BCB Student Publications

[Note for student authors: please list BCB as one of your affiliations, doing so as either “Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, North Carolina 27599” or “Curriculum in Bioinformatics and Computational Biology” if part of a long list of other UNC-CH affiliations.]

2022

Reed KSM, Davis ES, Bond ML, Cabrera A, Thulson E, Quiroga IY, Cassel S, Woolery KT, Hilton I, Won H, Love MI, Phanstiel DH. Temporal analysis suggests a reciprocal relationship between 3D chromatin structure and transcription. Cell Rep 2022 Nov 41:111567 PMID: 36323252 DOI: 10.1016/j.celrep.2022.111567

Wolter JM, Le BD, Matoba N, Lafferty MJ, Aygün N, Liang D, Courtney K, Song J, Piven J, Zylka MJ, Stein JL. Cellular Genome-wide Association Study Identifies Common Genetic Variation Influencing Lithium-Induced Neural Progenitor Proliferation. Biol Psychiatry 2022 Aug PMID: 36307327 DOI: 10.1016/j.biopsych.2022.08.014

Conway JM, Walton WG, Salas-González I, Law TF, Lindberg CA, Crook LE, Kosina SM, Fitzpatrick CR, Lietzan AD, Northen TR, Jones CD, Finkel OM, Redinbo MR, Dangl JL. Diverse MarR bacterial regulators of auxin catabolism in the plant microbiome. Nat Microbiol 2022 Nov 7:1817-1833 PMID: 36266335 DOI: 10.1038/s41564-022-01244-3

Herron JC, Hu S, Liu B, Watanabe T, Hahn KM, Elston TC. Spatial models of pattern formation during phagocytosis. PLoS Comput Biol 2022 10 18:e1010092 PMID: 36190993 DOI: 10.1371/journal.pcbi.1010092

Thulson E, Davis ES, D’Costa S, Coryell PR, Kramer NE, Mohlke KL, Loeser RF, Diekman BO, Phanstiel DH. 3D Chromatin Structure in Chondrocytes Identifies Putative Osteoarthritis Risk Genes. Genetics 2022 Sep PMID: 36099032 DOI: 10.1093/genetics/iyac141

Coria A, Wienecke A, Knight ML, Desirò D, Laederach A, Borodavka A. Rotavirus RNA chaperone mediates global transcriptome-wide increase in RNA backbone flexibility. Nucleic Acids Res 2022 09 50:10078-10092 PMID: 36062555 DOI: 10.1093/nar/gkac738

Jiang Y, Harigaya Y, Zhang Z, Zhang H, Zang C, Zhang NR. Nonparametric single-cell multiomic characterization of trio relationships between transcription factors, target genes, and cis-regulatory regions. Cell Syst 2022 Sep 13:737-751.e4 PMID: 36055233 DOI: 10.1016/j.cels.2022.08.004

Liang D, Aygün N, Matoba N, Ideraabdullah FY, Love MI, Stein JL. Inference of putative cell-type specific imprinted regulatory elements and genes during human neuronal differentiation. Hum Mol Genet 2022 Aug PMID: 35994039 DOI: 10.1093/hmg/ddac207

Roden CA, Dai Y, Giannetti CA, Seim I, Lee M, Sealfon R, McLaughlin GA, Boerneke MA, Iserman C, Wey SA, Ekena JL, Troyanskaya OG, Weeks KM, You L, Chilkoti A, Gladfelter AS. Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures. Nucleic Acids Res 2022 08 50:8168-8192 PMID: 35871289 (erratum 34159327) DOI: 10.1093/nar/gkac596

Hochuli JE, Jain S, Melo-Filho C, Sessions ZL, Bobrowski T, Choe J, Zheng J, Eastman R, Talley DC, Rai G, Simeonov A, Tropsha A, Muratov EN, Baljinnyam B, Zakharov AV. Allosteric Binders of ACE2 Are Promising Anti-SARS-CoV-2 Agents. ACS Pharmacol Transl Sci 2022 Jul 5:468-478 PMID: 35821746 (erratum 35313579) DOI: 10.1021/acsptsci.2c00049

Kumar J, Lackey L, Waldern JM, Dey A, Mustoe AM, Weeks KM, Mathews DH, Laederach A. Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing. Elife 2022 06 11: PMID: 35695373 DOI: e73888

Li X, Lee L, Abnousi A, Yu M, Liu W, Huang L, Li Y, Hu M. SnapHiC2: A computationally efficient loop caller for single cell Hi-C data. Comput Struct Biotechnol J 2022 20:2778-2783 PMID: 35685374 DOI: 10.1016/j.csbj.2022.05.046

Xia Y, He X, Renshaw L, Martinez-Perez C, Kay C, Gray M, Meehan J, Parker JS, Perou CM, Carey LA, Dixon JM, Turnbull A. Integrated DNA and RNA Sequencing Reveals Drivers of Endocrine Resistance in Estrogen Receptor-Positive Breast Cancer. Clin Cancer Res 2022 08 28:3618-3629 PMID: 35653148 DOI: 10.1158/1078-0432.CCR-21-3189

Weir WH, Mucha PJ, Kim WY. A bipartite graph-based expected networks approach identifies DDR genes not associated with TMB yet predictive of immune checkpoint blockade response. Cell Rep Med 2022 05 3:100602 PMID: 35584624 DOI: 10.1016/j.xcrm.2022.100602

Qi M, Berry JC, Veley KW, O’Connor L, Finkel OM, Salas-González I, Kuhs M, Jupe J, Holcomb E, Glavina Del Rio T, Creech C, Liu P, Tringe SG, Dangl JL, Schachtman DP, Bart RS. Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons. ISME J 2022 08 16:1957-1969 PMID: 35523959 DOI: 10.1038/s41396-022-01245-4

Huang L, Rosen JD, Sun Q, Chen J, Wheeler MM, Zhou Y, Min YI, Kooperberg C, Conomos MP, Stilp AM, Rich SS, Rotter JI, Manichaikul A, Loos RJF, Kenny EE, Blackwell TW, Smith AV, Jun G, Sedlazeck FJ, Metcalf G, Boerwinkle E, Raffield LM, Reiner AP, Auer PL, Li Y. TOP-LD: A tool to explore linkage disequilibrium with TOPMed whole-genome sequence data. Am J Hum Genet 2022 06 109:1175-1181 PMID: 35504290 DOI: 10.1016/j.ajhg.2022.04.006

Talkington AM, Davis RB, Datto NC, Goodwin ER, Miller LA, Caron KM. Dermal Lymphatic Capillaries Do Not Obey Murray’s Law. Front Cardiovasc Med 2022 9:840305 PMID: 35498025 DOI: 10.3389/fcvm.2022.840305

Huang L, Yang Y, Li G, Jiang M, Wen J, Abnousi A, Rosen JD, Hu M, Li Y. A systematic evaluation of Hi-C data enhancement methods for enhancing PLAC-seq and HiChIP data. Brief Bioinform 2022 05 23: PMID: 35488276 DOI: 10.1093/bib/bbac145

Snead WT, Jalihal AP, Gerbich TM, Seim I, Hu Z, Gladfelter AS. Membrane surfaces regulate assembly of ribonucleoprotein condensates. Nat Cell Biol 2022 04 24:461-470 PMID: 35411085 (erratum 35411084) DOI: 10.1038/s41556-022-00882-3

Hoffner O’Connor M, Berglind A, Kennedy Ng MM, Keith BP, Lynch ZJ, Schaner MR, Steinbach EC, Herzog J, Trad OK, Jeck WR, Arthur JC, Simon JM, Sartor RB, Furey TS, Sheikh SZ. BET Protein Inhibition Regulates Macrophage Chromatin Accessibility and Microbiota-Dependent Colitis. Front Immunol 2022 13:856966 PMID: 35401533 DOI: 10.3389/fimmu.2022.856966

Hinton AL, Mucha PJ. A Simultaneous Feature Selection and Compositional Association Test for Detecting Sparse Associations in High-Dimensional Metagenomic Data. Front Microbiol 2022 13:837396 PMID: 35387076 DOI: 10.3389/fmicb.2022.837396

Seim I, Posey AE, Snead WT, Stormo BM, Klotsa D, Pappu RV, Gladfelter AS. Dilute phase oligomerization can oppose phase separation and modulate material properties of a ribonucleoprotein condensate. Proc Natl Acad Sci U S A 2022 03 119:e2120799119 PMID: 35333653 DOI: 10.1073/pnas.2120799119

Hochuli JE, Jain S, Melo-Filho C, Sessions ZL, Bobrowski T, Choe J, Zheng J, Eastman R, Talley DC, Rai G, Simeonov A, Tropsha A, Muratov EN, Baljinnyam B, Zakharov AV. Allosteric binders of ACE2 are promising anti-SARS-CoV-2 agents. bioRxiv 2022 Mar PMID: 35313579 (erratum 35821746) DOI: 10.1101/2022.03.15.484484

Liu W, Sun Q, Huang L, Bhattacharya A, Wang GW, Tan X, Kuban KCK, Joseph RM, O’Shea TM, Fry RC, Li Y, Santos HP. Innovative computational approaches shed light on genetic mechanisms underlying cognitive impairment among children born extremely preterm. J Neurodev Disord 2022 03 14:16 PMID: 35240980 DOI: 10.1186/s11689-022-09429-x

Burclaff J, Bliton RJ, Breau KA, Ok MT, Gomez-Martinez I, Ranek JS, Bhatt AP, Purvis JE, Woosley JT, Magness ST. A Proximal-to-Distal Survey of Healthy Adult Human Small Intestine and Colon Epithelium by Single-Cell Transcriptomics. Cell Mol Gastroenterol Hepatol 2022 13:1554-1589 PMID: 35176508 DOI: 10.1016/j.jcmgh.2022.02.007

Kramer NE, Davis ES, Wenger CD, Deoudes EM, Parker SM, Love MI, Phanstiel DH. Plotgardener: Cultivating precise multi-panel figures in R. Bioinformatics 2022 Feb PMID: 35134826 DOI: 10.1093/bioinformatics/btac057

Sun Q, Liu W, Rosen JD, Huang L, Pace RG, Dang H, Gallins PJ, Blue EE, Ling H, Corvol H, Strug LJ, Bamshad MJ, Gibson RL, Pugh EW, Blackman SM, Cutting GR, O’Neal WK, Zhou YH, Wright FA, Knowles MR, Wen J, Li Y. Leveraging TOPMed imputation server and constructing a cohort-specific imputation reference panel to enhance genotype imputation among cystic fibrosis patients. HGG Adv 2022 Apr 3:100090 PMID: 35128485 DOI: 10.1016/j.xhgg.2022.100090

Wen J, Lagler TM, Sun Q, Yang Y, Chen J, Harigaya Y, Sankaran VG, Hu M, Reiner AP, Raffield LM, Li Y. Super interactive promoters provide insight into cell type-specific regulatory networks in blood lineage cell types. PLoS Genet 2022 01 18:e1009984 PMID: 35100265 DOI: 10.1371/journal.pgen.1009984

