The Huck Institutes of the Life Sciences

Student Publications

List of BG student co-authored papers during last five years

2017

 

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  

 

 

 

 

2016

 

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. 2016Apr 11. pii: S1874-9399(16)30062-1. doi: 10.1016/j.bbagrm.2016.04.002. [Epubahead 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 ASSOCIATION 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

 

2015

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 U S A. 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

Lynch VJ, Bedoya-Reina OC, Ratan A, Sulak M, Drautz-Moses DI, Perry GH, Miller W, Schuster SC. Elephantid Genomes Reveal the Molecular Bases of Woolly Mammoth Adaptations to the Arctic. Cell Rep. 2015 Jul 14;12(2):217-28. doi:10.1016/j.celrep.2015.06.027. Epub 2015 Jul 2. PubMed

Yan C, Zhang D, Raygoza Garay JA, Mwangi MM, Bai L. Decoupling of divergent gene regulation by sequence-specific DNA binding factors. Nucleic Acids Res. 2015 Sep 3;43(15):7292-305. doi: 10.1093/nar/gkv618. Epub 2015 Jun 16. PubMed PMID: 26082499; PubMed

Kim D, Li R, Dudek SM, Ritchie MD. Predicting censored survival data based on the interactions between meta-dimensional omics data in breast cancer. J Biomed Inform. 2015 Aug;56:220-8. doi: 10.1016/j.jbi.2015.05.019. Epub 2015 Jun 3. PubMed

Kim D, Li R, Dudek SM, Wallace JR, Ritchie MD. Binning somatic mutations based on biological knowledge for predicting survival: an application in renal cell carcinoma. Pac Symp Biocomput. 2015:96-107. PubMed

Schneider M, Hellerschmied D, Schubert T, Amlacher S, Vinayachandran V, Reja R, Pugh BF, Clausen T, Köhler A. The Nuclear Pore-Associated TREX-2 Complex Employs Mediator to Regulate Gene Expression. Cell. 2015 Aug 27;162(5):1016-28. doi: 10.1016/j.cell.2015.07.059. PubMed

Pardos de la Gandara M, Raygoza Garay JA, Mwangi M, Tobin JN, Tsang A, Khalida C, D'Orazio B, Kost RG, Leinberger-Jabari A, Coffran C, Evering TH, Coller BS, Balachandra S, Urban T, Parola C, Salvato S, Jenks N, Wu D, Burgess R, Chung M, de Lencastre H, Tomasz A. Molecular Types of Methicillin-Resistant Staphylococcus aureus and Methicillin-Sensitive S. aureus Strains Causing Skin and Soft Tissue Infections and Nasal Colonization, Identified in Community Health Centers in New  York City. J Clin Microbiol. 2015 Aug;53(8):2648-58. doi: 10.1128/JCM.00591-15. Epub 2015 Jun 10. PubMed

Tang Y, Bouvier E, Kwok CK, Ding Y, Nekrutenko A, Bevilacqua PC, Assmann SM. StructureFold: genome-wide RNA secondary structure mapping and reconstruction in  vivo. Bioinformatics. 2015 Aug 15;31(16):2668-75. doi:10.1093/bioinformatics/btv213. Epub 2015 Apr 16. PubMed

Hall MA, Verma SS, Wallace J, Lucas A, Berg RL, Connolly J, Crawford DC, Crosslin DR, de Andrade M, Doheny KF, Haines JL, Harley JB, Jarvik GP, Kitchner T, Kuivaniemi H, Larson EB, Carrell DS, Tromp G, Vrabec TR, Pendergrass SA, McCarty CA, Ritchie MD. Biology-Driven Gene-Gene Interaction Analysis of Age-Related Cataract in the eMERGE Network. Genet Epidemiol. 2015 Jul;39(5):376-84. doi: 10.1002/gepi.21902. Epub 2015 May 17. PubMed

Pendergrass SA, Verma A, Okula A, Hall MA, Crawford DC, Ritchie MD. Phenome-Wide Association Studies: Embracing Complexity for Discovery. Hum Hered.  2015;79(3-4):111-23. doi: 10.1159/000381851. Epub 2015 Jul 28. Review. PubMed

Hester SE, Goodfield LL, Park J, Feaga HA, Ivanov YV, Bendor L, Taylor DL, Harvill ET. Host Specificity of Ovine Bordetella parapertussis and the Role of Complement. PLoS One. 2015 Jul 9;10(7):e0130964. doi: 10.1371/journal.pone.0130964. eCollection 2015. PubMed

