Malinowski J, Rasmussen-Torvik LJ, Borthwick KM, Smelser DT, Crosslin DR, de Andrade M, Ryer EJ, McCarty CA, Böttinger EP, Pacheco JA, Crawford DC, Carrell DS, Gerhard GS, Franklin DP, Carey DJ, Phillips VL, Williams MJ, Wei W, Blair R, Hill AA, Vasudevan TM, Lewis DR, Thomson IA, Krysa J, Hill GB, Roake J, Merriman TR,Oszkinis G, Galora S, Saracini C, Abbate R, Pulli R, Pratesi C, Saratzis A, Verissimo AR, Bumpstead S, Badger SA, Clough RE, Cockerill G, Hafez H, Scott DJ, Futers TS, Romaine SP, Bridge K, Griffin KJ, Bailey MA, Smith A, Thompson MM, van Bockxmeer FM, Matthiasson SE, Thorleifsson G, Thorsteinsdottir U, Blankensteijn JD, Teijink JA, Wijmenga C, de Graaf J, Kiemeney LA, Lindholt JS, Hughes A, Bradley DT, Stirrups K, Golledge J, Norman PE, Powell JT, Humphries SE, Hamby SE, Goodall AH, Nelson CP, Sakalihasan N, Courtois A, Ferrell RE, Eriksson P,Folkersen L, Franco-Cereceda A, Eicher JD, Johnson AD, Betsholtz C, Ruusalepp A, Franzén O, Schadt EE, Björkegren JL, Lipovich L, Drolet AM, Verhoeven EL, Zeebregts CJ, Geelkerken RH, van Sambeek MR, van Sterkenburg SM, de Vries JP, Stefansson K, Thompson JR, de Bakker PI, Deloukas P, Sayers RD, Harrison SC, van Rij AM, Samani NJ, Bown MJ. Meta-analysis of genome-wide association studies for abdominal aortic aneurysm identifies four new disease-specific risk loci. Circ Res. 2017 Jan 20;120(2):341-353. doi: 10.1161/CIRCRESAHA.116.308765. PubMed

Verma SS, Lucas AM, Lavage DR, Leader JB, Metpally R, Krishnamurthy S, Dewey F, Borecki I, Lopez A, Overton J, Penn J, Reid J, Pendergrass SA, Breitwieser G, Ritchie MD. Identifying genetic associations with variability in metabolic health and blood count laboratory values: Diving into the quantitative traits by leveraging longitudinal data from an EHR. Pac Symp Biocomput. 2016;22:533-544. PubMed

De R, Verma SS, Holzinger E, Hall M, Burt A, Carrell DS, Crosslin DR, Jarvik GP, Kuivaniemi H, Kullo IJ, Lange LA, Lanktree MB, Larson EB, North KE, Reiner AP, Tragante V, Tromp G, Wilson JG, Asselbergs FW, Drenos F, Moore JH, Ritchie MD, Keating B, Gilbert-Diamond D. Identifying gene-gene interactions that are highly associated with four quantitative lipid traits across multiple cohorts. Hum Genet. 2017 Feb;136(2):165-178. doi: 10.1007/s00439-016-1738-7. PubMed

Kim D, Li R , Lucas A, Verma SS, Dudek SM, Ritchie MD. Using knowledge-driven genomic interactions for multi-omics data analysis: metadimensional models for predicting clinical outcomes in ovarian carcinoma. J Am Med Inform Assoc. 2016 Dec 31. pii: ocw165. doi: 10.1093/jamia/ocw165. [Epub ahead of print] PubMed

Verma SS, Cooke Bailey JN, Lucas A, Bradford Y, Linneman JG, Hauser MA,Pasquale LR, Peissig PL, Brilliant MH, McCarty CA, Haines JL, Wiggs JL, Vrabec TR, Tromp G, Ritchie MD; eMERGE Network; NEIGHBOR Consortium. Epistatic Gene- Based Interaction Analyses for Glaucoma in eMERGE and NEIGHBOR Consortium. PLoS Genet. 2016 Sep 13;12(9):e1006186. doi: 10.1371/journal.pgen.1006186. eCollection 2016 Sep. PubMed

Stoler N, Arbeithuber B, Guiblet W, Makova KD, Nekrutenko A. Streamlined analysis of duplex sequencing data with Du Novo. Genome Biol. 2016 Aug 26;17(1):180. doi: 10.1186/s13059-016-1039-4. PubMed