Talkington AM, McSweeney MD, Wessler T, Rath MK, Li Z, Zhang T, Yuan H, Frank JE, Forest MG, Cao Y, Lai SK. A PBPK model recapitulates early kinetics of anti-PEG antibody-mediated clearance of PEG-liposomes. J Control Release 2022 03 343:518-527 PMID: 35066099 DOI: 10.1016/j.jconrel.2022.01.022

Sun Q, Crowley CA, Huang L, Wen J, Chen J, Bao EL, Auer PL, Lettre G, Reiner AP, Sankaran VG, Raffield LM, Li Y. From GWAS variant to function: A study of ∼148,000 variants for blood cell traits. HGG Adv 2022 Jan 3:100063 PMID: 35047852 DOI: 10.1016/j.xhgg.2021.100063

Palmer AC, Izar B, Hwangbo H, Sorger PK. Predictable Clinical Benefits without Evidence of Synergy in Trials of Combination Therapies with Immune-Checkpoint Inhibitors. Clin Cancer Res 2022 01 28:368-377 PMID: 35045958 DOI: 10.1158/1078-0432.CCR-21-2275

Shepherd JH, Ballman K, Polley MC, Campbell JD, Fan C, Selitsky S, Fernandez-Martinez A, Parker JS, Hoadley KA, Hu Z, Li Y, Soloway MG, Spears PA, Singh B, Tolaney SM, Somlo G, Port ER, Ma C, Kuzma C, Mamounas E, Golshan M, Bellon JR, Collyar D, Hahn OM, Hudis CA, Winer EP, Partridge A, Hyslop T, Carey LA, Perou CM, Sikov WM. CALGB 40603 (Alliance): Long-Term Outcomes and Genomic Correlates of Response and Survival After Neoadjuvant Chemotherapy With or Without Carboplatin and Bevacizumab in Triple-Negative Breast Cancer. J Clin Oncol 2022 04 40:1323-1334 PMID: 35044810 DOI: 10.1200/JCO.21.01506

Brotman SM, Raulerson CK, Vadlamudi S, Currin KW, Shen Q, Parsons VA, Iyengar AK, Roman TS, Furey TS, Kuusisto J, Collins FS, Boehnke M, Laakso M, Pajukanta P, Mohlke KL. Subcutaneous adipose tissue splice quantitative trait loci reveal differences in isoform usage associated with cardiometabolic traits. Am J Hum Genet 2022 01 109:66-80 PMID: 34995504 DOI: 10.1016/j.ajhg.2021.11.019

Prat A, Guarneri V, Pascual T, Brasó-Maristany F, Sanfeliu E, Paré L, Schettini F, Martínez D, Jares P, Griguolo G, Dieci MV, Cortés J, Llombart-Cussac A, Conte B, Marín-Aguilera M, Chic N, Puig-Butillé JA, Martínez A, Galván P, Tsai YH, González-Farré B, Mira A, Vivancos A, Villagrasa P, Parker JS, Conte P, Perou CM. Development and validation of the new HER2DX assay for predicting pathological response and survival outcome in early-stage HER2-positive breast cancer. EBioMedicine 2022 Jan 75:103801 PMID: 34990895 DOI: 10.1016/j.ebiom.2021.103801

Wienecke A, Laederach A. A novel algorithm for ranking RNA structure candidates. Biophys J 2022 01 121:7-10 PMID: 34896370 (erratum 34798137) DOI: 10.1016/j.bpj.2021.12.004

Tovar A, Crouse WL, Smith GJ, Thomas JM, Keith BP, McFadden KM, Moran TP, Furey TS, Kelada SNP. Integrative analysis reveals mouse strain-dependent responses to acute ozone exposure associated with airway macrophage transcriptional activity. Am J Physiol Lung Cell Mol Physiol 2022 01 322:L33-L49 PMID: 34755540 DOI: 10.1152/ajplung.00237.2021

Waldern JM, Kumar J, Laederach A. Disease-associated human genetic variation through the lens of precursor and mature RNA structure. Hum Genet 2022 Oct 141:1659-1672 PMID: 34741198 DOI: 10.1007/s00439-021-02395-9

2021

Le KH, Adolf-Bryfogle J, Klima JC, Lyskov S, Labonte J, Bertolani S, Burman SSR, Leaver-Fay A, Weitzner B, Maguire J, Rangan R, Adrianowycz MA, Alford RF, Adal A, Nance ML, Wu Y, Willis J, Kulp DW, Das R, Dunbrack RL, Schief W, Kuhlman B, Siegel JB, Gray JJ. PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design. Biophysicist (Rockv) 2021 Apr 2:108-122 PMID: 35128343 DOI: 10.35459/tbp.2019.000147

Christy TW, Giannetti CA, Laederach A, Weeks KM. Identifying proximal RNA interactions from cDNA-encoded crosslinks with ShapeJumper. PLoS Comput Biol 2021 12 17:e1009632 PMID: 34905538 DOI: 10.1371/journal.pcbi.1009632

Koehler Leman J, Lyskov S, Lewis SM, Adolf-Bryfogle J, Alford RF, Barlow K, Ben-Aharon Z, Farrell D, Fell J, Hansen WA, Harmalkar A, Jeliazkov J, Kuenze G, Krys JD, Ljubetič A, Loshbaugh AL, Maguire J, Moretti R, Mulligan VK, Nance ML, Nguyen PT, Ó Conchúir S, Roy Burman SS, Samanta R, Smith ST, Teets F, Tiemann JKS, Watkins A, Woods H, Yachnin BJ, Bahl CD, Bailey-Kellogg C, Baker D, Das R, DiMaio F, Khare SD, Kortemme T, Labonte JW, Lindorff-Larsen K, Meiler J, Schief W, Schueler-Furman O, Siegel JB, Stein A, Yarov-Yarovoy V, Kuhlman B, Leaver-Fay A, Gront D, Gray JJ, Bonneau R. Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks. Nat Commun 2021 11 12:6947 PMID: 34845212 DOI: 10.1038/s41467-021-27222-7

Marcel SS, Quimby AL, Noel MP, Jaimes OC, Mehrab-Mohseni M, Ashur SA, Velasco B, Tsuruta JK, Kasoji SK, Santos CM, Dayton PA, Parker JS, Davis IJ, Pattenden SG. Genome-wide cancer-specific chromatin accessibility patterns derived from archival processed xenograft tumors. Genome Res 2021 Nov PMID: 34815311 DOI: 10.1101/gr.275219.121

Talkington AM, Wessler T, Lai SK, Cao Y, Forest MG. Experimental Data and PBPK Modeling Quantify Antibody Interference in PEGylated Drug Carrier Delivery. Bull Math Biol 2021 11 83:123 PMID: 34751832 DOI: 10.1007/s11538-021-00950-z

Regner MJ, Wisniewska K, Garcia-Recio S, Thennavan A, Mendez-Giraldez R, Malladi VS, Hawkins G, Parker JS, Perou CM, Bae-Jump VL, Franco HL. A multi-omic single-cell landscape of human gynecologic malignancies. Mol Cell 2021 12 81:4924-4941.e10 PMID: 34739872 DOI: 10.1016/j.molcel.2021.10.013

Perrin HJ, Currin KW, Vadlamudi S, Pandey GK, Ng KK, Wabitsch M, Laakso M, Love MI, Mohlke KL. Chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci. PLoS Genet 2021 10 17:e1009865 PMID: 34699533 DOI: 10.1371/journal.pgen.1009865

Kudlacek ST, Metz S, Thiono D, Payne AM, Phan TTN, Tian S, Forsberg LJ, Maguire J, Seim I, Zhang S, Tripathy A, Harrison J, Nicely NI, Soman S, McCracken MK, Gromowski GD, Jarman RG, Premkumar L, de Silva AM, Kuhlman B. Designed, highly expressing, thermostable dengue virus 2 envelope protein dimers elicit quaternary epitope antibodies. Sci Adv 2021 Oct 7:eabg4084 PMID: 34652943 DOI: 10.1126/sciadv.abg4084

Talkington AM, McSweeney MD, Zhang T, Li Z, Nyborg AC, LaMoreaux B, Livingston EW, Frank JE, Yuan H, Lai SK. High MW polyethylene glycol prolongs circulation of pegloticase in mice with anti-PEG antibodies. J Control Release 2021 10 338:804-812 PMID: 34481925 DOI: 10.1016/j.jconrel.2021.08.051

Mosedale M, Cai Y, Eaddy JS, Kirby PJ, Wolenski FS, Dragan Y, Valdar W. Human-relevant mechanisms and risk factors for TAK-875-Induced liver injury identified via a gene pathway-based approach in Collaborative Cross mice. Toxicology 2021 09 461:152902 PMID: 34418498 DOI: 10.1016/j.tox.2021.152902

Aygün N, Elwell AL, Liang D, Lafferty MJ, Cheek KE, Courtney KP, Mory J, Hadden-Ford E, Krupa O, de la Torre-Ubieta L, Geschwind DH, Love MI, Stein JL. Brain-trait-associated variants impact cell-type-specific gene regulation during neurogenesis. Am J Hum Genet 2021 09 108:1647-1668 PMID: 34416157 DOI: 10.1016/j.ajhg.2021.07.011

Liu S, Thennavan A, Garay JP, Marron JS, Perou CM. MultiK: an automated tool to determine optimal cluster numbers in single-cell RNA sequencing data. Genome Biol 2021 08 22:232 PMID: 34412669 DOI: 10.1186/s13059-021-02445-5

Seim I, Roden CA, Gladfelter AS. Role of spatial patterning of N-protein interactions in SARS-CoV-2 genome packaging. Biophys J 2021 07 120:2771-2784 PMID: 34214535 (erratum 33442696) DOI: 10.1016/j.bpj.2021.06.018

Toyonaga T, Araba KC, Kennedy MM, Keith BP, Wolber EA, Beasley C, Steinbach EC, Schaner MR, Jain A, Long MD, Barnes EL, Herfarth HH, Isaacs KL, Hansen JJ, Kapadia MR, Guillem JG, Gulati AS, Sethupathy P, Furey TS, Ehre C, Sheikh SZ. Increased colonic expression of ACE2 associates with poor prognosis in Crohn’s disease. Sci Rep 2021 06 11:13533 PMID: 34188154 (erratum 33269348) DOI: 10.1038/s41598-021-92979-2

Ahn JH, Davis ES, Daugird TA, Zhao S, Quiroga IY, Uryu H, Li J, Storey AJ, Tsai YH, Keeley DP, Mackintosh SG, Edmondson RD, Byrum SD, Cai L, Tackett AJ, Zheng D, Legant WR, Phanstiel DH, Wang GG. Phase separation drives aberrant chromatin looping and cancer development. Nature 2021 07 595:591-595 PMID: 34163069 (erratum 34244676) DOI: 10.1038/s41586-021-03662-5