Ding Y, Kwok CK, Tang Y, Bevilacqua PC, Assmann SM. Genome-wide profiling of in vivo RNA structure at single-nucleotide resolution using structure-seq. Nat Protoc. 2015 Jul;10(7):1050-66. doi: 10.1038/nprot.2015.064. Epub 2015 Jun 18. PubMed

Liu Y, Chiaromonte F, Ross H, Malhotra R, Elleder D, Poss M. Error correction  and statistical analyses for intra-host comparisons of feline immunodeficiency virus diversity from high-throughput sequencing data. BMC Bioinformatics. 2015 Jun 30;16:202. doi: 10.1186/s12859-015-0607-z. PubMed

Jain D, Mishra T, Giardine BM, Keller CA, Morrissey CS, Magargee S, Dorman CM, Long M, Weiss MJ, Hardison RC. Dynamics of GATA1 binding and expression response  in a GATA1-induced erythroid differentiation system. Genom Data. 2015 Jun 1;4:1-7. PubMed

Fungtammasan A, Ananda G, Hile SE, Su MS, Sun C, Harris R, Medvedev P, Eckert  K, Makova KD. Accurate typing of short tandem repeats from genome-wide sequencing data and its applications. Genome Res. 2015 May;25(5):736-49. doi: 10.1101/gr.185892.114. Epub 2015 Mar 30. PubMed

Wan Y, Renner DW, Albert I, Szpara ML. VirAmp: a galaxy-based viral genome assembly pipeline. Gigascience. 2015 Apr 28;4:19. doi: 10.1186/s13742-015-0060-y. eCollection 2015. PubMed

Katani R, Cote R, Raygoza Garay JA, Li L, Arthur TM, DebRoy C, Mwangi MM,Kapur V. Complete Genome Sequence of SS52, a Strain of Escherichia coli O157:H7 Recovered from Supershedder Cattle. Genome Announc. 2015 Mar 19;3(2). pii: e01569-14. doi: 10.1128/genomeA.01569-14. PubMed  

Dogan N, Wu W, Morrissey CS, Chen KB, Stonestrom A, Long M, Keller CA, Cheng Y, Jain D, Visel A, Pennacchio LA, Weiss MJ, Blobel GA, Hardison RC. Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility. Epigenetics Chromatin. 2015 Apr 23;8:16. doi: 10.1186/s13072-015-0009-5. eCollection 2015. PubMed

Shabbir MZ, Malys T, Ivanov YV, Park J, Shabbir MA, Rabbani M, Yaqub T, Harvill ET. Microbial communities present in the lower respiratory tract of clinically healthy birds in Pakistan. Poult Sci. 2015 Apr;94(4):612-20. doi:10.3382/ps/pev010. Epub 2015 Feb 9. PubMed

Kwok CK, Tang Y, Assmann SM, Bevilacqua PC. The RNA structurome: transcriptome-wide structure probing with next-generation sequencing. Trends Biochem Sci. 2015 Apr;40(4):221-32. doi: 10.1016/j.tibs.2015.02.005. Epub 2015 Mar 18. Review. 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

Hsiung CC, Morrissey CS, Udugama M, Frank CL, Keller CA, Baek S, Giardine B, Crawford GE, Sung MH, Hardison RC, Blobel GA. Genome accessibility is widely preserved and locally modulated during mitosis. Genome Res. 2015 Feb;25(2):213-25. doi: 10.1101/gr.180646.114. Epub 2014 Nov 4. PubMed

Cote R, Katani R, Moreau MR, Kudva IT, Arthur TM, DebRoy C, Mwangi MM, Albert  I, Raygoza Garay JA, Li L, Brandl MT, Carter MQ, Kapur V. Comparative analysis of super-shedder strains of Escherichia coli O157:H7 reveals distinctive genomic features and a strongly aggregative adherent phenotype on bovine rectoanal junction squamous epithelial cells. PLoS One. 2015 Feb 9;10(2):e0116743. doi: 10.1371/journal.pone.0116743. eCollection 2015. PubMed

