2016

Lackey P, Welch JD, Marzluff WM. TUT7 Catalyzes the Uridylation of the 3’ End of Histone mRNA for Rapid Degradation. RNA 2016 (in press).

Welch JD*, Williams LA*, DiSalvo M*, Brandt AT, Marayati R, Sims CE, Allbritton NL, Prins JF, Yeh JJ, Jones CD. Selective Single Cell Isolation for Genomics Using Microraft Arrays. Nucleic Acids Research 2016 (in press) *Equal contribution.

Mansouri K1, Abdelaziz A, Rybacka A, Roncaglioni A, Tropsha A, Varnek A, Zakharov A, Worth A, Richard AM, Grulke CM, Trisciuzzi D, Fourches D, Horvath D, Benfenati E, Muratov E, Wedebye EB, Grisoni F, Mangiatordi GF, Incisivo GM, Hong H, Ng HW, Tetko IV, Balabin I, Kancherla J, Shen J, Burton J, Nicklaus M, Cassotti M, Nikolov NG, Nicolotti O, Andersson PL, Zang Q, Politi R, Beger RD, Todeschini R, Huang R, Farag S, Rosenberg SA, Slavov S, Hu X, Judson RS. CERAPP: Collaborative Estrogen Receptor Activity Prediction Project. Environ Health Perspect. 2016 Jul;124(7):1023-33. doi: 10.1289/ehp.1510267. Epub 2016 Feb 23. PubMed PMID: 26908244.

Lyons SM, Cunningham CH, Welch JD, Groh B, Guo AY, Wei B, Whitfield ML, Xiong Y, Marzluff WF. A subset of replication-dependent histone mRNAs are expressed as polyadenylated RNAs in terminally differentiated tissues. Nucleic Acids Research 2016 July 8. doi: 10.1093/nar/gkw620 [PDF] PubMed PMID: 27402160.

Taylor D, Shai S, Stanley N, Mucha PJ. “Enhanced detectability of community structure in multilayer networks through layer aggregation.” Physical Review Letters 2016 Jun 3; 116, no. 22 (2016): 228301. Epub 2016 Jun 2. PubMed PMID: 27314740.

Welch JD, Hartemink AJ, Prins JF. SLICER: Inferring branched, nonlinear cellular trajectories from single cell RNA-seq data. Genome Biology 2016 May 23; 17:106 doi:10.1186/s13059-016-0975-3 [PDF] *Also accepted at RECOMB 2016 (doi: http://dx.doi.org/10.1101/047845 [PDF]) PubMed PMID: 27215581.

Welch JD, Hu Y, Prins JF. Robust Detection of Alternative Splicing in a Population of Single Cells. Nucleic Acids Research 2016 May 5; doi: 10.1093/nar/gkv1525 [PDF] Epub 2016 Jan 5. *Also accepted as a highlight at ISMB 2016. PubMed PMID: 26740580.

Stanley N, Shai S, Taylor D, Mucha PJ, “Clustering Network Layers with the Strata Multilayer Stochastic Block Model,” in IEEE Transactions on Network Science and Engineering, vol. 3, no. 2, pp. 95-105, April-June 1 2016. doi: 10.1109/TNSE.2016.2537545. 

Parry TL, Desai G, Schisler JC, Li L, Quintana MT, Stanley N, Lockyer P, Patterson C, Willis MS. “Fenofibrate unexpectedly induces cardiac hypertrophy in mice lacking MuRF1.” Cardiovascular Pathology 2016 Mar-Apr;25(2):127-40. doi: 10.1016/j.carpath.2015.09.008. Epub 2015 Oct 29. PubMed PMID: 26764147.

Kardos, J., Chai, S., Mose, L. E., Selitsky, S. R., Krishnan, B., Saito, R., … & Vincent, B. G. (2016). Claudin-low bladder tumors are immune infiltrated and actively immune suppressed. JCI Insight, 2016 Mar 17; 1(3): e85902. doi: 10.1172/jci.insight.85902.

Xu, Z., Zhang, G., Duan, Q., Chai, S., Zhang, B., Wu, C., … & Hu, M. (2016). HiView: an integrative genome browser to leverage Hi-C results for the interpretation of GWAS variants. BMC research notes, 2016 Mar 11; 9(1), 1. PubMed PMID: 26969411.

Shobair, M., Dagliyan, O., Kota, P., Dang, Y. L., He, H., Stutts, M. J., & Dokholyan, N. V. (2016). Gain-of-function mutation W493R in the epithelial sodium channel allosterically reconfigures intersubunit couplingJournal of Biological Chemistry 2016 Feb 19; 291(8), 3682-3692. Paper of the Week. DOI: 10.1074/jbc.M115.678052 PubMed PMID: 26668308.

2015

Swanson CI, Meserve JH, McCarter PC, Thieme A, Mathew T, Elston TC, Duronio RJ. “Expression of an S phase-stabilized version of the CDK inhibitor Dacapo can alter endoreplication” Development: 2015 Dec 15; doi:10.1242/dev.115006. PubMed PMID 26493402.

Nagiec MJ, McCarter PC, Kelley JB, Dixit G, Elston TC, Dohlman HG.  “Signal inhibition by a dynamically-regulated pool of mono-phosphorylated MAPK” Mol. Biol. Cell 2015 Sep 15 26, 3359–3371. PubMed PMID: 26179917.