Christy TW, Giannetti CA, Houlihan G, Smola MJ, Rice GM, Wang J, Dokholyan NV, Laederach A, Holliger P, Weeks KM. Direct Mapping of Higher-Order RNA Interactions by SHAPE-JuMP. Biochemistry 2021 06 60:1971-1982 PMID: 34121404 DOI: 10.1021/acs.biochem.1c00270

Suzuki SK, Kelley JB, Elston TC, Dohlman HG. Gradient Tracking by Yeast GPCRs in a Microfluidics Chamber. Methods Mol Biol 2021 2268:275-287 PMID: 34085275 DOI: 10.1007/978-1-0716-1221-7_18

Chen J, Spracklen CN, Marenne G, Varshney A, Corbin LJ, Luan J, Willems SM, Wu Y, Zhang X, Horikoshi M, Boutin TS, Mägi R, Waage J, Li-Gao R, Chan KHK, Yao J, Anasanti MD, Chu AY, Claringbould A, Heikkinen J, Hong J, Hottenga JJ, Huo S, Kaakinen MA, Louie T, März W, Moreno-Macias H, Ndungu A, Nelson SC, Nolte IM, North KE, Raulerson CK, Ray D, Rohde R, Rybin D, Schurmann C, Sim X, Southam L, Stewart ID, Wang CA, Wang Y, Wu P, Zhang W, Ahluwalia TS, Appel EVR, Bielak LF, Brody JA, Burtt NP, Cabrera CP, Cade BE, Chai JF, Chai X, Chang LC, Chen CH, Chen BH, Chitrala KN, Chiu YF, de Haan HG, Delgado GE, Demirkan A, Duan Q, Engmann J, Fatumo SA, Gayán J, Giulianini F, Gong JH, Gustafsson S, Hai Y, Hartwig FP, He J, Heianza Y, Huang T, Huerta-Chagoya A, Hwang MY, Jensen RA, Kawaguchi T, Kentistou KA, Kim YJ, Kleber ME, Kooner IK, Lai S, Lange LA, Langefeld CD, Lauzon M, Li M, Ligthart S, Liu J, Loh M, Long J, Lyssenko V, Mangino M, Marzi C, Montasser ME, Nag A, Nakatochi M, Noce D, Noordam R, Pistis G, Preuss M, Raffield L, Rasmussen-Torvik LJ, Rich SS, Robertson NR, Rueedi R, Ryan K, Sanna S, Saxena R, Schraut KE, Sennblad B, Setoh K, Smith AV, Sparsø T, Strawbridge RJ, Takeuchi F, Tan J, Trompet S, van den Akker E, van der Most PJ, Verweij N, Vogel M, Wang H, Wang C, Wang N, Warren HR, Wen W, Wilsgaard T, Wong A, Wood AR, Xie T, Zafarmand MH, Zhao JH, Zhao W, Amin N, Arzumanyan Z, Astrup A, Bakker SJL, Baldassarre D, Beekman M, Bergman RN, Bertoni A, Blüher M, Bonnycastle LL, Bornstein SR, Bowden DW, Cai Q, Campbell A, Campbell H, Chang YC, de Geus EJC, Dehghan A, Du S, Eiriksdottir G, Farmaki AE, Frånberg M, Fuchsberger C, Gao Y, Gjesing AP, Goel A, Han S, Hartman CA, Herder C, Hicks AA, Hsieh CH, Hsueh WA, Ichihara S, Igase M, Ikram MA, Johnson WC, Jørgensen ME, Joshi PK, Kalyani RR, Kandeel FR, Katsuya T, Khor CC, Kiess W, Kolcic I, Kuulasmaa T, Kuusisto J, Läll K, Lam K, Lawlor DA, Lee NR, Lemaitre RN, Li H, Lin SY, Lindström J, Linneberg A, Liu J, Lorenzo C, Matsubara T, Matsuda F, Mingrone G, Mooijaart S, Moon S, Nabika T, Nadkarni GN, Nadler JL, Nelis M, Neville MJ, Norris JM, Ohyagi Y, Peters A, Peyser PA, Polasek O, Qi Q, Raven D, Reilly DF, Reiner A, Rivideneira F, Roll K, Rudan I, Sabanayagam C, Sandow K, Sattar N, Schürmann A, Shi J, Stringham HM, Taylor KD, Teslovich TM, Thuesen B, Timmers PRHJ, Tremoli E, Tsai MY, Uitterlinden A, van Dam RM, van Heemst D, van Hylckama Vlieg A, van Vliet-Ostaptchouk JV, Vangipurapu J, Vestergaard H, Wang T, Willems van Dijk K, Zemunik T, Abecasis GR, Adair LS, Aguilar-Salinas CA, Alarcón-Riquelme ME, An P, Aviles-Santa L, Becker DM, Beilin LJ, Bergmann S, Bisgaard H, Black C, Boehnke M, Boerwinkle E, Böhm BO, Bønnelykke K, Boomsma DI, Bottinger EP, Buchanan TA, Canouil M, Caulfield MJ, Chambers JC, Chasman DI, Chen YI, Cheng CY, Collins FS, Correa A, Cucca F, de Silva HJ, Dedoussis G, Elmståhl S, Evans MK, Ferrannini E, Ferrucci L, Florez JC, Franks PW, Frayling TM, Froguel P, Gigante B, Goodarzi MO, Gordon-Larsen P, Grallert H, Grarup N, Grimsgaard S, Groop L, Gudnason V, Guo X, Hamsten A, Hansen T, Hayward C, Heckbert SR, Horta BL, Huang W, Ingelsson E, James PS, Jarvelin MR, Jonas JB, Jukema JW, Kaleebu P, Kaplan R, Kardia SLR, Kato N, Keinanen-Kiukaanniemi SM, Kim BJ, Kivimaki M, Koistinen HA, Kooner JS, Körner A, Kovacs P, Kuh D, Kumari M, Kutalik Z, Laakso M, Lakka TA, Launer LJ, Leander K, Li H, Lin X, Lind L, Lindgren C, Liu S, Loos RJF, Magnusson PKE, Mahajan A, Metspalu A, Mook-Kanamori DO, Mori TA, Munroe PB, Njølstad I, O’Connell JR, Oldehinkel AJ, Ong KK, Padmanabhan S, Palmer CNA, Palmer ND, Pedersen O, Pennell CE, Porteous DJ, Pramstaller PP, Province MA, Psaty BM, Qi L, Raffel LJ, Rauramaa R, Redline S, Ridker PM, Rosendaal FR, Saaristo TE, Sandhu M, Saramies J, Schneiderman N, Schwarz P, Scott LJ, Selvin E, Sever P, Shu XO, Slagboom PE, Small KS, Smith BH, Snieder H, Sofer T, Sørensen TIA, Spector TD, Stanton A, Steves CJ, Stumvoll M, Sun L, Tabara Y, Tai ES, Timpson NJ, Tönjes A, Tuomilehto J, Tusie T, Uusitupa M, van der Harst P, van Duijn C, Vitart V, Vollenweider P, Vrijkotte TGM, Wagenknecht LE, Walker M, Wang YX, Wareham NJ, Watanabe RM, Watkins H, Wei WB, Wickremasinghe AR, Willemsen G, Wilson JF, Wong TY, Wu JY, Xiang AH, Yanek LR, Yengo L, Yokota M, Zeggini E, Zheng W, Zonderman AB, Rotter JI, Gloyn AL, McCarthy MI, Dupuis J, Meigs JB, Scott RA, Prokopenko I, Leong A, Liu CT, Parker SCJ, Mohlke KL, Langenberg C, Wheeler E, Morris AP, Barroso I, de Haan HG, van den Akker E, van der Most PJ, de Geus EJC, van Dam RM, van Heemst D, van Hylckama Vlieg A, van Willems van Dijk K, de Silva HJ, van der Harst P, van Duijn C. The trans-ancestral genomic architecture of glycemic traits. Nat Genet 2021 06 53:840-860 PMID: 34059833 DOI: 10.1038/s41588-021-00852-9

Currin KW, Erdos MR, Narisu N, Rai V, Vadlamudi S, Perrin HJ, Idol JR, Yan T, Albanus RD, Broadaway KA, Etheridge AS, Bonnycastle LL, Orchard P, Didion JP, Chaudhry AS, Innocenti F, Schuetz EG, Scott LJ, Parker SCJ, Collins FS, Mohlke KL, Barnabas BB, Black S, Bouffard GG, Brooks SY, Coleman H, Dekhtyar L, Han J, Ho SL, Kim J, Legaspi R, Maduro QL, Masiello CA, McDowell JC, Montemayor C, Mullikin JC, Park M, Riebow NL, Schandler K, Schmidt B, Sison C, Stantripop S, Thomas JW, Thomas PJ, Vemulapalli M, Young AC. Genetic effects on liver chromatin accessibility identify disease regulatory variants. Am J Hum Genet 2021 07 108:1169-1189 PMID: 34038741 DOI: 10.1016/j.ajhg.2021.05.001

Liang D, Elwell AL, Aygün N, Krupa O, Wolter JM, Kyere FA, Lafferty MJ, Cheek KE, Courtney KP, Yusupova M, Garrett ME, Ashley-Koch A, Crawford GE, Love MI, de la Torre-Ubieta L, Geschwind DH, Stein JL. Cell-type-specific effects of genetic variation on chromatin accessibility during human neuronal differentiation. Nat Neurosci 2021 07 24:941-953 PMID: 34017130 DOI: 10.1038/s41593-021-00858-w

Angus SP, Stuhlmiller TJ, Mehta G, Bevill SM, Goulet DR, Olivares-Quintero JF, East MP, Tanioka M, Zawistowski JS, Singh D, Sciaky N, Chen X, He X, Rashid NU, Chollet-Hinton L, Fan C, Soloway MG, Spears PA, Jefferys S, Parker JS, Gallagher KK, Forero-Torres A, Krop IE, Thompson AM, Murthy R, Gatza ML, Perou CM, Earp HS, Carey LA, Johnson GL. FOXA1 and adaptive response determinants to HER2 targeted therapy in TBCRC 036. NPJ Breast Cancer 2021 May 7:51 PMID: 33980863 DOI: 10.1038/s41523-021-00258-0

Yi H, Huang L, Mishne G, Chi EC. COBRAC: a fast implementation of convex biclustering with compression. Bioinformatics 2021 Apr PMID: 33904580 DOI: 10.1093/bioinformatics/btab248

Morton LM, Karyadi DM, Stewart C, Bogdanova TI, Dawson ET, Steinberg MK, Dai J, Hartley SW, Schonfeld SJ, Sampson JN, Maruvka YE, Kapoor V, Ramsden DA, Carvajal-Garcia J, Perou CM, Parker JS, Krznaric M, Yeager M, Boland JF, Hutchinson A, Hicks BD, Dagnall CL, Gastier-Foster JM, Bowen J, Lee O, Machiela MJ, Cahoon EK, Brenner AV, Mabuchi K, Drozdovitch V, Masiuk S, Chepurny M, Zurnadzhy LY, Hatch M, Berrington de Gonzalez A, Thomas GA, Tronko MD, Getz G, Chanock SJ. Radiation-related genomic profile of papillary thyroid carcinoma after the Chernobyl accident. Science 2021 05 372: PMID: 33888599 DOI: 10.1126/science.abg2538