Perez-Andreu V, Roberts KG, Xu H, Smith C, Zhang H, Yang W, Harvey RC,Payne-Turner D, Devidas M, Cheng IM, Carroll WL, Heerema NA, Carroll AJ, Raetz EA, Gastier-Foster JM, Marcucci G, Bloomfield CD, Mrózek K, Kohlschmidt J, Stock  W, Kornblau SM, Konopleva M, Paietta E, Rowe JM, Luger SM, Tallman MS, Dean M,Burchard EG, Torgerson DG, Yue F, Wang Y, Pui CH, Jeha S, Relling MV, Evans WE, Gerhard DS, Loh ML, Willman CL, Hunger SP, Mullighan CG, Yang JJ. A genome-wide association study of susceptibility to acute lymphoblastic leukemia in adolescents and young adults. Blood. 2015 Jan 22;125(4):680-6. doi: 10.1182/blood-2014-09-595744. Epub 2014 Dec 2. Pubmed

Ritchie MD, Holzinger ER, Li R, Pendergrass SA, Kim D. Methods of integrating  data to uncover genotype-phenotype interactions. Nat Rev Genet. 2015 Feb;16(2):85-97. doi: 10.1038/nrg3868. Epub 2015 Jan 13. Review. PubMed

Moore CB, Verma A, Pendergrass S, Verma SS, Johnson DH, Daar ES, Gulick RM, Haubrich R, Robbins GK, Ritchie MD, Haas DW. Phenome-wide Association Study Relating Pretreatment Laboratory Parameters With Human Genetic Variants in AIDS Clinical Trials Group Protocols. Open Forum Infect Dis. 2015 Jan 9;2(1):ofu113. doi: 10.1093/ofid/ofu113. eCollection 2015 Jan. PubMed

Pendergrass SA, Verma SS, Hall MA, Holzinger ER, Moore CB, Wallace JR, Dudek  SM, Huggins W, Kitchner T, Waudby C, Berg R, Mccarty CA, Ritchie MD. Next-generation analysis of cataracts: determining knowledge driven gene-gene interactions using biofilter, and gene-environment interactions using the Phenx Toolkit*. Pac Symp Biocomput. 2015:495-505. PubMed

 

2014

 

Pimkin M, Kossenkov AV, Mishra T, Morrissey CS, Wu W, Keller CA, Blobel GA, Lee D, Beer MA, Hardison RC, Weiss MJ. Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis. Genome Res. 2014 Dec;24(12):1932-44. doi: 10.1101/gr.164178.113. Epub 2014 Oct 15. PubMed

Kumar A, Maranas CD. CLCA: maximum common molecular substructure queries within the MetRxn database. J Chem Inf Model. 2014 Dec 22;54(12):3417-38. doi: 10.1021/ci5003922. Epub 2014 Dec 1. PubMed

Wu W, Morrissey CS, Keller CA, Mishra T, Pimkin M, Blobel GA, Weiss MJ, Hardison RC. Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis. Genome Res. 2014 Dec;24(12):1945-62. doi: 10.1101/gr.164830.113. Epub 2014 Oct 15. PubMed

Hall MA, Verma A, Brown-Gentry KD, Goodloe R, Boston J, Wilson S, McClellan B, Sutcliffe C, Dilks HH, Gillani NB, Jin H, Mayo P, Allen M, Schnetz-Boutaud N, Crawford DC, Ritchie MD, Pendergrass SA. Detection of pleiotropy through a Phenome-wide association study (PheWAS) of epidemiologic data as part of the Environmental Architecture for Genes Linked to Environment (EAGLE) study. PLoS Genet. 2014 Dec 4;10(12):e1004678. doi: 10.1371/journal.pgen.1004678. eCollection 2014 Dec. PubMed

Verma SS, de Andrade M, Tromp G, Kuivaniemi H, Pugh E, Namjou-Khales B, Mukherjee S, Jarvik GP, Kottyan LC, Burt A, Bradford Y, Armstrong GD, Derr K, Crawford DC, Haines JL, Li R, Crosslin D, Ritchie MD. Imputation and quality control steps for combining multiple genome-wide datasets. Front Genet. 2014 Dec  11;5:370. doi: 10.3389/fgene.2014.00370. eCollection 2014. PubMed