Lebeis SL, Herrera Paredes S, Lundberg DS, Breakfield N, Gehring J, McDonald M, et al. Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Science. 2015 Aug 21;349(6250):860–4. Available from: http://www.sciencemag.org/cgi/doi/10.1126/science.aaa8764 PubMed PMID: 26184915.

Coleman KE, Grant GD, Haggerty RA, Brantley K, Shibata E, Workman BD, Dutta A, Varma D, Purvis JE, Cook JG. Sequential replication-coupled destruction at G1/S ensures genome stability. Genes & Development 2015 Aug 15; 29(16):1734-46. doi: 10.1101/gad.263731.115 PubMed PMID: 26272819.

Herrera Paredes S, Lebeis SL. Giving back to the community: microbial mechanisms of plant-soil interactions. Bailey JK, editor. Funct Ecol. 2016 Jul;30(7):1043–52. Available from: http://doi.wiley.com/10.1111/1365-2435.12684

Morgan AP, Welsh CE. Informatics resources for the Collaborative Cross and related mouse populations. Mamm Genome. 2015 Jul 2. [Epub ahead of print] No abstract available. PubMed PMID: 26135136.

Solem AC, Halvorsen M, Ramos SB, Laederach A. The potential of the riboSNitch in personalized medicine. Wiley Interdiscip Rev RNA. 2015 Jun 26. doi: 10.1002/wrna.1291. [Epub ahead of print] PubMed PMID: 26115028.

Crowley JJ, Zhabotynsky V, Sun W, Huang S, Pakatci IK, Kim Y, Wang JR, Morgan AP, Calaway JD, Aylor DL, Yun Z, Bell TA, Buus RJ, Calaway ME, Didion JP, Gooch TJ, Hansen SD, Robinson NN, Shaw GD, Spence JS, Quackenbush CR, Barrick CJ, Nonneman RJ, Kim K, Xenakis J, Xie Y, Valdar W, Lenarcic AB, Wang W, Welsh CE, Fu CP, Zhang Z, Holt J, Guo Z, Threadgill DW, Tarantino LM, Miller DR, Zou F, McMillan L, Sullivan PF, de Villena FP. Corrigendum: Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance. Nat Genet. 2015 May 27;47(6):690. doi: 10.1038/ng0615-690a. No abstract available. PubMed PMID: 26018903.

Welch JD, Slevin MK, Tatomer DC, Duronio RJ, Prins JF, Marzluff WF. EnD-Seq and AppEnD: sequencing 3′ ends to identify nontemplated tails and degradation intermediates. RNA. 2015 Jul;21(7):1375-89. doi: 10.1261/rna.048785.114. Epub 2015 May 26. PubMed PMID: 26015596.

Kutchko KM, Sanders W, Ziehr B, Phillips G, Solem A, Halvorsen M, Weeks KM, Moorman N, Laederach A. Multiple conformations are a conserved and regulatory feature of the RB1 5′ UTR. RNA. 2015 Jul;21(7):1274-85. doi: 10.1261/rna.049221.114. Epub 2015 May 21. PubMed PMID: 25999316.

Tsai YS, Dominguez D, Gomez SM, Wang Z. Transcriptome-wide identification and study of cancer-specific splicing events across multiple tumors. Oncotarget. 2015 Mar 30;6(9):6825-39. PubMed PMID: 25749525.

Xu Z, Duan Q, Yan S, Chen W, Li M, Lange E, Li Y. DISSCO: direct imputation of summary statistics allowing covariates. Bioinformatics. 2015 Mar 24. pii: btv168. [Epub ahead of print] PubMed PMID: 25810429.

Crowley JJ, Zhabotynsky V, Sun W, Huang S, Pakatci IK, Kim Y, Wang JR, Morgan AP, Calaway JD, Aylor DL, Yun Z, Bell TA, Buus RJ, Calaway ME, Didion JP, Gooch TJ, Hansen SD, Robinson NN, Shaw GD, Spence JS, Quackenbush CR, Barrick CJ, Nonneman RJ, Kim K, Xenakis J, Xie Y, Valdar W, Lenarcic AB, Wang W, Welsh CE, Fu CP, Zhang Z, Holt J, Guo Z, Threadgill DW, Tarantino LM, Miller DR, Zou F, McMillan L, Sullivan PF, Pardo-Manuel de Villena F. Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance. Nat Genet. 2015 Apr;47(4):353-60. doi: 10.1038/ng.3222. Epub 2015 Mar 2. PubMed PMID: 25730764.

Welch JD, Baran-Gale J, Perou CM, Sethupathy P, Prins JF. Pseudogenes transcribed in breast invasive carcinoma show subtype-specific expression and ceRNA potential. BMC Genomics. 2015 Feb 22;16:113. doi: 10.1186/s12864-015-1227-8. PubMed PMID: 25765044.

Didion JP, Morgan AP, Clayshulte AM, Mcmullan RC, Yadgary L, Petkov PM, Bell TA, Gatti DM, Crowley JJ, Hua K, Aylor DL, Bai L, Calaway M, Chesler EJ, French JE, Geiger TR, Gooch TJ, Garland T Jr, Harrill AH, Hunter K, McMillan L, Holt M, Miller DR, O’Brien DA, Paigen K, Pan W, Rowe LB, Shaw GD, Simecek P, Sullivan PF, Svenson KL, Weinstock GM, Threadgill DW, Pomp D, Churchill GA, Pardo-Manuel de Villena F. A multi-megabase copy number gain causes maternal transmission ratio distortion on mouse chromosome 2. PLoS Genet. 2015 Feb 13;11(2):e1004850. doi: 10.1371/journal.pgen.1004850. eCollection 2015 Feb. PubMed PMID: 25679959.