Teixeira PJPL, Colaianni NR, Law TF, Conway JM, Gilbert S, Li H, Salas-González I, Panda D, Del Risco NM, Finkel OM, Castrillo G, Mieczkowski P, Jones CD, Dangl JL. Specific modulation of the root immune system by a community of commensal bacteria. Proc Natl Acad Sci U S A 2021 04 118: PMID: 33879573 DOI: 10.1073/pnas.2100678118

Reyt G, Ramakrishna P, Salas-González I, Fujita S, Love A, Tiemessen D, Lapierre C, Morreel K, Calvo-Polanco M, Flis P, Geldner N, Boursiac Y, Boerjan W, George MW, Castrillo G, Salt DE. Two chemically distinct root lignin barriers control solute and water balance. Nat Commun 2021 04 12:2320 PMID: 33875659 DOI: 10.1038/s41467-021-22550-0

Colaianni NR, Parys K, Lee HS, Conway JM, Kim NH, Edelbacher N, Mucyn TS, Madalinski M, Law TF, Jones CD, Belkhadir Y, Dangl JL. A complex immune response to flagellin epitope variation in commensal communities. Cell Host Microbe 2021 04 29:635-649.e9 PMID: 33713602 (erratum 33713601) DOI: 10.1016/j.chom.2021.02.006

Parys K, Colaianni NR, Lee HS, Hohmann U, Edelbacher N, Trgovcevic A, Blahovska Z, Lee D, Mechtler A, Muhari-Portik Z, Madalinski M, Schandry N, Rodríguez-Arévalo I, Becker C, Sonnleitner E, Korte A, Bläsi U, Geldner N, Hothorn M, Jones CD, Dangl JL, Belkhadir Y. Signatures of antagonistic pleiotropy in a bacterial flagellin epitope. Cell Host Microbe 2021 04 29:620-634.e9 PMID: 33713601 (erratum 33713602) DOI: 10.1016/j.chom.2021.02.008

Sun KY, Oreper D, Schoenrock SA, McMullan R, Giusti-Rodríguez P, Zhabotynsky V, Miller DR, Tarantino LM, Pardo-Manuel de Villena F, Valdar W. Bayesian modeling of skewed X inactivation in genetically diverse mice identifies a novel Xce allele associated with copy number changes. Genetics 2021 05 218: PMID: 33693696 DOI: 10.1093/genetics/iyab034

Pomeroy AE, Peña MI, Houser JR, Dixit G, Dohlman HG, Elston TC, Errede B. A predictive model of gene expression reveals the role of network motifs in the mating response of yeast. Sci Signal 2021 02 14: PMID: 33593998 DOI: 10.1126/scisignal.abb5235

Haggerty RA, Purvis JE. Inferring the structures of signaling motifs from paired dynamic traces of single cells. PLoS Comput Biol 2021 02 17:e1008657 PMID: 33539338 DOI: 10.1371/journal.pcbi.1008657

Seim I, Roden CA, Gladfelter AS. Role of spatial patterning of N-protein interactions in SARS-CoV-2 genome packaging. bioRxiv 2021 Apr PMID: 33442696 (erratum 34214535) DOI: 10.1101/2021.01.06.425605

Kirk JM, Sprague D, Calabrese JM. Classification of Long Noncoding RNAs by k-mer Content. Methods Mol Biol 2021 2254:41-60 PMID: 33326069 DOI: 10.1007/978-1-0716-1158-6_4

Tilot AK, Khramtsova EA, Liang D, Grasby KL, Jahanshad N, Painter J, Colodro-Conde L, Bralten J, Hibar DP, Lind PA, Liu S, Brotman SM, Thompson PM, Medland SE, Macciardi F, Stranger BE, Davis LK, Fisher SE, Stein JL. The Evolutionary History of Common Genetic Variants Influencing Human Cortical Surface Area. Cereb Cortex 2021 03 31:1873-1887 PMID: 33290510 DOI: 10.1093/cercor/bhaa327

Maguire JB, Haddox HK, Strickland D, Halabiya SF, Coventry B, Griffin JR, Pulavarti SVSRK, Cummins M, Thieker DF, Klavins E, Szyperski T, DiMaio F, Baker D, Kuhlman B. Perturbing the energy landscape for improved packing during computational protein design. Proteins 2021 04 89:436-449 PMID: 33249652 DOI: 10.1002/prot.26030

Salas-González I, Reyt G, Flis P, Custódio V, Gopaulchan D, Bakhoum N, Dew TP, Suresh K, Franke RB, Dangl JL, Salt DE, Castrillo G. Coordination between microbiota and root endodermis supports plant mineral nutrient homeostasis. Science 2021 01 371: PMID: 33214288 (erratum 33414209) DOI: 10.1126/science.abd0695

2020

Smeekens JM, Johnson-Weaver BT, Hinton AL, Azcarate-Peril MA, Moran TP, Immormino RM, Kesselring JR, Steinbach EC, Orgel KA, Staats HF, Burks AW, Mucha PJ, Ferris MT, Kulis MD. Fecal IgA, Antigen Absorption, and Gut Microbiome Composition Are Associated With Food Antigen Sensitization in Genetically Susceptible Mice. Front Immunol 2020 11:599637 PMID: 33542716 DOI: 10.3389/fimmu.2020.599637

Kumar RJ, Chao HX, Simpson DA, Feng W, Cho MG, Roberts VR, Sullivan AR, Shah SJ, Wozny AS, Fagan-Solis K, Kumar S, Luthman A, Ramsden DA, Purvis JE, Gupta GP. Dual inhibition of DNA-PK and DNA polymerase theta overcomes radiation resistance induced by p53 deficiency. NAR Cancer 2020 Dec 2:zcaa038 PMID: 33385162 DOI: 10.1093/narcan/zcaa038

Prat A, Guarneri V, Paré L, Griguolo G, Pascual T, Dieci MV, Chic N, González-Farré B, Frassoldati A, Sanfeliu E, Cejalvo JM, Muñoz M, Bisagni G, Brasó-Maristany F, Urso L, Vidal M, Brandes AA, Adamo B, Musolino A, Miglietta F, Conte B, Oliveira M, Saura C, Pernas S, Alarcón J, Llombart-Cussac A, Cortés J, Manso L, López R, Ciruelos E, Schettini F, Villagrasa P, Carey LA, Perou CM, Piacentini F, D’Amico R, Tagliafico E, Parker JS, Conte P. A multivariable prognostic score to guide systemic therapy in early-stage HER2-positive breast cancer: a retrospective study with an external evaluation. Lancet Oncol 2020 11 21:1455-1464 PMID: 33152285 (erratum 33152281) DOI: 10.1016/S1470-2045(20)30450-2

Mitros T, Session AM, James BT, Wu GA, Belaffif MB, Clark LV, Shu S, Dong H, Barling A, Holmes JR, Mattick JE, Bredeson JV, Liu S, Farrar K, Głowacka K, Jeżowski S, Barry K, Chae WB, Juvik JA, Gifford J, Oladeinde A, Yamada T, Grimwood J, Putnam NH, De Vega J, Barth S, Klaas M, Hodkinson T, Li L, Jin X, Peng J, Yu CY, Heo K, Yoo JH, Ghimire BK, Donnison IS, Schmutz J, Hudson ME, Sacks EJ, Moose SP, Swaminathan K, Rokhsar DS. Genome biology of the paleotetraploid perennial biomass crop Miscanthus. Nat Commun 2020 10 11:5442 PMID: 33116128 DOI: 10.1038/s41467-020-18923-6

Fernandez-Martinez A, Krop IE, Hillman DW, Polley MY, Parker JS, Huebner L, Hoadley KA, Shepherd J, Tolaney S, Henry NL, Dang C, Harris L, Berry D, Hahn O, Hudis C, Winer E, Partridge A, Perou CM, Carey LA. Survival, Pathologic Response, and Genomics in CALGB 40601 (Alliance), a Neoadjuvant Phase III Trial of Paclitaxel-Trastuzumab With or Without Lapatinib in HER2-Positive Breast Cancer. J Clin Oncol 2020 12 38:4184-4193 PMID: 33095682 DOI: 10.1200/JCO.20.01276

Crouse WL, Kelada SNP, Valdar W. Inferring the Allelic Series at QTL in Multiparental Populations. Genetics 2020 12 216:957-983 PMID: 33082282 DOI: 10.1534/genetics.120.303393

Finkel OM, Salas-González I, Castrillo G, Conway JM, Law TF, Teixeira PJPL, Wilson ED, Fitzpatrick CR, Jones CD, Dangl JL. A single bacterial genus maintains root growth in a complex microbiome. Nature 2020 11 587:103-108 PMID: 32999461 DOI: 10.1038/s41586-020-2778-7

Spracklen CN, Iyengar AK, Vadlamudi S, Raulerson CK, Jackson AU, Brotman SM, Wu Y, Cannon ME, Davis JP, Crain AT, Currin KW, Perrin HJ, Narisu N, Stringham HM, Fuchsberger C, Locke AE, Welch RP, Kuusisto JK, Pajukanta P, Scott LJ, Li Y, Collins FS, Boehnke M, Laakso M, Mohlke KL. Adiponectin GWAS loci harboring extensive allelic heterogeneity exhibit distinct molecular consequences. PLoS Genet 2020 09 16:e1009019 PMID: 32915782 DOI: 10.1371/journal.pgen.1009019

Reyt G, Chao Z, Flis P, Salas-González I, Castrillo G, Chao DY, Salt DE. Uclacyanin Proteins Are Required for Lignified Nanodomain Formation within Casparian Strips. Curr Biol 2020 10 30:4103-4111.e6 PMID: 32857976 (erratum 33080201) DOI: 10.1016/j.cub.2020.07.095

Ramirez-Villacis DX, Finkel OM, Salas-González I, Fitzpatrick CR, Dangl JL, Jones CD, Leon-Reyes A. Root Microbiome Modulates Plant Growth Promotion Induced by Low Doses of Glyphosate. mSphere 2020 08 5: PMID: 32817451 DOI: 10.1128/mSphere.00484-20

Matoba N, Liang D, Sun H, Aygün N, McAfee JC, Davis JE, Raffield LM, Qian H, Piven J, Li Y, Kosuri S, Won H, Stein JL. Common genetic risk variants identified in the SPARK cohort support DDHD2 as a candidate risk gene for autism. Transl Psychiatry 2020 08 10:265 PMID: 32747698 DOI: 10.1038/s41398-020-00953-9

Crosby EJ, Acharya CR, Haddad AF, Rabiola CA, Lei G, Wei JP, Yang XY, Wang T, Liu CX, Wagner KU, Muller WJ, Chodosh LA, Broadwater G, Hyslop T, Shepherd JH, Hollern DP, He X, Perou CM, Chai S, Ashby BK, Vincent BG, Snyder JC, Force J, Morse MA, Lyerly HK, Hartman ZC. Stimulation of Oncogene-Specific Tumor-Infiltrating T Cells through Combined Vaccine and αPD-1 Enable Sustained Antitumor Responses against Established HER2 Breast Cancer. Clin Cancer Res 2020 09 26:4670-4681 PMID: 32732224 DOI: 10.1158/1078-0432.CCR-20-0389