Barrie ES, Weinshenker D, Verma A, Pendergrass SA, Lange LA, Ritchie MD, Wilson JG, Kuivaniemi H, Tromp G, Carey DJ, Gerhard GS, Brilliant MH, Hebbring SJ, Cubells JF, Pinsonneault JK, Norman GJ, Sadee W. Regulatory polymorphisms in human DBH affect peripheral gene expression and sympathetic activity. Circ Res. 2014 Dec 5;115(12):1017-25. doi: 10.1161/CIRCRESAHA.116.304398. Epub 2014 Oct 17. PubMed  

Pope BD, Ryba T, Dileep V, Yue F, Wu W, Denas O, Vera DL, Wang Y, Hansen RS, Canfield TK, Thurman RE, Cheng Y, Gülsoy G, Dennis JH, Snyder MP, Stamatoyannopoulos JA, Taylor J, Hardison RC, Kahveci T, Ren B, Gilbert DM. Topologically associating domains are stable units of replication-timing regulation. Nature. 2014 Nov 20;515(7527):402-5. doi: 10.1038/nature13986. PubMed

Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, Yang X, Patacsil D, Keller CA, Giardine B; Mouse ENCODE Consortium, Kundaje A, Wang T, Pennacchio LA, Weng Z, Hardison RC, Snyder MP. Principles of regulatory information conservation between mouse and human. Nature. 2014 Nov 20;515(7527):371-5. doi: 10.1038/nature13985. PubMed [Yanli Wang]

Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis  C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R,  Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler  EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B; Mouse ENCODE Consortium. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 2014 Nov 20;515(7527):355-64. doi: 10.1038/nature13992. PubMed

Namjou B, Marsolo K, Caroll RJ, Denny JC, Ritchie MD, Verma SS, Lingren T, Porollo A, Cobb BL, Perry C, Kottyan LC, Rothenberg ME, Thompson SD, Holm IA, Kohane IS, Harley JB. Phenome-wide association study (PheWAS) in EMR-linked pediatric cohorts, genetically links PLCL1 to speech language development and IL5-IL13 to Eosinophilic Esophagitis. Front Genet. 2014 Nov 18;5:401. doi:10.3389/fgene.2014.00401. eCollection 2014. PubMed

Simons M, Saha R, Amiour N, Kumar A, Guillard L, Clément G, Miquel M, Li Z, Mouille G, Lea PJ, Hirel B, Maranas CD. Assessing the metabolic impact of nitrogen availability using a compartmentalized maize leaf genome-scale model. Plant Physiol. 2014 Nov;166(3):1659-74. doi: 10.1104/pp.114.245787. Epub 2014 Sep 23. PubMed

Ritchie MD, Verma SS, Hall MA, Goodloe RJ, Berg RL, Carrell DS, Carlson CS, Chen L, Crosslin DR, Denny JC, Jarvik G, Li R, Linneman JG, Pathak J, Peissig P,  Rasmussen LV, Ramirez AH, Wang X, Wilke RA, Wolf WA, Torstenson ES, Turner SD, McCarty CA. Electronic medical records and genomics (eMERGE) network exploration  in cataract: several new potential susceptibility loci. Mol Vis. 2014 Sep 19;20:1281-95. eCollection 2014. PubMed

Crosslin DR, Tromp G, Burt A, Kim DS, Verma SS, Lucas AM, Bradford Y, Crawford DC, Armasu SM, Heit JA, Hayes MG, Kuivaniemi H, Ritchie MD, Jarvik GP, de Andrade M; electronic Medical Records and Genomics (eMERGE) Network. Controlling for population structure and genotyping platform bias in the eMERGE multi-institutional biobank linked to electronic health records. Front Genet. 2014 Nov 4;5:352. doi: 10.3389/fgene.2014.00352. eCollection 2014. PubMed  

Kim D, Li R, Dudek SM, Frase AT, Pendergrass SA, Ritchie MD. Knowledge-driven  genomic interactions: an application in ovarian cancer. BioData Min. 2014 Sep 9;7:20. doi: 10.1186/1756-0381-7-20. eCollection 2014. PubMed

Kuruppumullage Don P, Ananda G, Chiaromonte F, Makova KD. Segmenting the human genome based on states of neutral genetic divergence. Proc Natl Acad Sci U S A. 2013 Sep 3;110(36):14699-704. doi: 10.1073/pnas.1221792110. Epub 2013 Aug 19. PubMed

Chang GS, Chen XA, Park B, Rhee HS, Li P, Han KH, Mishra T, Chan-Salis KY, Li  Y, Hardison RC, Wang Y, Pugh BF. A comprehensive and high-resolution genome-wide  response of p53 to stress. Cell Rep. 2014 Jul 24;8(2):514-27. doi: 10.1016/j.celrep.2014.06.030. Epub 2014 Jul 17. PubMed