Proctor EA, Kota P, Aleksandrov AA, He L, Riordan JR, Dokholyan NV. Rational Coupled Dynamics Network Manipulation Rescues Disease-Relevant Mutant Cystic Fibrosis Transmembrane Conductance Regulator. Chem Sci. 2015 Feb;6(2):1237-1246. PubMed PMID: 25685315.

Corley M, Solem A, Qu K, Chang HY, Laederach A. Detecting riboSNitches with RNA folding algorithms: a genome-wide benchmark. Nucleic Acids Res. 2015 Jan 23. pii: gkv010. [Epub ahead of print] PubMed PMID: 25618847.

Li J, Shi J, Huang W, Sun J, Wu Y, Duan Q, Luo J, Lange LA, Gordon-Larsen P, Zheng SL, Yuan W, Wang Y, Popkin BM, Mo Z, Xu J, Du S, Mohlke KL, Lange EM. Variant Near FGF5 Has Stronger Effects on Blood Pressure in Chinese With a Higher Body Mass Index. Am J Hypertens. 2015 Jan 23. pii: hpu263. [Epub ahead of print] PubMed PMID: 25618516.

Selitsky SR, Baran-Gale J, Honda M, Yamane D, Masaki T, Fannin EE, Guerra B, Shirasaki T, Shimakami T, Kaneko S, Lanford RE, Lemon SM, Sethupathy P. Small tRNA-derived RNAs are increased and more abundant than microRNAs in chronic hepatitis B and C. Sci Rep. 2015 Jan 8;5:7675. doi: 10.1038/srep07675. PubMed PMID: 25567797.

Kelley JB, Dixit G, Sheetz JB, Venkatapurapu SP, Elston TC, Dohlman HG. RGS proteins and septins cooperate to promote chemotropism by regulating polar cap mobility. Curr Biol. 2015 Feb 2;25(3):275-85. doi: 10.1016/j.cub.2014.11.047. Epub 2015 Jan 15. PubMed PMID: 25601550.

English JG, Shellhammer JP, Malahe M, McCarter PC, Elston TC, Dohlman HG. MAPK feedback encodes a switch and timer for tunable stress adaptation in yeast. Sci Signal. 2015 Jan 13;8(359):ra5. doi: 10.1126/scisignal.2005774. PubMed PMID: 25587192.

2014

Morgan AP, Crowley JJ, Nonneman RJ, Quackenbush CR, Miller CN, Ryan AK, Bogue MA, Paredes SH, Yourstone S, Carroll IM, Kawula TH, Bower MA, Sartor RB, Sullivan PF. The antipsychotic olanzapine interacts with the gut microbiome to cause weight gain in mouse. PLoS One. 2014 Dec 15;9(12):e115225. doi: 10.1371/journal.pone.0115225. eCollection 2014. PubMed PMID: 25506936.

Blatt J, Farag S, Corey SJ, Sarrimanolis Z, Muratov E, Fourches D, Tropsha A, Janzen WP. Expanding the scope of drug repurposing in pediatrics: the Children’s Pharmacy Collaborative. Drug Discov Today. 2014 Nov;19(11):1696-8. doi: 10.1016/j.drudis.2014.08.003. Epub 2014 Aug 19. PubMed PMID: 25149597.

Hasan SS, Proctor EA, Yamashita E, Dokholyan NV, Cramer WA. Traffic within the cytochrome b6f lipoprotein complex: gating of the quinone portal. Biophys J. 2014 Oct 7;107(7):1620-8. doi: 10.1016/j.bpj.2014.08.003. PubMed PMID: 25296314.

Weiser M, Mukherjee S, Furey TS. Novel distal eQTL analysis demonstrates effect of population genetic architecture on detecting and interpreting associations. Genetics. 2014 Nov;198(3):879-93. doi: 10.1534/genetics.114.167791. Epub 2014 Sep 16. PubMed PMID: 25230953.

Baran-Gale J, Fannin EE, Kurtz CL, Sethupathy P. Beta cell 5′-shifted isomiRs are candidate regulatory hubs in type 2 diabetes. PLoS One. 2013 Sep 9;8(9):e73240. doi: 10.1371/journal.pone.0073240. eCollection 2013. PubMed PMID: 24039891.

Wang Y, Chen D, Qian H, Tsai YS, Shao S, Liu Q, Dominguez D, Wang Z. The splicing factor RBM4 controls apoptosis, proliferation, and migration to suppress tumor progression. Cancer Cell. 2014 Sep 8;26(3):374-89. doi: 10.1016/j.ccr.2014.07.010. PubMed PMID: 25203323.

Miller LA, Santhanakrishnan A, Jones S, Hamlet C, Mertens K, Zhu L. J Exp Biol. 2012 Aug 1;215(Pt 15):2716-27. doi: 10.1242/jeb.064501. Reconfiguration and the reduction of vortex-induced vibrations in broad leaves. PubMed PMID: 22786650.

Gatza ML, Silva GO, Parker JS, Fan C, Perou CM. An integrated genomics approach identifies drivers of proliferation in luminal-subtype human breast cancer. Nat Genet. 2014 Oct;46(10):1051-9. doi: 10.1038/ng.3073. Epub 2014 Aug 24. PubMed PMID: 25151356.