Verma A, Verma SS, Pendergrass SA, Crawford DC, Crosslin DR, Kuivaniemi H, Bush WS, Bradford Y, Kullo I, Bielinski SJ, Li R, Denny JC, Peissig P, Hebbring S, De Andrade M, Ritchie MD, Tromp G. eMERGE Phenome-Wide Association Study (PheWAS) identifies clinical associations and pleiotropy for stop-gain variants. BMC Med Genomics. 2016 Aug 12;9 Suppl 1:32. doi: 10.1186/s12920-016-0191-8. PubMed

Verma A, Basile AO, Bradford Y, Kuivaniemi H, Tromp G, Carey D, Gerhard GS, Crowe JE Jr, Ritchie MD, Pendergrass SA. Phenome-wide association study to explore relationships between immune system related genetic loci and complex traits and diseases. PLOS ONE. 2016 Aug 10;11(8):e0160573. doi: 10.1371/journal.pone.0160573. eCollection 2016. PubMed

van't Hof FN, Ruigrok YM, Lee CH, Ripke S, Anderson G, de Andrade M, Baas AF, Blankensteijn JD, Böttinger EP, Bown MJ, Broderick J, Bijlenga P, Carrell DS, Crawford DC, Crosslin DR, Ebeling C, Eriksson JG, Fornage M, Foroud T, von Und Zu Fraunberg M, Friedrich CM, Gaál EI, Gottesman O, Guo DC, Harrison SC, Hernesniemi J, Hofman A, Inoue I, Jääskeläinen JE, Jones GT, Kiemeney LA, Kivisaari R, Ko N, Koskinen S, Kubo M, Kullo IJ, Kuivaniemi H, Kurki MI, Laakso A, Lai D, Leal SM, Lehto H, LeMaire SA, Low SK, Malinowski J, McCarty CA, Milewicz DM, Mosley TH, Nakamura Y, Nakaoka H, Niemelä M, Pacheco J, Peissig PL, Pera J, Rasmussen-Torvik L, Ritchie MD, Rivadeneira F, van Rij AM, Santos-Cortez RL, Saratzis A, Slowik A, Takahashi A, Tromp G, Uitterlinden AG, Verma SS, Vermeulen SH, Wang GT; Aneurysm Consortium; Vascular Research Consortium of New Zealand, Han B, Rinkel GJ, de Bakker PI. Shared genetic risk factors of Intracranial, abdominal, and thoracic aneurysms. J Am Heart Assoc. 2016 Jul 14;5(7). pii: e002603. doi:10.1161/JAHA.115.002603. PubMed

Fungtammasan A, Tomaszkiewicz M, Campos-Sanchez R, Eckert K, DeGiorgio M, Makova KD. Reverse transcription errors and RNA-DNA differences at short tandem repeats. Mol Biol Evol. 2016 Jul 12. pii: msw139. [Epub ahead of print] PubMed

Oetjens MT, Bush WS, Denny JC, Birdwell K, Kodaman N, Verma A, Dilks HH, Pendergrass SA, Ritchie MD, Crawford DC. Evidence for extensive pleiotropy among pharmacogenes. Pharmacogenomics. 2016 Jun 1:0. [Epub ahead of print] PubMed

Aguilar-Gurrieri C, Larabi A, Vinayachandran V, Patel NA, Yen K, Reja R, Ebong IO, Schoehn G, Robinson CV, Pugh BF, Panne D. Structural evidence for Nap1-dependent H2A-H2B deposition and nucleosome assembly. EMBO J. 2016, May 25.pii: e201694105. PubMed

Agaba M, Ishengoma E, Miller WC, McGrath BC, Hudson CN, Bedoya Reina OC, Ratan A, Burhans R, Chikhi R, Medvedev P, Praul CA, Wu-Cavener L, Wood B, Robertson H, Penfold L, Cavener DR. Giraffe genome sequence reveals clues to its unique morphology and physiology. Nat Commun. 2016, May 17; 7:11519. PubMed

Li R, Dudek SM, Kim D, Hall MA, Bradford Y, Peissig PL, Brilliant MH, Linneman JG, McCarty CA, Bao L, Ritchie MD. Identification of genetic interaction networks via an evolutionary algorithm evolved Bayesian network. BioData Min. 2016 May 10; 9:18. doi: 10.1186/s13040-016-0094-4. eCollection 2016. PubMed