Ananda G, Hile SE, Breski A, Wang Y, Kelkar Y, Makova KD, Eckert KA. Microsatellite interruptions stabilize primate genomes and exist as population-specific single nucleotide polymorphisms within individual human genomes. PLoS Genet. 2014 Jul 17;10(7):e1004498. doi: 10.1371/journal.pgen.1004498. eCollection 2014 Jul. PubMed PMID: 25033203; PubMed     

Kim D, Shin H, Sohn KA, Verma A, Ritchie MD, Kim JH. Incorporating inter-relationships between different levels of genomic data into cancer clinical outcome prediction. Methods. 2014 Jun 1;67(3):344-53. doi: 10.1016/j.ymeth.2014.02.003. Epub 2014 Feb 18. Pubmed

Weyrich LS, Feaga HA, Park J, Muse SJ, Safi CY, Rolin OY, Young SE, Harvill ET. Resident microbiota affect Bordetella pertussis infectious dose and host specificity. J Infect Dis. 2014 Mar;209(6):913-21. doi: 10.1093/infdis/jit597. Epub 2013 Nov 13. PubMed

Mahony S, Edwards MD, Mazzoni EO, Sherwood RI, Kakumanu A, Morrison CA, Wichterle H, Gifford DK. An integrated model of multiple-condition ChIP-Seq data  reveals predeterminants of Cdx2 binding. PLoS Comput Biol. 2014 Mar 27;10(3):e1003501. doi: 10.1371/journal.pcbi.1003501. eCollection 2014 Mar. PubMed  

Lawrence CW, Kumar S, Noid WG, Showalter SA. Role of Ordered Proteins in the Folding-Upon-Binding of Intrinsically Disordered Proteins. J Phys Chem Lett. 2014 Mar 6;5(5):833-8. doi: 10.1021/jz402729x. Epub 2014 Feb 17. PubMed

Dickins B, Rebolledo-Jaramillo B, Su MS, Paul IM, Blankenberg D, Stoler N, Makova KD, Nekrutenko A. Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach. Biotechniques. 2014 Mar 1;56(3):134-6, 138-41. doi: 10.2144/000114146. eCollection 2014. PubMed

Blankenberg D, Von Kuster G, Bouvier E, Baker D, Afgan E, Stoler N; Galaxy Team, Taylor J, Nekrutenko A. Dissemination of scientific software with Galaxy ToolShed. Genome Biol. 2014 Feb 20;15(2):403. doi: 10.1186/gb4161. PubMed

Bannantine JP, Li L, Mwangi M, Cote R, Raygoza Garay JA, Kapur V. Complete Genome Sequence of Mycobacterium avium subsp. paratuberculosis, Isolated from Human Breast Milk. Genome Announc. 2014 Feb 6;2(1). pii: e01252-13. doi: 10.1128/genomeA.01252-13. PubMed

Welch AJ, Bedoya-Reina OC, Carretero-Paulet L, Miller W, Rode KD, Lindqvist C. Polar bears exhibit genome-wide signatures of bioenergetic adaptation to life in the arctic environment. Genome Biol Evol. 2014 Feb;6(2):433-50. doi: 10.1093/gbe/evu025. PubMed

Ding Y, Tang Y, Kwok CK, Zhang Y, Bevilacqua PC, Assmann SM. In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features. Nature. 2014 Jan 30;505(7485):696-700. doi: 10.1038/nature12756. Epub 2013 Nov 24. PubMed

2013

Bedoya-Reina OC, Ratan A, Burhans R, Kim HL, Giardine B, Riemer C, Li Q, Olson TL, Loughran TP Jr, Vonholdt BM, Perry GH, Schuster SC, Miller W. Galaxy tools to study genome diversity. Gigascience. 2013 Dec 30;2(1):17. doi: 10.1186/2047-217X-2-17. PubMed

Kim D, Li R, Dudek SM, Ritchie MD. ATHENA: Identifying interactions between different levels of genomic data associated with cancer clinical outcomes using grammatical evolution neural network. BioData Min. 2013 Dec 20;6(1):23. doi: 10.1186/1756-0381-6-23. PubMed PMID: 24359638; PubMed 