Yourstone SM, Lundberg DS, Dangl JL, Jones CD. MT-Toolbox: improved amplicon sequencing using molecule tags. BMC Bioinformatics. 2014 Aug 22;15:284. doi: 10.1186/1471-2105-15-284. PubMed PMID: 25149069.

Mellnik J, Vasquez PA, McKinley SA, Witten J, Hill DB, Forest MG. Micro-heterogeneity metrics for diffusion in soft matter. Soft Matter. 2014 Oct 21;10(39):7781-96. doi: 10.1039/c4sm00676c. Epub 2014 Aug 21. PubMed PMID: 25144347.

Orvis T, Hepperla A, Walter V, Song S, Simon J, Parker J, Wilkerson MD, Desai N, Major MB, Hayes DN, Davis IJ, Weissman B. BRG1/SMARCA4 inactivation promotes non-small cell lung cancer aggressiveness by altering chromatin organization. Cancer Res. 2014 Nov 15;74(22):6486-98. doi: 10.1158/0008-5472.CAN-14-0061. Epub 2014 Aug 12. PubMed PMID: 25115300.

Nedd S, Redler RL, Proctor EA, Dokholyan NV, Alexandrova AN. Cu,Zn-superoxide dismutase without Zn is folded but catalytically inactive. J Mol Biol. 2014 Dec 12;426(24):4112-24. doi: 10.1016/j.jmb.2014.07.016. Epub 2014 Jul 30. PubMed PMID: 25083917.

Zhao W, He X, Hoadley KA, Parker JS, Hayes DN, Perou CM. Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling. BMC Genomics. 2014 Jun 2;15:419. doi: 10.1186/1471-2164-15-419. PubMed PMID: 24888378.

Choudhury R, Roy SG, Tsai YS, Tripathy A, Graves LM, Wang Z. The splicing activator DAZAP1 integrates splicing control into MEK/Erk-regulated cell proliferation and migration. Nat Commun. 2014;5:3078. doi: 10.1038/ncomms4078. PubMed PMID: 24452013.

Haoqian Zhang*, Min Lin*, Handuo Shi, Longwen Huang, Xiaomeng Zhang, Shan Shen, Rencheng Gao, Shuke Wu, Chengzhe Tian, Zhenglin Yang, Guosheng Zhang, Siheng He, Hao Wang, Tiffany Saw, Yiwei Chen, Weiyue Ji, and Qi Ouyang. Programming a Pavlovian conditioning circuit in Escherichia coli. 2014;5:3102. doi: 10.1038/ncomms4102. PubMed PMID: 24434523.

Liu CT, Buchkovich ML, Winkler TW, Heid IM; African Ancestry Anthropometry Genetics Consortium; GIANT Consortium, Borecki IB, Fox CS, Mohlke KL, North KE, Adrienne Cupples L. Multi-ethnic fine-mapping of 14 central adiposity loci. Hum Mol Genet. 2014 Sep 1;23(17):4738-44. doi: 10.1093/hmg/ddu183. Epub 2014 Apr 23. PubMed PMID: 24760767.

Tsai YS, Gomez SM, Wang Z. Prevalent RNA recognition motif duplication in the human genome. RNA. 2014 May;20(5):702-12. doi: 10.1261/rna.044081.113. Epub 2014 Mar 25. PubMed PMID: 24667216.

Liu EY, Morgan AP, Chesler EJ, Wang W, Churchill GA, Pardo-Manuel de Villena F. High-resolution sex-specific linkage maps of the mouse reveal polarized distribution of crossovers in male germline. Genetics. 2014 May;197(1):91-106. doi: 10.1534/genetics.114.161653. Epub 2014 Feb 27. PubMed PMID: 24578350.

Rogala AR, Morgan AP, Christensen AM, Gooch TJ, Bell TA, Miller DR, Godfrey VL, de Villena FP. The Collaborative Cross as a resource for modeling human disease: CC011/Unc, a new mouse model for spontaneous colitis. Mamm Genome. 2014 Apr;25(3-4):95-108. doi: 10.1007/s00335-013-9499-2. Epub 2014 Feb 1. PubMed PMID: 24487921.

Mucyn TS, Yourstone S, Lind AL, Biswas S, Nishimura MT, Baltrus DA, Cumbie JS, Chang JH, Jones CD, Dangl JL, Grant SR. Variable suites of non-effector genes are co-regulated in the type III secretion virulence regulon across the Pseudomonas syringae phylogeny. PLoS Pathog. 2014 Jan;10(1):e1003807. doi: 10.1371/journal.ppat.1003807. Epub 2014 Jan 2. PubMed PMID: 24391493.

2013

Simon JM, Hacker KE, Singh D, Brannon AR, Parker JS, Weiser M, Ho TH, Kuan PF, Jonasch E, Furey TS, Prins JF, Lieb JD, Rathmell WK, Davis IJ. Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects. Genome Res. 2014 Feb;24(2):241-50. doi: 10.1101/gr.158253.113. Epub 2013 Oct 24. PubMed PMID: 24158655.

Kutchko KM, Fröhlich F. Emergence of metastable state dynamics in interconnected cortical networks with propagation delays. PLoS Comput Biol. 2013 Oct;9(10):e1003304. doi: 10.1371/journal.pcbi.1003304. Epub 2013 Oct 24. PubMed PMID: 24204238.