Lundberg A, Lindström LS, Parker JS, Löverli E, Perou CM, Bergh J, Tobin NP. A pan-cancer analysis of the frequency of DNA alterations across cell cycle activity levels. Oncogene 2020 08 39:5430-5440 PMID: 32581248 DOI: 10.1038/s41388-020-1367-4

Garcia-Recio S, Thennavan A, East MP, Parker JS, Cejalvo JM, Garay JP, Hollern DP, He X, Mott KR, Galván P, Fan C, Selitsky SR, Coffey AR, Marron D, Brasó-Maristany F, Burgués O, Albanell J, Rojo F, Lluch A, de Dueñas EM, Rosen JM, Johnson GL, Carey LA, Prat A, Perou CM. FGFR4 regulates tumor subtype differentiation in luminal breast cancer and metastatic disease. J Clin Invest 2020 09 130:4871-4887 PMID: 32573490 DOI: 130323

Toyonaga T, Steinbach EC, Keith BP, Barrow JB, Schaner MR, Wolber EA, Beasley C, Huling J, Wang Y, Allbritton NL, Chaumont N, Sadiq TS, Koruda MJ, Jain A, Long MD, Barnes EL, Herfarth HH, Isaacs KL, Hansen JJ, Shanahan MT, Rahbar R, Furey TS, Sethupathy P, Sheikh SZ. Decreased Colonic Activin Receptor-Like Kinase 1 Disrupts Epithelial Barrier Integrity in Patients With Crohn’s Disease. Cell Mol Gastroenterol Hepatol 2020 10:779-796 PMID: 32561494 DOI: 10.1016/j.jcmgh.2020.06.005

Fitzpatrick CR, Salas-González I, Conway JM, Finkel OM, Gilbert S, Russ D, Teixeira PJPL, Dangl JL. The Plant Microbiome: From Ecology to Reductionism and Beyond. Annu Rev Microbiol 2020 09 74:81-100 PMID: 32530732 DOI: 10.1146/annurev-micro-022620-014327

Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, Bradley P, Bystroff C, Conway P, Cooper S, Correia BE, Coventry B, Das R, De Jong RM, DiMaio F, Dsilva L, Dunbrack R, Ford AS, Frenz B, Fu DY, Geniesse C, Goldschmidt L, Gowthaman R, Gray JJ, Gront D, Guffy S, Horowitz S, Huang PS, Huber T, Jacobs TM, Jeliazkov JR, Johnson DK, Kappel K, Karanicolas J, Khakzad H, Khar KR, Khare SD, Khatib F, Khramushin A, King IC, Kleffner R, Koepnick B, Kortemme T, Kuenze G, Kuhlman B, Kuroda D, Labonte JW, Lai JK, Lapidoth G, Leaver-Fay A, Lindert S, Linsky T, London N, Lubin JH, Lyskov S, Maguire J, Malmström L, Marcos E, Marcu O, Marze NA, Meiler J, Moretti R, Mulligan VK, Nerli S, Norn C, Ó’Conchúir S, Ollikainen N, Ovchinnikov S, Pacella MS, Pan X, Park H, Pavlovicz RE, Pethe M, Pierce BG, Pilla KB, Raveh B, Renfrew PD, Burman SSR, Rubenstein A, Sauer MF, Scheck A, Schief W, Schueler-Furman O, Sedan Y, Sevy AM, Sgourakis NG, Shi L, Siegel JB, Silva DA, Smith S, Song Y, Stein A, Szegedy M, Teets FD, Thyme SB, Wang RY, Watkins A, Zimmerman L, Bonneau R. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nat Methods 2020 07 17:665-680 PMID: 32483333 DOI: 10.1038/s41592-020-0848-2

Shahir NM, Wang JR, Wolber EA, Schaner MS, Frank DN, Ir D, Robertson CE, Chaumont N, Sadiq TS, Koruda MJ, Rahbar R, Nix BD, Newberry RD, Sartor RB, Sheikh SZ, Furey TS. Crohn’s Disease Differentially Affects Region-Specific Composition and Aerotolerance Profiles of Mucosally Adherent Bacteria. Inflamm Bowel Dis 2020 11 26:1843-1855 PMID: 32469069 DOI: 10.1093/ibd/izaa103

Froning K, Maguire J, Sereno A, Huang F, Chang S, Weichert K, Frommelt AJ, Dong J, Wu X, Austin H, Conner EM, Fitchett JR, Heng AR, Balasubramaniam D, Hilgers MT, Kuhlman B, Demarest SJ. Computational stabilization of T cell receptors allows pairing with antibodies to form bispecifics. Nat Commun 2020 05 11:2330 PMID: 32393818 DOI: 10.1038/s41467-020-16231-7

Morgan AP, Brazeau NF, Ngasala B, Mhamilawa LE, Denton M, Msellem M, Morris U, Filer DL, Aydemir O, Bailey JA, Parr JB, Mårtensson A, Bjorkman A, Juliano JJ. Falciparum malaria from coastal Tanzania and Zanzibar remains highly connected despite effective control efforts on the archipelago. Malar J 2020 Jan 19:47 PMID: 31992305 DOI: 10.1186/s12936-020-3137-8

Selitsky SR, Marron D, Hollern D, Mose LE, Hoadley KA, Jones C, Parker JS, Dittmer DP, Perou CM. Virus expression detection reveals RNA-sequencing contamination in TCGA. BMC Genomics 2020 Jan 21:79 PMID: 31992194 DOI: 10.1186/s12864-020-6483-6

Keele GR, Quach BC, Israel JW, Chappell GA, Lewis L, Safi A, Simon JM, Cotney P, Crawford GE, Valdar W, Rusyn I, Furey TS. Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation. PLoS Genet 2020 01 16:e1008537 PMID: 31961859 DOI: 10.1371/journal.pgen.1008537

Tovar A, Smith GJ, Thomas JM, Crouse WL, Harkema JR, Kelada SNP. Transcriptional Profiling of the Murine Airway Response to Acute Ozone Exposure. Toxicol Sci 2020 01 173:114-130 PMID: 31626304 DOI: 10.1093/toxsci/kfz219

2019

Patwardhan MN, Wenger CD, Davis ES, Phanstiel DH. Bedtoolsr: An R package for genomic data analysis and manipulation. J Open Source Softw 2019 4: PMID: 31903447 DOI: 10.21105/joss.01742

Min A, Deoudes E, Bond ML, Davis ES, Phanstiel DH. CoralP: Flexible visualization of the human phosphatome. J Open Source Softw 2019 4: PMID: 31903446 DOI: 10.21105/joss.01837

Xia Y, Fan C, Hoadley KA, Parker JS, Perou CM. Genetic determinants of the molecular portraits of epithelial cancers. Nat Commun 2019 12 10:5666 PMID: 31827079 DOI: 10.1038/s41467-019-13588-2

Hollern DP, Xu N, Thennavan A, Glodowski C, Garcia-Recio S, Mott KR, He X, Garay JP, Carey-Ewend K, Marron D, Ford J, Liu S, Vick SC, Martin M, Parker JS, Vincent BG, Serody JS, Perou CM. B Cells and T Follicular Helper Cells Mediate Response to Checkpoint Inhibitors in High Mutation Burden Mouse Models of Breast Cancer. Cell 2019 11 179:1191-1206.e21 PMID: 31730857 DOI: 10.1016/j.cell.2019.10.028

Finkel OM, Salas-González I, Castrillo G, Spaepen S, Law TF, Teixeira PJPL, Jones CD, Dangl JL. The effects of soil phosphorus content on plant microbiota are driven by the plant phosphate starvation response. PLoS Biol 2019 11 17:e3000534 PMID: 31721759 DOI: 10.1371/journal.pbio.3000534

Wu Y, Broadaway KA, Raulerson CK, Scott LJ, Pan C, Ko A, He A, Tilford C, Fuchsberger C, Locke AE, Stringham HM, Jackson AU, Narisu N, Kuusisto J, Pajukanta P, Collins FS, Boehnke M, Laakso M, Lusis AJ, Civelek M, Mohlke KL. Colocalization of GWAS and eQTL signals at loci with multiple signals identifies additional candidate genes for body fat distribution. Hum Mol Genet 2019 12 28:4161-4172 PMID: 31691812 DOI: 10.1093/hmg/ddz263

Raulerson CK, Ko A, Kidd JC, Currin KW, Brotman SM, Cannon ME, Wu Y, Spracklen CN, Jackson AU, Stringham HM, Welch RP, Fuchsberger C, Locke AE, Narisu N, Lusis AJ, Civelek M, Furey TS, Kuusisto J, Collins FS, Boehnke M, Scott LJ, Lin DY, Love MI, Laakso M, Pajukanta P, Mohlke KL. Adipose Tissue Gene Expression Associations Reveal Hundreds of Candidate Genes for Cardiometabolic Traits. Am J Hum Genet 2019 10 105:773-787 PMID: 31564431 DOI: 10.1016/j.ajhg.2019.09.001

Teixeira PJP, Colaianni NR, Fitzpatrick CR, Dangl JL. Beyond pathogens: microbiota interactions with the plant immune system. Curr Opin Microbiol 2019 06 49:7-17 PMID: 31563068 DOI: 10.1016/j.mib.2019.08.003

Smith CC, Chai S, Washington AR, Lee SJ, Landoni E, Field K, Garness J, Bixby LM, Selitsky SR, Parker JS, Savoldo B, Serody JS, Vincent BG. Machine-Learning Prediction of Tumor Antigen Immunogenicity in the Selection of Therapeutic Epitopes. Cancer Immunol Res 2019 10 7:1591-1604 PMID: 31515258 DOI: 10.1158/2326-6066.CIR-19-0155

Mosedale M, Cai Y, Eaddy JS, Corty RW, Nautiyal M, Watkins PB, Valdar W. Identification of Candidate Risk Factor Genes for Human Idelalisib Toxicity Using a Collaborative Cross Approach. Toxicol Sci 2019 12 172:265-278 PMID: 31501888 DOI: 10.1093/toxsci/kfz199