Iyer J, Wang Q, Le T, Pizzo L, Grönke S, Ambegaokar SS, Imai Y, Srivastava A, Troisí BL, Mardon G, Artero R, Jackson GR, Isaacs AM, Partridge L, Lu B, Kumar JP, Girirajan S. Quantitative assessment of eye phenotypes for functional genetic studies using Drosophila melanogaster. G3 (Bethesda). 2016 May 3; 6(5):1427-37. doi: 10.1534/g3.116.027060. PubMed

Kim D, Lucas A, Glessner J, Verma SS, Bradford Y, Li R, Frase AT, Hakonarson H, Peissig P, Brilliant M, Ritchie MD. Biofilter as a functional annotation pipeline for common and rare copy number burden. Pac Symp Biocomput. 2016;21:357-68. Pubmed

Tomaszkiewicz M, Rangavittal S, Cechova M, Sanchez RC, Fescemyer HW, Harris R, Ye D, O'Brien PC, Chikhi R, Ryder OA, Ferguson-Smith MA, Medvedev P, Makova KD. A time- and cost-effective strategy to sequence mammalian Y Chromosomes: An application to the de novo assembly of gorilla Y. Genome Res. 2016 Apr; 26(4):530-40. doi: 10.1101/gr.199448.115. Epub 2016 Mar 2. PubMed

Zhang Y, An L, Yue F, Hardison RC. Jointly characterizing epigenetic dynamics across multiple human cell types. Nucleic Acids Res. 2016 Apr 19. pii: gkw278. [Epub ahead of print] PubMed

Hao R, Su S, Wan Y, Shen F, Niu B, Coslo D, Albert I, Han X, Omiecinski CJ. Bioinformatic analysis of MicroRNA networks following the activation of the constitutive androstane receptor (CAR) in mouse liver. Biochim. Biophys Acta. 2016 Apr 11. pii: S1874-9399(16)30062-1. doi: 10.1016/j.bbagrm.2016.04.002. [Epub ahead of print] PubMed

Iwafuchi-Doi M, Donahue G, Kakumanu A, Watts JA, Mahony S, Pugh BF, Lee D, Kaestner KH, Zaret KS. The pioneer transcription factor FoxA maintains an accessible nucleosome configuration at enhancers for tissue-specific gene activation. Mol Cell. 2016 Apr 7;62(1):79-91. doi: 10.1016/j.molcel.2016.03.001. PubMed

Verma SS, Frase AT, Verma A, Pendergrass SA, Mahony S, Haas DW, Ritchie MD. Phenome-wide interaction study (PheWIS) in AIDS clinical trials group data (ACTG). Pac Symp Biocomput. 2016;21:57-68. PubMed PMID: 26776173. PubMed

Verma A, Leader JB, Verma SS, Frase A, Wallace J, Dudek S, Lavage DR, Van Hout CV, Dewey FE, Penn J, Lopez A, Overton JD, Carey DJ, Ledbetter DH, Kirchner HL, Ritchie MD, Pendergrass SA. Integrating clinical laboratory measures and ICD-9 code diagnoses in phenome-wide associate studies. Pac Symp Biocomput. 2016; 21:168-79. PubMed

Hughes GL, Raygoza Garay JA, Koundal V, Rasgon JL, Mwangi MM. Genome sequence of Stenotrophomonas maltophilia strain SmAs1, isolated from the Asian malaria mosquito Anopheles stephensi. Genome Announc. 2016 Mar 10;4(2). pii: e00086-16. doi: 10.1128/genomeA.00086-16. PubMed

Raygoza Garay JA, Hughes GL, Koundal V, Rasgon JL, Mwangi MM. Genome sequence of Elizabethkingia anophelis strain EaAs1, Isolated from the Asian malaria mosquito Anopheles stephensi. Genome Announc. 2016 Mar 10;4(2). pii: e00084-16. doi: 10.1128/genomeA.00084-16. PubMed

Ariyachet C, Tovaglieri A, Xiang G, Lu J, Shah MS, Richmond CA, Verbeke C, Melton DA, Stanger BZ, Mooney D, Shivdasani RA, Mahony S, Xia Q, Breault DT, Zhou Q. Reprogrammed stomach tissue as a renewable source of functional β cells for blood glucose regulation. Cell Stem Cell. 2016 Mar 3;18(3):410-21. doi:10.1016/j.stem.2016.01.003. Epub 2016 Feb 18. PubMed