Spaniel C, Honda M, Selitsky SR, Yamane D, Shimakami T, Kaneko S, Lanford RE, and Lemon SM (2013). microRNA-122 Abundance in Malignant and Non-malignant Liver Tissue from Japanese Patients with Persistent HCV versus HBV Infection. Plos One 2013 Oct 9;8(10):e76867. doi: 10.1371/journal.pone.0076867. eCollection 2013. PubMed PMID: 24130799.

Jacobs TM, Kuhlman B. Using anchoring motifs for the computational design of protein-protein interactions. Biochem Soc Trans. 2013 Oct;41(5):1141-5. doi: 10.1042/BST20130108. Review. PubMed PMID: 24059499.

Cleary SP, Jeck WR, Zhao X, Kuichen, Selitsky SR, Savich GL, Tan TX, Wu MC, Getz G, Lawrence MS, Parker JS, Li J, Powers S, Kim H, Fischer S, Giundi M,Ghanekar A, Chiang DY. (2013). Identification of Driver Genes in Hepatocellular Carcinoma by Exome Sequencing. Hepatology. 2013 Nov;58(5):1693-702. doi: 10.1002/hep.26540. Epub 2013 Sep 24.PubMed PMID: 23728943

Kelly SA, Bell TA, Selitsky SR, Buus RJ, Hua K, Weinstock GM, Garland T Jr., Pardo-Manuel de Villena F, Pomp D. A novel intronic SNP in the Myosin heavy polypeptide 4 gene is responsible for the Mini-Muscle phenotype characterized by major reduction in hindlimb muscle mass in mice. Genetics. 2013 Dec;195(4):1385-95. doi: 10.1534/genetics.113.154476. Epub 2013 Sep 20. PubMed PMID: 24056412.

Wu Y, Marvelle AF, Li J, Croteau-Chonka DC, Feranil AB, Kuzawa CW, Li Y, Adair LS, Mohlke KL. Genetic association with lipids in CLHNS: waist circumference modifies an APOA5 effect on triglyceride levels. J Lipid Res. 2013 Sep 10. PubMed PMID: 24023260.

Baran-Gale J, Fannin EE, Kurtz CL, Sethupathy P. Beta cell 5′-shifted isomiRs are candidate regulatory hubs in type 2 diabetes. PLoS One. 2013 Sep 9;8(9):e73240. doi: 10.1371/journal.pone.0073240. eCollection 2013. PubMed PMID: 24039891.

Rogler LE, Kosmyna B, Moskowitz D, Bebawee R, Rahimzadeh J, Kutchko K, Laederach A, Notarangelo LD, Giliani S, Bouhassira E, Frenette P, Roy-Chowdhury J, Rogler CE. Small RNAs derived from lncRNA RNase MRP have gene-silencing activity relevant to human Cartilage Hair Hypoplasia. Hum Mol Genet. 2014 Jan 15;23(2):368-82. doi: 10.1093/hmg/ddt427. Epub 2013 Sep 5. PubMed PMID: 24009312.

Franceschini, N, Duan, Q, … Genome-wide Association Analysis of Blood-Pressure Traits in African-Ancestry Individuals Reveals Common Associated Genes in African and Non-African Populations. American Journal of Human Genetics, 2013 Sep 5;93(3):545-54. doi: 10.1016/j.ajhg.2013.07.010. Epub 2013 Aug 22. PubMed PMID: 23972371.

Duan Q, Liu EY, Auer PL, Zhang G, Lange EM, Jun G, Bizon C, Jiao S, Buyske S, Franceschini N, Carlson CS, Hsu L, Reiner AP, Peters U, Haessler J, Curtis K, Wassel CL, Robinson JG, Martin LW, Haiman CA, Le Marchand L, Matise TC, Hindorff LA, Crawford DC, Assimes TL, Kang HM, Heiss G, Jackson RD, Kooperberg C, Wilson JG, Abecasis GR, North KE, Nickerson DA, Lange LA, Li Y. Imputation of coding variants in African Americans: better performance using data from the exome sequencing project. Bioinformatics. 2013 Nov 1;29(21):2744-9. doi: 10.1093/bioinformatics/btt477. Epub 2013 Aug 16. PubMed PMID: 23956302.

Coram MA, Duan, Q., Hoffmann TJ, Thornton T, Knowles JW, Johnson NA, Ochs-Balcom HM, Donlon TA, Martin LW, Eaton CB, Li Y, et al. Genome-wide Characterization of Shared and Distinct Genetic Components that Influence Blood Lipid Levels in Ethnically Diverse Human Populations. American Journal of Human Genetics, 2013 Jun 6;92(6):904-16. doi: 10.1016/j.ajhg.2013.04.025. Epub 2013 May 30. PubMed PMID: 23726366.

Bulik-Sullivan B, Selitsky S, & Sethupathy P. Prioritization of Genetic Variants in the microRNA Regulome as Functional Candidates in Genome-Wide Association Studies. Human mutation, 2013 Aug;34(8):1049-56. doi: 10.1002/humu.22337. Epub 2013 May 8. PubMed PMID: 23595788.

Simon JM, Giresi PG, Davis IJ, Lieb JD. A Detailed Protocol for Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE). Curr Protoc Mol Biol. 2013 Apr;Chapter 21:Unit21.26. doi: 10.1002/0471142727.mb2126s102. PubMed PMID: 23547014.