Spracklen CN, Karaderi T, Yaghootkar H, Schurmann C, Fine RS, Kutalik Z, Preuss MH, Lu Y, Wittemans LBL, Adair LS, Allison M, Amin N, Auer PL, Bartz TM, Blüher M, Boehnke M, Borja JB, Bork-Jensen J, Broer L, Chasman DI, Chen YI, Chirstofidou P, Demirkan A, van Duijn CM, Feitosa MF, Garcia ME, Graff M, Grallert H, Grarup N, Guo X, Haesser J, Hansen T, Harris TB, Highland HM, Hong J, Ikram MA, Ingelsson E, Jackson R, Jousilahti P, Kähönen M, Kizer JR, Kovacs P, Kriebel J, Laakso M, Lange LA, Lehtimäki T, Li J, Li-Gao R, Lind L, Luan J, Lyytikäinen LP, MacGregor S, Mackey DA, Mahajan A, Mangino M, Männistö S, McCarthy MI, McKnight B, Medina-Gomez C, Meigs JB, Molnos S, Mook-Kanamori D, Morris AP, de Mutsert R, Nalls MA, Nedeljkovic I, North KE, Pennell CE, Pradhan AD, Province MA, Raitakari OT, Raulerson CK, Reiner AP, Ridker PM, Ripatti S, Roberston N, Rotter JI, Salomaa V, Sandoval-Zárate AA, Sitlani CM, Spector TD, Strauch K, Stumvoll M, Taylor KD, Thuesen B, Tönjes A, Uitterlinden AG, Venturini C, Walker M, Wang CA, Wang S, Wareham NJ, Willems SM, Willems van Dijk K, Wilson JG, Wu Y, Yao J, Young KL, Langenberg C, Frayling TM, Kilpeläinen TO, Lindgren CM, Loos RJF, Mohlke KL. Exome-Derived Adiponectin-Associated Variants Implicate Obesity and Lipid Biology. Am J Hum Genet 2019 Sep 105:670-671 PMID: 31491410 (erratum 31178129) DOI: 10.1016/j.ajhg.2019.08.001

Robinson JI, Weir WH, Crowley JR, Hink T, Reske KA, Kwon JH, Burnham CD, Dubberke ER, Mucha PJ, Henderson JP. Metabolomic networks connect host-microbiome processes to human Clostridioides difficile infections. J Clin Invest 2019 08 129:3792-3806 PMID: 31403473 (erratum 31403467) DOI: 126905

Rangarajan N, Gordy CL, Askew L, Bevill SM, Elston TC, Errede B, Hurst JH, Kelley JB, Sheetz JB, Suzuki SK, Valentin NH, Young E, Dohlman HG. Systematic analysis of F-box proteins reveals a new branch of the yeast mating pathway. J Biol Chem 2019 10 294:14717-14731 PMID: 31399514 DOI: 10.1074/jbc.RA119.010063

Smith CC, Selitsky SR, Chai S, Armistead PM, Vincent BG, Serody JS. Alternative tumour-specific antigens. Nat Rev Cancer 2019 08 19:465-478 PMID: 31278396 DOI: 10.1038/s41568-019-0162-4

Maurizio PL, Fuseini H, Tegha G, Hosseinipour M, De Paris K. Signatures of divergent anti-malarial treatment responses in peripheral blood from adults and young children in Malawi. Malar J 2019 Jun 18:205 PMID: 31234875 DOI: 10.1186/s12936-019-2842-7

Cannon ME, Currin KW, Young KL, Perrin HJ, Vadlamudi S, Safi A, Song L, Wu Y, Wabitsch M, Laakso M, Crawford GE, Mohlke KL. Open Chromatin Profiling in Adipose Tissue Marks Genomic Regions with Functional Roles in Cardiometabolic Traits. G3 (Bethesda) 2019 08 9:2521-2533 PMID: 31186305 DOI: 10.1534/g3.119.400294

Spracklen CN, Karaderi T, Yaghootkar H, Schurmann C, Fine RS, Kutalik Z, Preuss MH, Lu Y, Wittemans LBL, Adair LS, Allison M, Amin N, Auer PL, Bartz TM, Blüher M, Boehnke M, Borja JB, Bork-Jensen J, Broer L, Chasman DI, Chen YI, Chirstofidou P, Demirkan A, van Duijn CM, Feitosa MF, Garcia ME, Graff M, Grallert H, Grarup N, Guo X, Haesser J, Hansen T, Harris TB, Highland HM, Hong J, Ikram MA, Ingelsson E, Jackson R, Jousilahti P, Kähönen M, Kizer JR, Kovacs P, Kriebel J, Laakso M, Lange LA, Lehtimäki T, Li J, Li-Gao R, Lind L, Luan J, Lyytikäinen LP, MacGregor S, Mackey DA, Mahajan A, Mangino M, Männistö S, McCarthy MI, McKnight B, Medina-Gomez C, Meigs JB, Molnos S, Mook-Kanamori D, Morris AP, de Mutsert R, Nalls MA, Nedeljkovic I, North KE, Pennell CE, Pradhan AD, Province MA, Raitakari OT, Raulerson CK, Reiner AP, Ridker PM, Ripatti S, Roberston N, Rotter JI, Salomaa V, Sandoval-Zárate AA, Sitlani CM, Spector TD, Strauch K, Stumvoll M, Taylor KD, Thuesen B, Tönjes A, Uitterlinden AG, Venturini C, Walker M, Wang CA, Wang S, Wareham NJ, Willems SM, Willems van Dijk K, Wilson JG, Wu Y, Yao J, Young KL, Langenberg C, Frayling TM, Kilpeläinen TO, Lindgren CM, Loos RJF, Mohlke KL. Exome-Derived Adiponectin-Associated Variants Implicate Obesity and Lipid Biology. Am J Hum Genet 2019 07 105:15-28 PMID: 31178129 (erratum 31491410) DOI: 10.1016/j.ajhg.2019.05.002

Sprague D, Waters SA, Kirk JM, Wang JR, Samollow PB, Waters PD, Calabrese JM. Nonlinear sequence similarity between the Xist and Rsx long noncoding RNAs suggests shared functions of tandem repeat domains. RNA 2019 08 25:1004-1019 PMID: 31097619 DOI: 10.1261/rna.069815.118

Morgan AP, Bell TA, Crowley JJ, Pardo-Manuel de Villena F. Instability of the Pseudoautosomal Boundary in House Mice. Genetics 2019 06 212:469-487 PMID: 31028113 DOI: 10.1534/genetics.119.302232

Shellhammer JP, Pomeroy AE, Li Y, Dujmusic L, Elston TC, Hao N, Dohlman HG. Quantitative analysis of the yeast pheromone pathway. Yeast 2019 08 36:495-518 PMID: 31022772 DOI: 10.1002/yea.3395

Azam SH, Porrello A, Harrison EB, Leslie PL, Liu X, Waugh TA, Belanger A, Mangala LS, Lopez-Berestein G, Wilson HL, McCann JV, Kim WY, Sood AK, Liu J, Dudley AC, Pecot CV. Quaking orchestrates a post-transcriptional regulatory network of endothelial cell cycle progression critical to angiogenesis and metastasis. Oncogene 2019 06 38:5191-5210 PMID: 30918328 DOI: 10.1038/s41388-019-0786-6

Keele GR, Crouse WL, Kelada SNP, Valdar W. Determinants of QTL Mapping Power in the Realized Collaborative Cross. G3 (Bethesda) 2019 05 9:1707-1727 PMID: 30914424 DOI: 10.1534/g3.119.400194

Chao HX, Fakhreddin RI, Shimerov HK, Kedziora KM, Kumar RJ, Perez J, Limas JC, Grant GD, Cook JG, Gupta GP, Purvis JE. Evidence that the human cell cycle is a series of uncoupled, memoryless phases. Mol Syst Biol 2019 03 15:e8604 PMID: 30886052 (erratum 30952682) DOI: 10.15252/msb.20188604

Shorter JR, Maurizio PL, Bell TA, Shaw GD, Miller DR, Gooch TJ, Spence JS, McMillan L, Valdar W, Pardo-Manuel de Villena F. A Diallel of the Mouse Collaborative Cross Founders Reveals Strong Strain-Specific Maternal Effects on Litter Size. G3 (Bethesda) 2019 05 9:1613-1622 PMID: 30877080 DOI: 10.1534/g3.118.200847

Wong KY, Fan C, Tanioka M, Parker JS, Nobel AB, Zeng D, Lin DY, Perou CM. I-Boost: an integrative boosting approach for predicting survival time with multiple genomics platforms. Genome Biol 2019 03 20:52 PMID: 30845957 DOI: 10.1186/s13059-019-1640-4

Alzubi MA, Turner TH, Olex AL, Sohal SS, Tobin NP, Recio SG, Bergh J, Hatschek T, Parker JS, Sartorius CA, Perou CM, Dozmorov MG, Harrell JC. Separation of breast cancer and organ microenvironment transcriptomes in metastases. Breast Cancer Res 2019 03 21:36 PMID: 30841919 DOI: 10.1186/s13058-019-1123-2

Farag S, Bleich RM, Shank EA, Isayev O, Bowers AA, Tropsha A. Inter-Modular Linkers play a crucial role in governing the biosynthesis of non-ribosomal peptides. Bioinformatics 2019 10 35:3584-3591 PMID: 30785185 DOI: 10.1093/bioinformatics/btz127