Ma Z, Axtell MJ. Long-range genomic enrichment, sequencing, and assembly to determine unknown sequences flanking a known microRNA. PLoS One. 2013 Dec 20;8(12):e83721. doi: 10.1371/journal.pone.0083721. eCollection 2013. PubMed

Zheng R, Rebolledo-Jaramillo B, Zong Y, Wang L, Russo P, Hancock W, Stanger BZ, Hardison RC, Blobel GA. Function of GATA factors in the adult mouse liver. PLoS One. 2013 Dec 18;8(12):e83723. doi: 10.1371/journal.pone.0083723. eCollection 2013. PubMed

Bar-Yaacov D, Avital G, Levin L, Richards AL, Hachen N, Rebolledo Jaramillo B, Nekrutenko A, Zarivach R, Mishmar D. RNA-DNA differences in human mitochondria restore ancestral form of 16S ribosomal RNA. Genome Res. 2013 Nov;23(11):1789-96. doi: 10.1101/gr.161265.113. Epub 2013 Aug 2. PubMed

Gottesman O, Kuivaniemi H, Tromp G, Faucett WA, Li R, Manolio TA, Sanderson SC, Kannry J, Zinberg R, Basford MA, Brilliant M, Carey DJ, Chisholm RL, Chute CG, Connolly JJ, Crosslin D, Denny JC, Gallego CJ, Haines JL, Hakonarson H, Harley J, Jarvik GP, Kohane I, Kullo IJ, Larson EB, McCarty C, Ritchie MD, Roden  DM, Smith ME, Böttinger EP, Williams MS; eMERGE Network. The Electronic Medical Records and Genomics (eMERGE) Network: past, present, and future. Genet Med. 2013 Oct;15 (10):761-71. doi: 10.1038/gim.2013.72. Epub 2013 Jun 6. Review. PubMed 

Yue XP, Chang TC, DeJarnette JM, Marshall CE, Lei CZ, Liu WS. Copy number variation of PRAMEY across breeds and its association with male fertility in Holstein sires. J Dairy Sci. 2013;96(12):8024-34. doi: 10.3168/jds.2013-7037. Epub 2013 Oct 11. PubMed

Hester SE, Park J, Goodfield LL, Feaga HA, Preston A, Harvill ET. Horizontally acquired divergent O-antigen contributes to escape from cross-immunity in the classical bordetellae. BMC Evol Biol. 2013 Sep 25;13:209. doi: 10.1186/1471-2148-13-209. PubMed

Zhang Q, Yoon Y, Yu Y, Parnell EJ, Garay JA, Mwangi MM, Cross FR, Stillman DJ, Bai L. Stochastic expression and epigenetic memory at the yeast HO promoter.  Proc Natl Acad Sci U S A. 2013 Aug 20;110(34):14012-7. doi: 10.1073/pnas.1306113110. Epub 2013 Jul 8. PubMed

Girirajan S, Johnson RL, Tassone F, Balciuniene J, Katiyar N, Fox K, Baker C,  Srikanth A, Yeoh KH, Khoo SJ, Nauth TB, Hansen R, Ritchie M, Hertz-Picciotto I, Eichler EE, Pessah IN, Selleck SB. Global increases in both common and rare copy  number load associated with autism. Hum Mol Genet. 2013 Jul 15;22(14):2870-80. doi: 10.1093/hmg/ddt136. Epub 2013 Mar 27. PubMed

Chang TC, Yang Y, Retzel EF, Liu WS. Male-specific region of the bovine Y chromosome is gene rich with a high transcriptomic activity in testis development. Proc Natl Acad Sci U S A. 2013 Jul 23;110(30):12373-8. doi: 10.1073/pnas.1221104110. Epub 2013 Jul 10. Erratum in: Proc Natl Acad Sci U S A.  2014 Feb 25;111(8):3195. PubMed

Montgomery SB, Goode DL, Kvikstad E, Albers CA, Zhang ZD, Mu XJ, Ananda G, Howie B, Karczewski KJ, Smith KS, Anaya V, Richardson R, Davis J; 1000 Genomes Project Consortium, MacArthur DG, Sidow A, Duret L, Gerstein M, Makova KD, Marchini J, McVean G, Lunter G. The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes. Genome Res. 2013 May;23(5):749-61. doi: 10.1101/gr.148718.112. Epub 2013 Mar 11. PubMed