Tang Y, Assmann SM, Bevilacqua PC. Protein structure is related to RNA structural reactivity in vivo. J Mol Biol. 2016 Feb 27;428(5 Pt A):758-66. doi:10.1016/j.jmb.2015.11.012. Epub 2015 Nov 17. PubMed

Nissley DA, Sharma AK, Ahmed N, Friedrich UA, Kramer G, Bukau B, O'Brien EP. Accurate prediction of cellular co-translational folding indicates proteins can switch from post- to co-translational folding. Nat Commun. 2016 Feb 18;7:10341. doi: 10.1038/ncomms10341. PubMed

Simonti CN, Vernot B, Bastarache L, Bottinger E, Carrell DS, Chisholm RL, Crosslin DR, Hebbring SJ, Jarvik GP, Kullo IJ, Li R, Pathak J, Ritchie MD, Roden DM, Verma SS, Tromp G, Prato JD, Bush WS, Akey JM, Denny JC, Capra JA. The phenotypic legacy of admixture between modern humans and Neandertals. Science. 2016 Feb 12;351(6274):737-41. doi: 10.1126/science.aad2149. PubMed

Bailey JN, Loomis SJ, Kang JH, Allingham RR, Gharahkhani P, Khor CC, Burdon KP, Aschard H, Chasman DI, Igo RP Jr, Hysi PG, Glastonbury CA, Ashley-Koch A, Brilliant M, Brown AA, Budenz DL, Buil A, Cheng CY, Choi H, Christen WG, Curhan G, De Vivo I, Fingert JH, Foster PJ, Fuchs C, Gaasterland D, Gaasterland T, Hewitt AW, Hu F, Hunter DJ, Khawaja AP, Lee RK, Li Z, Lichter PR, Mackey DA, McGuffin P, Mitchell P, Moroi SE, Perera SA, Pepper KW, Qi Q, Realini T, Richards JE, Ridker PM, Rimm E, Ritch R, Ritchie M, Schuman JS, Scott WK, Singh K, Sit AJ, Song YE, Tamimi RM, Topouzis F, Viswanathan AC, Verma SS, Vollrath D, Wang JJ, Weisschuh N, Wissinger B, Wollstein G, Wong TY, Yaspan BL, Zack DJ, Zhang K, Study EN; ANZRAG Consortium, Weinreb RN, Pericak-Vance MA, Small K, Hammond CJ, Aung T, Liu Y, Vithana EN, MacGregor S, Craig JE, Kraft P, Howell G, Hauser MA, Pasquale LR, Haines JL, Wiggs JL. Genome-wide association analysis identifies TXNRD2, ATXN2 and FOXC1 as susceptibility loci for primary open-angle glaucoma. Nat Genet. 2016 Feb;48(2):189-94. doi: 10.1038/ng.3482. Epub 2016 Jan 11. PubMed

DebRoy C, Fratamico PM, Yan X, Baranzoni G, Liu Y, Needleman DS, Tebbs R, O'Connell CD, Allred A, Swimley M, Mwangi M, Kapur V, Raygoza Garay JA, Roberts EL, Katani R. Comparison of O-antigen gene clusters of all O-Serogroups of Escherichia coli and proposal for adopting a new nomenclature for O-typing. PLOS ONE. 2016 Jan 29;11(1):e0147434. PubMed

Lyu Y, Li Q. A semi-parametric statistical model for integrating gene expression profiles across different platforms. BMC Bioinformatics. 2016 Jan 11;17 Suppl 1:5. doi: 10.1186/s12859-015-0847-y. PubMed

Park J, Zhang Y, Chen C, Dudley EG, Harvill ET. Diversity of secretion systems associated with virulence characteristics of the classical bordetellae. Microbiology. 2015 Dec;161(12):2328-40. doi: 10.1099/mic.0.000197. Epub 2015 Oct 9. PubMed

De R, Verma SS, Drenos F, Holzinger ER, Holmes MV, Hall MA, Crosslin DR, Carrell DS, Hakonarson H, Jarvik G, Larson E, Pacheco JA, Rasmussen-Torvik LJ, Moore CB, Asselbergs FW, Moore JH, Ritchie MD, Keating BJ, Gilbert-Diamond D. Identifying gene-gene interactions that are highly associated with Body Mass Index using Quantitative Multifactor Dimensionality Reduction (QMDR). BioData Min. 2015 Dec 14;8:41. doi: 10.1186/s13040-015-0074-0. eCollection 2015. PubMed