Justice AE, Karaderi T, Highland HM, Young KL, Graff M, Lu Y, Turcot V, Auer PL, Fine RS, Guo X, Schurmann C, Lempradl A, Marouli E, Mahajan A, Winkler TW, Locke AE, Medina-Gomez C, Esko T, Vedantam S, Giri A, Lo KS, Alfred T, Mudgal P, Ng MCY, Heard-Costa NL, Feitosa MF, Manning AK, Willems SM, Sivapalaratnam S, Abecasis G, Alam DS, Allison M, Amouyel P, Arzumanyan Z, Balkau B, Bastarache L, Bergmann S, Bielak LF, Blüher M, Boehnke M, Boeing H, Boerwinkle E, Böger CA, Bork-Jensen J, Bottinger EP, Bowden DW, Brandslund I, Broer L, Burt AA, Butterworth AS, Caulfield MJ, Cesana G, Chambers JC, Chasman DI, Chen YI, Chowdhury R, Christensen C, Chu AY, Collins FS, Cook JP, Cox AJ, Crosslin DS, Danesh J, de Bakker PIW, Denus S, Mutsert R, Dedoussis G, Demerath EW, Dennis JG, Denny JC, Di Angelantonio E, Dörr M, Drenos F, Dubé MP, Dunning AM, Easton DF, Elliott P, Evangelou E, Farmaki AE, Feng S, Ferrannini E, Ferrieres J, Florez JC, Fornage M, Fox CS, Franks PW, Friedrich N, Gan W, Gandin I, Gasparini P, Giedraitis V, Girotto G, Gorski M, Grallert H, Grarup N, Grove ML, Gustafsson S, Haessler J, Hansen T, Hattersley AT, Hayward C, Heid IM, Holmen OL, Hovingh GK, Howson JMM, Hu Y, Hung YJ, Hveem K, Ikram MA, Ingelsson E, Jackson AU, Jarvik GP, Jia Y, Jørgensen T, Jousilahti P, Justesen JM, Kahali B, Karaleftheri M, Kardia SLR, Karpe F, Kee F, Kitajima H, Komulainen P, Kooner JS, Kovacs P, Krämer BK, Kuulasmaa K, Kuusisto J, Laakso M, Lakka TA, Lamparter D, Lange LA, Langenberg C, Larson EB, Lee NR, Lee WJ, Lehtimäki T, Lewis CE, Li H, Li J, Li-Gao R, Lin LA, Lin X, Lind L, Lindström J, Linneberg A, Liu CT, Liu DJ, Luan J, Lyytikäinen LP, MacGregor S, Mägi R, Männistö S, Marenne G, Marten J, Masca NGD, McCarthy MI, Meidtner K, Mihailov E, Moilanen L, Moitry M, Mook-Kanamori DO, Morgan A, Morris AP, Müller-Nurasyid M, Munroe PB, Narisu N, Nelson CP, Neville M, Ntalla I, O’Connell JR, Owen KR, Pedersen O, Peloso GM, Pennell CE, Perola M, Perry JA, Perry JRB, Pers TH, Ewing A, Polasek O, Raitakari OT, Rasheed A, Raulerson CK, Rauramaa R, Reilly DF, Reiner AP, Ridker PM, Rivas MA, Robertson NR, Robino A, Rudan I, Ruth KS, Saleheen D, Salomaa V, Samani NJ, Schreiner PJ, Schulze MB, Scott RA, Segura-Lepe M, Sim X, Slater AJ, Small KS, Smith BH, Smith JA, Southam L, Spector TD, Speliotes EK, Stefansson K, Steinthorsdottir V, Stirrups KE, Strauch K, Stringham HM, Stumvoll M, Sun L, Surendran P, Swart KMA, Tardif JC, Taylor KD, Teumer A, Thompson DJ, Thorleifsson G, Thorsteinsdottir U, Thuesen BH, Tönjes A, Torres M, Tsafantakis E, Tuomilehto J, Uitterlinden AG, Uusitupa M, van Duijn CM, Vanhala M, Varma R, Vermeulen SH, Vestergaard H, Vitart V, Vogt TF, Vuckovic D, Wagenknecht LE, Walker M, Wallentin L, Wang F, Wang CA, Wang S, Wareham NJ, Warren HR, Waterworth DM, Wessel J, White HD, Willer CJ, Wilson JG, Wood AR, Wu Y, Yaghootkar H, Yao J, Yerges-Armstrong LM, Young R, Zeggini E, Zhan X, Zhang W, Zhao JH, Zhao W, Zheng H, Zhou W, Zillikens MC, Rivadeneira F, Borecki IB, Pospisilik JA, Deloukas P, Frayling TM, Lettre G, Mohlke KL, Rotter JI, Kutalik Z, Hirschhorn JN, Cupples LA, Loos RJF, North KE, Lindgren CM. Protein-coding variants implicate novel genes related to lipid homeostasis contributing to body-fat distribution. Nat Genet 2019 03 51:452-469 PMID: 30778226 DOI: 10.1038/s41588-018-0334-2

Mose LE, Perou CM, Parker JS. Improved indel detection in DNA and RNA via realignment with ABRA2. Bioinformatics 2019 09 35:2966-2973 PMID: 30649250 DOI: 10.1093/bioinformatics/btz033

2018

Corty RW, Valdar W. vqtl: An R Package for Mean-Variance QTL Mapping. G3 (Bethesda) 2018 12 8:3757-3766 PMID: 30389795 DOI: 10.1534/g3.118.200642

Corty RW, Valdar W. QTL Mapping on a Background of Variance Heterogeneity. G3 (Bethesda) 2018 12 8:3767-3782 PMID: 30389794 DOI: 10.1534/g3.118.200790

Corty RW, Kumar V, Tarantino LM, Takahashi JS, Valdar W. Mean-Variance QTL Mapping Identifies Novel QTL for Circadian Activity and Exploratory Behavior in Mice. G3 (Bethesda) 2018 12 8:3783-3790 PMID: 30389793 DOI: 10.1534/g3.118.200194

Keith BP, Barrow JB, Toyonaga T, Kazgan N, O’Connor MH, Shah ND, Schaner MS, Wolber EA, Trad OK, Gipson GR, Pitman WA, Kanke M, Saxena SJ, Chaumont N, Sadiq TS, Koruda MJ, Cotney PA, Allbritton N, Trembath DG, Sylvester F, Furey TS, Sethupathy P, Sheikh SZ. Colonic epithelial miR-31 associates with the development of Crohn’s phenotypes. JCI Insight 2018 10 3: PMID: 30282822 DOI: 122788

Kirk JM, Kim SO, Inoue K, Smola MJ, Lee DM, Schertzer MD, Wooten JS, Baker AR, Sprague D, Collins DW, Horning CR, Wang S, Chen Q, Weeks KM, Mucha PJ, Calabrese JM. Functional classification of long non-coding RNAs by k-mer content. Nat Genet 2018 10 50:1474-1482 PMID: 30224646 DOI: 10.1038/s41588-018-0207-8

Wolff SC, Kedziora KM, Dumitru R, Dungee CD, Zikry TM, Beltran AS, Haggerty RA, Cheng J, Redick MA, Purvis JE. Inheritance of OCT4 predetermines fate choice in human embryonic stem cells. Mol Syst Biol 2018 09 14:e8140 PMID: 30177503 DOI: 10.15252/msb.20178140

Metz KS, Deoudes EM, Berginski ME, Jimenez-Ruiz I, Aksoy BA, Hammerbacher J, Gomez SM, Phanstiel DH. Coral: Clear and Customizable Visualization of Human Kinome Data. Cell Syst 2018 09 7:347-350.e1 PMID: 30172842 DOI: 10.1016/j.cels.2018.07.001

Oreper D, Schoenrock SA, McMullan R, Ervin R, Farrington J, Miller DR, de Villena FP, Valdar W, Tarantino LM. Reciprocal F1 Hybrids of Two Inbred Mouse Strains Reveal Parent-of-Origin and Perinatal Diet Effects on Behavior and Expression. G3 (Bethesda) 2018 11 8:3447-3468 PMID: 30171036 DOI: 10.1534/g3.118.200135

Pan DZ, Garske KM, Alvarez M, Bhagat YV, Boocock J, Nikkola E, Miao Z, Raulerson CK, Cantor RM, Civelek M, Glastonbury CA, Small KS, Boehnke M, Lusis AJ, Sinsheimer JS, Mohlke KL, Laakso M, Pajukanta P, Ko A. Author Correction: Integration of human adipocyte chromosomal interactions with adipose gene expression prioritizes obesity-related genes from GWAS. Nat Commun 2018 08 9:3472 PMID: 30135520 (erratum 29666371) DOI: 10.1038/s41467-018-05849-3

Lansford JL, Dharmasiri U, Chai S, Hunsucker SA, Bortone DS, Keating JE, Schlup IM, Glish GL, Collins EJ, Alatrash G, Molldrem JJ, Armistead PM, Vincent BG. Computational modeling and confirmation of leukemia-associated minor histocompatibility antigens. Blood Adv 2018 08 2:2052-2062 PMID: 30115642 DOI: 10.1182/bloodadvances.2018022475

Borland D, Yi H, Grant GD, Kedziora KM, Chao HX, Haggerty RA, Kumar J, Wolff SC, Cook JG, Purvis JE. The Cell Cycle Browser: An Interactive Tool for Visualizing, Simulating, and Perturbing Cell-Cycle Progression. Cell Syst 2018 08 7:180-184.e4 PMID: 30077635 DOI: 10.1016/j.cels.2018.06.004

Stanley N, Kwitt R, Niethammer M, Mucha PJ. Compressing Networks with Super Nodes. Sci Rep 2018 Jul 8:10892 PMID: 30022035 DOI: 10.1038/s41598-018-29174-3

Bonacci T, Suzuki A, Grant GD, Stanley N, Cook JG, Brown NG, Emanuele MJ. Cezanne/OTUD7B is a cell cycle-regulated deubiquitinase that antagonizes the degradation of APC/C substrates. EMBO J 2018 08 37: PMID: 29973362 DOI: 10.15252/embj.201798701

de Moraes MH, Soto EB, Salas González I, Desai P, Chu W, Porwollik S, McClelland M, Teplitski M. Genome-Wide Comparative Functional Analyses Reveal Adaptations of Salmonella sv. Newport to a Plant Colonization Lifestyle. Front Microbiol 2018 9:877 PMID: 29867794 DOI: 10.3389/fmicb.2018.00877

Saito R, Smith CC, Utsumi T, Bixby LM, Kardos J, Wobker SE, Stewart KG, Chai S, Manocha U, Byrd KM, Damrauer JS, Williams SE, Vincent BG, Kim WY. Molecular Subtype-Specific Immunocompetent Models of High-Grade Urothelial Carcinoma Reveal Differential Neoantigen Expression and Response to Immunotherapy. Cancer Res 2018 07 78:3954-3968 PMID: 29784854 (erratum 32182171) DOI: 10.1158/0008-5472.CAN-18-0173

Pan DZ, Garske KM, Alvarez M, Bhagat YV, Boocock J, Nikkola E, Miao Z, Raulerson CK, Cantor RM, Civelek M, Glastonbury CA, Small KS, Boehnke M, Lusis AJ, Sinsheimer JS, Mohlke KL, Laakso M, Pajukanta P, Ko A. Integration of human adipocyte chromosomal interactions with adipose gene expression prioritizes obesity-related genes from GWAS. Nat Commun 2018 04 9:1512 PMID: 29666371 (erratum 30135520) DOI: 10.1038/s41467-018-03554-9

Maguire JB, Boyken SE, Baker D, Kuhlman B. Rapid Sampling of Hydrogen Bond Networks for Computational Protein Design. J Chem Theory Comput 2018 05 14:2751-2760 PMID: 29652499 (erratum 30221938) DOI: 10.1021/acs.jctc.8b00033

Collins KAL, Stuhlmiller TJ, Zawistowski JS, East MP, Pham TT, Hall CR, Goulet DR, Bevill SM, Angus SP, Velarde SH, Sciaky N, Oprea TI, Graves LM, Johnson GL, Gomez SM. Proteomic analysis defines kinase taxonomies specific for subtypes of breast cancer. Oncotarget 2018 Mar 9:15480-15497 PMID: 29643987 DOI: 10.18632/oncotarget.24337

Spracklen CN, Shi J, Vadlamudi S, Wu Y, Zou M, Raulerson CK, Davis JP, Zeynalzadeh M, Jackson K, Yuan W, Wang H, Shou W, Wang Y, Luo J, Lange LA, Lange EM, Popkin BM, Gordon-Larsen P, Du S, Huang W, Mohlke KL. Identification and functional analysis of glycemic trait loci in the China Health and Nutrition Survey. PLoS Genet 2018 04 14:e1007275 PMID: 29621232 DOI: 10.1371/journal.pgen.1007275