Wilson Sayres MA, Makova KD. Gene survival and death on the human Y chromosome. Mol Biol Evol. 2013 Apr;30(4):781-7. doi: 10.1093/molbev/mss267. Epub 2012 Dec 4. PubMed

Perry GH, Louis EE Jr, Ratan A, Bedoya-Reina OC, Burhans RC, Lei R, Johnson SE, Schuster SC, Miller W. Aye-aye population genomic analyses highlight an important center of endemism in northern Madagascar. Proc Natl Acad Sci U S A. 2013 Apr 9;110(15):5823-8. doi: 10.1073/pnas.1211990110. Epub 2013 Mar 25. PubMed

Mistry BV, Zhao Y, Chang TC, Yasue H, Chiba M, Oatley J, Diaz F, Liu WS. Differential expression of PRAMEL1, a cancer/testis antigen, during spermatogenesis in the mouse. PLoS One. 2013;8(4):e60611. doi: 10.1371/journal.pone.0060611. Epub 2013 Apr 2. PubMed

Kumar S, Showalter SA, Noid WG. Native-based simulations of the binding interaction between RAP74 and the disordered FCP1 peptide. J Phys Chem B. 2013 Mar 21;117(11):3074-85. doi: 10.1021/jp310293b. Epub 2013 Mar 12. PubMed

Baptiste BA, Ananda G, Strubczewski N, Lutzkanin A, Khoo SJ, Srikanth A, Kim N, Makova KD, Krasilnikova MM, Eckert KA. Mature microsatellites: mechanisms underlying dinucleotide microsatellite mutational biases in human cells. G3 (Bethesda). 2013 Mar;3(3):451-63. doi: 10.1534/g3.112.005173. Epub 2013 Mar 1. PubMed  

Ananda G, Walsh E, Jacob KD, Krasilnikova M, Eckert KA, Chiaromonte F, Makova  KD. Distinct mutational behaviors differentiate short tandem repeats from microsatellites in the human genome. Genome Biol Evol. 2013;5(3):606-20. doi: 10.1093/gbe/evs116. PubMed

Pendergrass SA, Verma SS, Holzinger ER, Moore CB, Wallace J, Dudek SM, Huggins W, Kitchner T, Waudby C, Berg R, McCarty CA, Ritchie MD. Next-generation  analysis of cataracts: determining knowledge driven gene-gene interactions using  Biofilter, and gene-environment interactions using the PhenX Toolkit. Pac Symp Biocomput. 2013:147-58. Corrected and republished in: Pac Symp Biocomput. 2015;:495-505. PubMed

 

 

2012

 

Ranganathan S, Tee TW, Chowdhury A, Zomorrodi AR, Yoon JM, Fu Y, Shanks JV,Maranas CD. An integrated computational and experimental study for overproducing  fatty acids in Escherichia coli. Metab Eng. 2012 Nov;14(6):687-704. doi: 10.1016/j.ymben.2012.08.008. Epub 2012 Oct 2. PubMed

Zomorrodi AR, Suthers PF, Ranganathan S, Maranas CD. Mathematical optimization applications in metabolic networks. Metab Eng. 2012 Nov;14(6):672-86. doi:10.1016/j.ymben.2012.09.005. Epub 2012 Sep 28. Review. PubMed  

Arif MA, Fattash I, Ma Z, Cho SH, Beike AK, Reski R, Axtell MJ, Frank W. DICER-LIKE3 activity in Physcomitrella patens DICER-LIKE4 mutants causes severe developmental dysfunction and sterility. Mol Plant. 2012 Nov;5(6):1281-94. doi: 10.1093/mp/sss036. Epub 2012 Apr 17. PubMed

Weyrich LS, Rolin OY, Muse SJ, Park J, Spidale N, Kennett MJ, Hester SE, Chen  C, Dudley EG, Harvill ET. A Type VI secretion system encoding locus is required for Bordetella bronchiseptica immunomodulation and persistence in vivo. PLoS One. 2012;7(10):e45892. doi: 10.1371/journal.pone.0045892. Epub 2012 Oct 12. PubMed

Park J, Zhang Y, Buboltz AM, Zhang X, Schuster SC, Ahuja U, Liu M, Miller JF,  Sebaihia M, Bentley SD, Parkhill J, Harvill ET. Comparative genomics of the classical Bordetella subspecies: the evolution and exchange of virulence-associated diversity amongst closely related pathogens. BMC Genomics. 2012 Oct 10;13:545. doi: 10.1186/1471-2164-13-545. PubMed