Vickers KC, Sethupathy P, Baran-Gale J, Remaley AT. The Complexity of microRNA Function and the Role of IsomiRs in Lipid Homeostasis. J Lipid Res. 2013 May;54(5):1182-91. doi: 10.1194/jlr.R034801. Epub 2013 Mar 15. PubMed PMID: 23505317.

Proctor EA, Kota P, Demarest SJ, Caravella JA, Dokholyan NV. Highly covarying residues have a functional role in antibody constant domains. Proteins. 2013 May;81(5):884-95. doi: 10.1002/prot.24247. Epub 2013 Feb 27. PubMed PMID: 23280585.

Nguyen DH, Fredlund E, Zhao W, Perou CM, Balmain A, Mao JH, Barcellos-Hoff MH. Murine microenvironment metaprofiles associate with human cancer etiology and intrinsic subtypes. Clin Cancer Res. 2013 Mar 15;19(6):1353-62. doi: 10.1158/1078-0432.CCR-12-3554. Epub 2013 Jan 21. PubMed PMID: 23339125.

Fogarty MP, Panhuis TM, Vadlamudi S, Buchkovich ML, Mohlke KL. Allele-Specific Transcriptional Activity at Type 2 Diabetes-Associated Single Nucleotide Polymorphisms in Regions of Pancreatic Islet Open Chromatin at the JAZF1 Locus. Diabetes. 2013 Jan 17. [Epub ahead of print] PubMed PMID: 23328127.

Duan Q, Liu EY, Croteau-Chonka DC, Mohlke KL, Li Y. A comprehensive SNP and indel imputability database. Bioinformatics. 2013 Feb 15;29(4):528-31. doi: 10.1093/bioinformatics/bts724. Epub 2013 Jan 3. PubMed PMID: 23292738.

2012

Huyghe JR, Jackson AU, Fogarty MP, Buchkovich ML, Stančáková A, Stringham HM, Sim X, Yang L, Fuchsberger C, Cederberg H, Chines PS, Teslovich TM, Romm JM, Ling H, McMullen I, Ingersoll R, Pugh EW, Doheny KF, Neale BM, Daly MJ, Kuusisto J, Scott LJ, Kang HM, Collins FS, Abecasis GR, Watanabe RM, Boehnke M, Laakso M, Mohlke KL. Exome array analysis identifies new loci and low-frequency variants influencing insulin processing and secretion. Nat Genet. 2013 Feb;45(2):197-201. doi: 10.1038/ng.2507. Epub 2012 Dec 23. PubMed PMID: 23263489.

Chao HH, He X, Parker JS, Zhao W, Perou CM. Micro-scale genomic DNA copy number aberrations as another means of mutagenesis in breast cancer. PLoS One. 2012;7(12):e51719. doi: 10.1371/journal.pone.0051719. Epub 2012 Dec 17. PubMed PMID: 23284754; PubMed Central PMCID: PMC3524128.

Didion JP, de Villena FP. Deconstructing Mus gemischus: advances in understanding ancestry, structure, and variation in the genome of the laboratory mouse. Mamm Genome. 2013 Feb;24(1-2):1-20. doi: 10.1007/s00335-012-9441-z. Epub 2012 Dec 9. PubMed PMID: 23223940.

Proctor EA, Kota P, Demarest SJ, Caravella JA, Dokholyan NV. Metric to distinguish closely related domain families using sequence information. J Mol Biol. 2013 Feb 8;425(3):475-8. doi: 10.1016/j.jmb.2012.11.031. Epub 2012 Dec 3. PubMed PMID: 23219465.

Reiner AP, Lange EM, Jenny NS, Chaves PH, Ellis J, Li J, Walston J, Lange LA, Cushman M, Tracy RP. Soluble CD14: genomewide association analysis and relationship to cardiovascular risk and mortality in older adults. Arterioscler Thromb Vasc Biol. 2013 Jan;33(1):158-64. doi: 10.1161/ATVBAHA.112.300421. Epub 2012 Nov 15. PubMed PMID: 23162014.

Paul L. Auer*, Jill M. Johnsen*, Andrew D. Johnson*, Benjamin A. Logsdon*, Leslie A. Lange*, Michael A. Nalls, Guosheng Zhang, Nora Franceschini, Keolu Fox, Ethan M. Lange, Stephen S. Rich, Christopher J. O’Donnell, Rebecca D. Jackson, Robert B. Wallace, Zhao Chen, Timothy A. Graubert, James G. Wilson, Hua Tang*, Guillaume Lettre*, Alex P. Reiner*, Santhi K. Ganesh*, Yun Li*, on behalf of the NHLBI GO Exome Sequencing Project. Imputation of exome sequence variants into population-based samples identifies blood cell trait-associated loci in African Americans: the NLHBI GO Exome Sequencing Project. The American Journal of Human Genetics. 2012 Nov 2;91(5):794-808. doi: 10.1016/j.ajhg.2012.08.031. Epub 2012 Oct 25. PubMed PMID: 23103231.

Paredes SH, Melgar MF, Sethupathy P. Promoter-proximal CCCTC-factor binding is associated with an increase in the transcriptional pausing index. Bioinformatics. 2013 Jun 15;29(12):1485-7. doi: 10.1093/bioinformatics/bts596. Epub 2012 Oct 9. PubMed PMID: 23047559.

Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee BK, Lee K, London D, Lotakis D, Neph S, Neri F, Nguyen ED, Qu H, Reynolds AP, Roach V, Safi A, Sanchez ME, Sanyal A, Shafer A, Simon JM, Song L, Vong S, Weaver M, Yan Y, Zhang Z, Zhang Z, Lenhard B, Tewari M, Dorschner MO, Hansen RS, Navas PA, Stamatoyannopoulos G, Iyer VR, Lieb JD, Sunyaev SR, Akey JM, Sabo PJ, Kaul R, Furey TS, Dekker J, Crawford GE, Stamatoyannopoulos JA. The accessible chromatin landscape of the human genome. Nature. 2012 Sep 6;489(7414):75-82. doi: 10.1038/nature11232. PubMed PMID: 22955617.

Solberg Woods LC, Holl KL, Oreper D, Xie Y, Tsaih SW, Valdar W. Fine-mapping diabetes-related traits, including insulin resistance, in heterogeneous stock rats. Physiol Genomics. 2012 Nov 1;44(21):1013-26. doi: 10.1152/physiolgenomics.00040.2012. Epub 2012 Sep 4. PubMed PMID: 22947656; PubMed Central PMCID: PMC3524769.

Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, Tremblay J, Engelbrektson A, Kunin V, del Rio TG, Edgar RC, Eickhorst T, Ley RE, Hugenholtz P, Tringe SG, Dangl JL. Defining the core Arabidopsis thaliana root microbiome. Nature. 2012 Aug 2;488(7409):86-90. doi: 10.1038/nature11237. PubMed PMID: 22859206.

Miller LA, Santhanakrishnan A, Jones S, Hamlet C, Mertens K, Zhu L. Reconfiguration and the reduction of vortex-induced vibrations in broad leaves. J Exp Biology. 2012 Aug 1;215(Pt 15):2716-27. doi: 10.1242/jeb.064501. PubMed PMID: 22786650.

Xu K., Usary J, Kousis PC, Prat A, Wang DY, Adams JR, Wang W, Loch AJ, Deng T, Zhao W, Cardiff RD, Yoon K, Gaiano N, Ling V, Beyene J, Zacksenhaus E, Gridley T, Leong WL, Guidos CJ, Perou CM, Egan SE (2012) Lunatic Fringe Deficiency Cooperates with the Met/Caveolin Gene Amplicon to Induce Basal-like Breast Cancer, Cancer Cell 2012 May 15;21(5):626-41. doi: 10.1016/j.ccr.2012.03.041. PubMed PMID: 22624713.

Bailey, J. A., Mvalo, T., Aragam, N., Weiser, M., Congdon, S., Kamwendo, D., Martinson, F., et al. (2012). Use of massively parallel pyrosequencing to evaluate the diversity of and selection on Plasmodium falciparum csp T-cell epitopes in Lilongwe, Malawi. The Journal of infectious diseases, 2012 Aug 15;206(4):580-7. doi: 10.1093/infdis/jis329. Epub 2012 May 2. PubMed PMID: 22551816.

Duncan JS, Whittle MC, Nakamura K, Abell AN, Midland AA, Zawistowski JS, Johnson NL, Granger DA, Jordan NV, Darr DB, Usary J, Kuan PF, Smalley DM, Major B, He X, Hoadley KA, Zhou B, Sharpless NE, Perou CM, Kim WY, Gomez SM, Chen X, Jin J, Frye SV, Earp HS, Graves LM, Johnson GL. Dynamic reprogramming of the kinome in response to targeted MEK inhibition in triple-negative breast cancer. Cell. 2012 Apr 13;149(2):307-21.doi: 10. 1016/j.cell.2012.02.053. PubMed PMID: 22500798.

Choudhury R, Tsai YS, Dominguez D, Wang Y, Wang Z. Engineering RNA endonucleases with customized sequence specificities. Nature communications. 2012;3:1147. doi: 10.1038/ncomms2154.PubMed PMID: 23093184.

Midland AA, Whittle MC, Duncan JS, Abell AN, Nakamura K, Zawistowski JS, Carey LA, Earp HS 3rd, Graves LM, Gomez SM, Johnson GL. Defining the expressed breast cancer kinome. Cell Res. 2012 Apr;22(4):620-3.doi:10.1038/cr.2012.25. Epub 2012 Feb 7. PubMed PMID: 22310242.

Didion JP, Yang H, Sheppard K, Fu CP, McMillan L, de Villena FP, Churchill GA. Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias. BMC Genomics. 2012 Jan 19;13:34. doi: 10.1186/1471-2164-13-34. PubMed PMID: 22260749; PubMed Central PMCID: PMC3305361.

2011

Dagliyan, E. A. Proctor, K. M. D’Auria, F. Ding, and N. V. Dokholyan. “Structural and dynamic determinants of protein-peptide recognition,” Structure 2011 Dec 7;19(12):1837-45. doi: 10.1016/j.str.2011.09.014. [Cover article] PubMed PMID: 22153506.

Martin JS, Halvorsen M, Davis-Neulander L, Ritz J, Gopinath C, Beauregard A, Laederach A. Structural effects of linkage disequilibrium on the transcriptome. RNA. 2012 Jan;18(1):77-87. doi: 10.1261/rna.029900.111. Epub 2011 Nov 22. PubMed PMID: 22109839; PubMed Central PMCID: PMC3261746.

Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M,Terashi G,Moal IH,Li X,Bates PA, Zacharias M,Park H,Ko JS,Lee H,Seok C, Bourquard T, Bernauer J, Poupon A,Azé J, Soner S, Ovali SK, Ozbek P, Tal NB, Haliloglu T, Hwang H, Vreven T, Pierce BG, Weng Z, Pérez-Cano L,Pons C,Fernández-Recio J,Jiang F,Yang F,Gong X,Cao L,Xu X,Liu B,Wang P,Li C,Wang C,Robert CH,Guharoy M,Liu S,Huang Y,Li L,Guo D,Chen Y,Xiao Y,London N,Itzhaki Z,Schueler-Furman O,Inbar Y,Potapov V,Cohen M,Schreiber G,Tsuchiya Y,Kanamori E,Standley DM,Nakamura H,Kinoshita K,Driggers CM,Hall RG,Morgan JL,Hsu VL,Zhan J,Yang Y,Zhou Y,Kastritis PL,Bonvin AM,Zhang W,Camacho CJ,Kilambi KP,Sircar A,Gray JJ,Ohue M,Uchikoga N,Matsuzaki Y,Ishida T,Akiyama Y,Khashan R, Bush, S, Fouches D, TropshaA, Esquivel-Rodríguez J,Kihara D,Stranges PB, Jacak R, Kuhlman B, Huang SY, Zou X, Wodak SJ, Janin J, Baker D. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. J Mol Bio414.2 2011 Nov 25;414(2):289-302. doi: 10.1016/j.jmb.2011.09.031. Epub 2011 Sep 29. PubMed PMID: 22001016.

Pelleymounter LL, Moon I, Johnson JA, Laederach A, Halvorsen M, Eckloffd B, Aboa R, Rossettie S. A novel application of pattern recognition for accurate SNP and indel discovery from high-throughput data: targeted resequencing of the glucocorticoid receptor co-chaperone FKBP5 in a Caucasian population. Mol Genet Metab 2011 Dec;104(4):457-69. doi: 10.1016/j.ymgme.2011.08.019. Epub 2011 Aug 24. PubMed PMID: 21917492.

L. Redler, K. C. Wilcox, E. A. Proctor, L. Fee, M. Caplow, and N. V. Dokholyan. “Glutathionylation at Cys 111 triggers dissociation of wild type and FALS mutant SOD1 dimers,” Biochemistry 2011 Aug 16;50(32):7057-66. doi: 10.1021/bi200614y. Epub 2011 Jul 18. PubMed PMID: 21739997

Song, Z. Zhang, L.L. Grasfeder, A.P.Boyle, P.G. Giresi, B.-K. Lee, N.C. Sheffield, S. Gräf, M. Huss, D. Keefe, Z. Liu, D. London, R.M. McDaniell, Y. Shibata, K.A. Showers, J.M. Simon, T. Vales, T. Wang, D. Winter, Zhuzhu Zhang, N.D. Clarke, E. Birney, V.R. Iyer, G.E. Crawford, J.D. Lieb, T.S. Furey. (2011) Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Research 2011 Oct;21(10):1757-67. doi: 10.1101/gr.121541.111. Epub 2011 Jul 12. PubMed PMID: 21750106.

Herschkowitz JI, Zhao W, Zhang M, Usary J, Murrow G, Edwards D, Knezevic J, Greene SB, Darr D, Troester MA, Hilsenbeck SG, Medina D, Perou CM, Rosen JM. (2012) Comparative oncogenomics identifies breast tumors enriched in functional tumor-initiating cells. Proc Natl Acad Sci U S A. 2012 Feb 21;109(8):2778-83. doi: 10.1073/pnas.1018862108. Epub 2011 Jun 1. PubMed PMID: 21633010.

Rocca-Serra P, Bellaousov S, Birmingham A,Chen C, Cordero Pablo, Das R, Davis-Neulander L, Duncan C, Halvorsen M, Knight R, Leontis NB, Mathews DH, Ritz J, Stombaugh J, Weeks KM, Zirbel CL, Laederach A. Sharing and archiving nucleic acid structure mapping data. RNA 2011 Jul;17(7):1204-12. doi: 10.1261/rna.2753211. Epub 2011 May 24. PubMed PMID: 21610212.

Abell AN, Jordan NV, Huang W, Prat A, Midland AA, Johnson NL, Granger DA, Mieczkowski PA, Perou CM, Gomez SM, Li L, Johnson GL. MAP3K4/CBP-regulated H2B acetylation controls epithelial-mesenchymal transition in trophoblast stem cells. Cell Stem Cell. 2011 May 6;8(5):525-37.doi: 10.1016/j.stem.2011.03.008. PubMed PMID: 21549327.

E.A. Proctor, F. Ding, and N. V. Dokholyan. “Structural and thermodynamic effects of post-translational modifications in mutant and wild-type Cu, Zn superoxide dismutase,” Journal of Molecular Biology, 2011 May 6;408(3):555-67. doi: 10.1016/j.jmb.2011.03.004. Epub 2011 Mar 23. [Featured in F1000] PubMed PMID: 21396374.

H. Hadi-Alijanvand, M. Rouhani, E. A. Proctor, N. V. Dokholyan, and A. A. Moosavi-Mohavedi. “A folding pathway-dependent score to recognize membrane proteins,” Public Library of Science ONE, 2011 Mar 1;6(3):e16778. doi: 10.1371/journal.pone.0016778. PubMed PMID: 21390303.

Doolittle JM, Gomez SM. Mapping protein interactions between Dengue virus and its human and insect hosts. PLoS Negl Trop Dis. 2011 Feb 15;5(2):e954. doi: 10.1371/ journal.pntd.0000954. PubMed PMID: 21358811.