Leader JB, Pendergrass SA, Verma A, Carey DJ, Hartzel DN, Ritchie MD, Kirchner HL. Contrasting association results between existing PheWAS phenotype definition methods and five validated electronic phenotypes. AMIA Annu Symp Proc. 2015 Nov 5; 2015:824-32. eCollection 2015. PubMed

Ivanov YV, Shariat N, Register KB, Linz B, Rivera I, Hu K, Dudley EG, Harvill ET. A newly discovered Bordetella species carries a transcriptionally active CRISPR-Cas with a small Cas9 endonuclease. BMC Genomics. 2015 Oct 26;16(1):863. doi: 10.1186/s12864-015-2028-9. PubMed PMID: 26502932. PubMed

Rebolledo-Jaramillo B, Su MS, Stoler N, McElhoe JA, Dickins B, Blankenberg D, Korneliussen TS, Chiaromonte F, Nielsen R, Holland MM, Paul IM, Nekrutenko A, Makova KD. Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA. Proc Natl Acad Sci USA. 2014 Oct 28;111(43):15474-9. doi: 10.1073/pnas.1409328111. Epub 2014 Oct 13. PubMed

Han GC, Vinayachandran V, Bataille AR, Park B, Chan-Salis KY, Keller CA, Long M, Mahony S, Hardison RC, Pugh BF. Genome-wide organization of GATA1 and TAL1 determined at high resolution. Mol Cell Biol. 2015 Oct 26; 36(1):157-72. doi: 10.1128/MCB.00806-15. PubMed

Li YR, van Setten J, Verma SS, Lu Y, Holmes MV, Gao H, Lek M, Nair N, Chandrupatla H, Chang B, Karczewski KJ, Wong C, Mohebnasab M, Mukhtar E, Phillips R, Tragante V, Hou C, Steel L, Lee T, Garifallou J, Guettouche T, Cao H, Guan W, Himes A, van Houten J, Pasquier A, Yu R, Carrigan E, Miller MB, Schladt D, Akdere A, Gonzalez A, Llyod KM, McGinn D, Gangasani A, Michaud Z, Colasacco A, Snyder J, Thomas K, Wang T, Wu B, Alzahrani AJ, Al-Ali AK, Al-Muhanna FA, Al-Rubaish AM, Al-Mueilo S, Monos DS, Murphy B, Olthoff KM, Wijmenga C, Webster T, Kamoun M, Balasubramanian S, Lanktree MB, Oetting WS, Garcia-Pavia P, MacArthur DG, de Bakker PI, Hakonarson H, Birdwell KA, Jacobson PA, Ritchie MD, Asselbergs FW, Israni AK, Shaked A, Keating BJ. Concept and design of a genome-wide association genotyping array tailored for transplantation-specific studies. Genome Med. 2015 Oct 1;7:90. doi: 10.1186/s13073-015-0211-x. PubMed

Namjou B, Marsolo K, Lingren T, Ritchie MD, Verma SS, Cobb BL, Perry C, Kitchner TE, Brilliant MH, Peissig PL, Borthwick KM, Williams MS, Grafton J, Jarvik GP, Holm IA, Harley JB. A GWAS study on liver function test using eMERGE network participants. PLOS ONE. 2015 Sep 28;10(9):e0138677. doi:10.1371/journal.pone.0138677. eCollection 2015. PubMed

Reja R, Vinayachandran V, Ghosh S, Pugh BF. Molecular mechanisms of ribosomal protein gene coregulation. Genes Dev. 2015 Sep 15;29(18):1942-54. doi: 10.1101/gad.268896.115. PubMed

Pang T, Guo L, Shim D, Cannon N, Tang S, Chen J, Xia X, Yin W, Carlson JE. Characterization of the transcriptome of the xerophyte Ammopiptanthus mongolicus leaves under drought stress by 454 pyrosequencing. PLOS ONE. 2015 Aug 27;10(8):e0136495. doi: 10.1371/journal.pone.0136495. eCollection 2015. Erratum in: PLOS ONE. 2015;10(10):e0140412. PubMed

Fuller ZL, Niño EL, Patch HM, Bedoya-Reina OC, Baumgarten T, Muli E, Mumoki F,Ratan A, McGraw J, Frazier M, Masiga D, Schuster S, Grozinger CM, Miller W. Genome-wide analysis of signatures of selection in populations of African honey bees (Apis mellifera) using new web-based tools. BMC Genomics. 2015 Jul 10;16:518. doi: 10.1186/s12864-015-1712-0. PubMed

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