Moktali V, Park J, Fedorova-Abrams ND, Park B, Choi J, Lee YH, Kang S. Systematic and searchable classification of cytochrome P450 proteins encoded by fungal and oomycete genomes. BMC Genomics. 2012 Oct 4;13:525. doi:10.1186/1471-2164-13-525. PubMed

Miller W, Schuster SC, Welch AJ, Ratan A, Bedoya-Reina OC, Zhao F, Kim HL, Burhans RC, Drautz DI, Wittekindt NE, Tomsho LP, Ibarra-Laclette E, Herrera-Estrella L, Peacock E, Farley S, Sage GK, Rode K, Obbard M,Montiel R, Bachmann L, Ingólfsson O, Aars J, Mailund T, Wiig O, Talbot SL, Lindqvist C. Polar and brown bear genomes reveal ancient admixture and demographic footprints  of past climate change. Proc Natl Acad Sci U S A. 2012 Sep 4;109(36):E2382-90. doi: 10.1073/pnas.1210506109. Epub 2012 Jul 23. PubMed

Mouse ENCODE Consortium, Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B,  Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, Byron R, Roach V, Sabo PJ, Sandstrom R, Stehling AS, Thurman RE, Weissman SM, Cayting P, Hariharan M, Lian J, Cheng Y, Landt SG, Ma Z, Wold BJ, Dekker J, Crawford GE, Keller CA, Wu W, Morrissey C, Kumar SA, Mishra T, Jain D, Byrska-Bishop M, Blankenberg D, Lajoie BR, Jain G, Sanyal A, Chen KB, Denas O, Taylor J, Blobel GA, Weiss MJ, Pimkin M, Deng W, Marinov GK, Williams BA, Fisher-Aylor KI, Desalvo G, Kiralusha A, Trout D, Amrhein H, Mortazavi A, Edsall L, McCleary D, Kuan S, Shen Y, Yue F, Ye Z, Davis  CA, Zaleski C, Jha S, Xue C, Dobin A, Lin W, Fastuca M, Wang H, Guigo R, Djebali  S, Lagarde J, Ryba T, Sasaki T, Malladi VS, Cline MS, Kirkup VM, Learned K, Rosenbloom KR, Kent WJ, Feingold EA, Good PJ, Pazin M, Lowdon RF, Adams LB. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol. 2012 Aug 13;13(8):418. doi: 10.1186/gb-2012-13-8-418. PubMed

Ahuja U, Liu M, Tomida S, Park J, Souda P, Whitelegge J, Li H, Harvill ET, Parkhill J, Miller JF. Phenotypic and genomic analysis of hypervirulent human-associated Bordetella bronchiseptica. BMC Microbiol. 2012 Aug 6;12:167. doi: 10.1186/1471-2180-12-167. PubMed

Fungtammasan A, Walsh E, Chiaromonte F, Eckert KA, Makova KD. A genome-wide analysis of common fragile sites: what features determine chromosomal instability in the human genome? Genome Res. 2012 Jun;22(6):993-1005. doi: 10.1101/gr.134395.111. Epub 2012 Mar 28. PubMed

Chang GS, Noegel AA, Mavrich TN, Müller R, Tomsho L, Ward E, Felder M, Jiang C, Eichinger L, Glöckner G, Schuster SC, Pugh BF. Unusual combinatorial involvement of poly-A/T tracts in organizing genes and chromatin in Dictyostelium. Genome Res. 2012 Jun;22(6):1098-106. doi: 10.1101/gr.131649.111. Epub 2012 Mar 20. PubMed

O'Donnell K, Humber RA, Geiser DM, Kang S, Park B, Robert VA, Crous PW, Johnston PR, Aoki T, Rooney AP, Rehner SA. Phylogenetic diversity of insecticolous fusaria inferred from multilocus DNA sequence data and their molecular identification via FUSARIUM-ID and Fusarium MLST. Mycologia. 2012 Mar-Apr;104(2):427-45. doi: 10.3852/11-179. Epub 2011 Nov 15. PubMed 

Kumar A, Suthers PF, Maranas CD. MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases. BMC Bioinformatics. 2012 Jan 10;13:6. doi: 10.1186/1471-2105-13-6. PubMed