Jayasinghe RG, Cao S, Gao Q, Wendl MC, Vo NS, Reynolds SM, Zhao Y, Climente-González H, Chai S, Wang F, Varghese R, Huang M, Liang WW, Wyczalkowski MA, Sengupta S, Li Z, Payne SH, Fenyö D, Miner JH, Walter MJ, Vincent B, Eyras E, Chen K, Shmulevich I, Chen F, Ding L, Caesar-Johnson SJ, Demchok JA, Felau I, Kasapi M, Ferguson ML, Hutter CM, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Zhang JJ, Chudamani S, Liu J, Lolla L, Naresh R, Pihl T, Sun Q, Wan Y, Wu Y, Cho J, DeFreitas T, Frazer S, Gehlenborg N, Getz G, Heiman DI, Kim J, Lawrence MS, Lin P, Meier S, Noble MS, Saksena G, Voet D, Zhang H, Bernard B, Chambwe N, Dhankani V, Knijnenburg T, Kramer R, Leinonen K, Liu Y, Miller M, Reynolds S, Shmulevich I, Thorsson V, Zhang W, Akbani R, Broom BM, Hegde AM, Ju Z, Kanchi RS, Korkut A, Li J, Liang H, Ling S, Liu W, Lu Y, Mills GB, Ng KS, Rao A, Ryan M, Wang J, Weinstein JN, Zhang J, Abeshouse A, Armenia J, Chakravarty D, Chatila WK, de Bruijn I, Gao J, Gross BE, Heins ZJ, Kundra R, La K, Ladanyi M, Luna A, Nissan MG, Ochoa A, Phillips SM, Reznik E, Sanchez-Vega F, Sander C, Schultz N, Sheridan R, Sumer SO, Sun Y, Taylor BS, Wang J, Zhang H, Anur P, Peto M, Spellman P, Benz C, Stuart JM, Wong CK, Yau C, Hayes DN, Parker JS, Wilkerson MD, Ally A, Balasundaram M, Bowlby R, Brooks D, Carlsen R, Chuah E, Dhalla N, Holt R, Jones SJM, Kasaian K, Lee D, Ma Y, Marra MA, Mayo M, Moore RA, Mungall AJ, Mungall K, Robertson AG, Sadeghi S, Schein JE, Sipahimalani P, Tam A, Thiessen N, Tse K, Wong T, Berger AC, Beroukhim R, Cherniack AD, Cibulskis C, Gabriel SB, Gao GF, Ha G, Meyerson M, Schumacher SE, Shih J, Kucherlapati MH, Kucherlapati RS, Baylin S, Cope L, Danilova L, Bootwalla MS, Lai PH, Maglinte DT, Van Den Berg DJ, Weisenberger DJ, Auman JT, Balu S, Bodenheimer T, Fan C, Hoadley KA, Hoyle AP, Jefferys SR, Jones CD, Meng S, Mieczkowski PA, Mose LE, Perou AH, Perou CM, Roach J, Shi Y, Simons JV, Skelly T, Soloway MG, Tan D, Veluvolu U, Fan H, Hinoue T, Laird PW, Shen H, Zhou W, Bellair M, Chang K, Covington K, Creighton CJ, Dinh H, Doddapaneni H, Donehower LA, Drummond J, Gibbs RA, Glenn R, Hale W, Han Y, Hu J, Korchina V, Lee S, Lewis L, Li W, Liu X, Morgan M, Morton D, Muzny D, Santibanez J, Sheth M, Shinbrot E, Wang L, Wang M, Wheeler DA, Xi L, Zhao F, Hess J, Appelbaum EL, Bailey M, Cordes MG, Ding L, Fronick CC, Fulton LA, Fulton RS, Kandoth C, Mardis ER, McLellan MD, Miller CA, Schmidt HK, Wilson RK, Crain D, Curley E, Gardner J, Lau K, Mallery D, Morris S, Paulauskis J, Penny R, Shelton C, Shelton T, Sherman M, Thompson E, Yena P, Bowen J, Gastier-Foster JM, Gerken M, Leraas KM, Lichtenberg TM, Ramirez NC, Wise L, Zmuda E, Corcoran N, Costello T, Hovens C, Carvalho AL, de Carvalho AC, Fregnani JH, Longatto-Filho A, Reis RM, Scapulatempo-Neto C, Silveira HCS, Vidal DO, Burnette A, Eschbacher J, Hermes B, Noss A, Singh R, Anderson ML, Castro PD, Ittmann M, Huntsman D, Kohl B, Le X, Thorp R, Andry C, Duffy ER, Lyadov V, Paklina O, Setdikova G, Shabunin A, Tavobilov M, McPherson C, Warnick R, Berkowitz R, Cramer D, Feltmate C, Horowitz N, Kibel A, Muto M, Raut CP, Malykh A, Barnholtz-Sloan JS, Barrett W, Devine K, Fulop J, Ostrom QT, Shimmel K, Wolinsky Y, Sloan AE, De Rose A, Giuliante F, Goodman M, Karlan BY, Hagedorn CH, Eckman J, Harr J, Myers J, Tucker K, Zach LA, Deyarmin B, Hu H, Kvecher L, Larson C, Mural RJ, Somiari S, Vicha A, Zelinka T, Bennett J, Iacocca M, Rabeno B, Swanson P, Latour M, Lacombe L, Têtu B, Bergeron A, McGraw M, Staugaitis SM, Chabot J, Hibshoosh H, Sepulveda A, Su T, Wang T, Potapova O, Voronina O, Desjardins L, Mariani O, Roman-Roman S, Sastre X, Stern MH, Cheng F, Signoretti S, Berchuck A, Bigner D, Lipp E, Marks J, McCall S, McLendon R, Secord A, Sharp A, Behera M, Brat DJ, Chen A, Delman K, Force S, Khuri F, Magliocca K, Maithel S, Olson JJ, Owonikoko T, Pickens A, Ramalingam S, Shin DM, Sica G, Van Meir EG, Zhang H, Eijckenboom W, Gillis A, Korpershoek E, Looijenga L, Oosterhuis W, Stoop H, van Kessel KE, Zwarthoff EC, Calatozzolo C, Cuppini L, Cuzzubbo S, DiMeco F, Finocchiaro G, Mattei L, Perin A, Pollo B, Chen C, Houck J, Lohavanichbutr P, Hartmann A, Stoehr C, Stoehr R, Taubert H, Wach S, Wullich B, Kycler W, Murawa D, Wiznerowicz M, Chung K, Edenfield WJ, Martin J, Baudin E, Bubley G, Bueno R, De Rienzo A, Richards WG, Kalkanis S, Mikkelsen T, Noushmehr H, Scarpace L, Girard N, Aymerich M, Campo E, Giné E, Guillermo AL, Van Bang N, Hanh PT, Phu BD, Tang Y, Colman H, Evason K, Dottino PR, Martignetti JA, Gabra H, Juhl H, Akeredolu T, Stepa S, Hoon D, Ahn K, Kang KJ, Beuschlein F, Breggia A, Birrer M, Bell D, Borad M, Bryce AH, Castle E, Chandan V, Cheville J, Copland JA, Farnell M, Flotte T, Giama N, Ho T, Kendrick M, Kocher JP, Kopp K, Moser C, Nagorney D, O’Brien D, O’Neill BP, Patel T, Petersen G, Que F, Rivera M, Roberts L, Smallridge R, Smyrk T, Stanton M, Thompson RH, Torbenson M, Yang JD, Zhang L, Brimo F, Ajani JA, Gonzalez AMA, Behrens C, Bondaruk J, Broaddus 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Landen CN, Phillips J, Prados M, Simko J, Smith-McCune K, VandenBerg S, Roggin K, Fehrenbach A, Kendler A, Sifri S, Steele R, Jimeno A, Carey F, Forgie I, Mannelli M, Carney M, Hernandez B, Campos B, Herold-Mende C, Jungk C, Unterberg A, von Deimling A, Bossler A, Galbraith J, Jacobus L, Knudson M, Knutson T, Ma D, Milhem M, Sigmund R, Godwin AK, Madan R, Rosenthal HG, Adebamowo C, Adebamowo SN, Boussioutas A, Beer D, Giordano T, Mes-Masson AM, Saad F, Bocklage T, Landrum L, Mannel R, Moore K, Moxley K, Postier R, Walker J, Zuna R, Feldman M, Valdivieso F, Dhir R, Luketich J, Pinero EMM, Quintero-Aguilo M, Carlotti CG, Dos Santos JS, Kemp R, Sankarankuty A, Tirapelli D, Catto J, Agnew K, Swisher E, Creaney J, Robinson B, Shelley CS, Godwin EM, Kendall S, Shipman C, Bradford C, Carey T, Haddad A, Moyer J, Peterson L, Prince M, Rozek L, Wolf G, Bowman R, Fong KM, Yang I, Korst R, Rathmell WK, Fantacone-Campbell JL, Hooke JA, Kovatich AJ, Shriver CD, DiPersio J, Drake B, Govindan R, Heath S, Ley T, Van Tine B, Westervelt P, Rubin MA, Lee JI, Aredes ND, Mariamidze A. Systematic Analysis of Splice-Site-Creating Mutations in Cancer. Cell Rep 2018 04 23:270-281.e3 PMID: 29617666 DOI: 10.1016/j.celrep.2018.03.052

Teslovich TM, Kim DS, Yin X, Stancáková A, Jackson AU, Wielscher M, Naj A, Perry JRB, Huyghe JR, Stringham HM, Davis JP, Raulerson CK, Welch RP, Fuchsberger C, Locke AE, Sim X, Chines PS, Narisu N, Kangas AJ, Soininen P, Ala-Korpela M, Gudnason V, Musani SK, Jarvelin MR, Schellenberg GD, Speliotes EK, Kuusisto J, Collins FS, Boehnke M, Laakso M, Mohlke KL. Identification of seven novel loci associated with amino acid levels using single-variant and gene-based tests in 8545 Finnish men from the METSIM study. Hum Mol Genet 2018 05 27:1664-1674 PMID: 29481666 DOI: 10.1093/hmg/ddy067

Herrera Paredes S, Gao T, Law TF, Finkel OM, Mucyn T, Teixeira PJPL, Salas González I, Feltcher ME, Powers MJ, Shank EA, Jones CD, Jojic V, Dangl JL, Castrillo G. Design of synthetic bacterial communities for predictable plant phenotypes. PLoS Biol 2018 02 16:e2003962 PMID: 29462153 DOI: 10.1371/journal.pbio.2003962

Kutchko KM, Madden EA, Morrison C, Plante KS, Sanders W, Vincent HA, Cruz Cisneros MC, Long KM, Moorman NJ, Heise MT, Laederach A. Structural divergence creates new functional features in alphavirus genomes. Nucleic Acids Res 2018 04 46:3657-3670 PMID: 29361131 DOI: 10.1093/nar/gky012

de la Torre-Ubieta L, Stein JL, Won H, Opland CK, Liang D, Lu D, Geschwind DH. The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis. Cell 2018 01 172:289-304.e18 PMID: 29307494 (erratum 29328907) DOI: 10.1016/j.cell.2017.12.014

Duan Q, Xu Z, Raffield LM, Chang S, Wu D, Lange EM, Reiner AP, Li Y. A robust and powerful two-step testing procedure for local ancestry adjusted allelic association analysis in admixed populations. Genet Epidemiol 2018 04 42:288-302 PMID: 29226381 DOI: 10.1002/gepi.22104

Maurizio PL, Ferris MT, Keele GR, Miller DR, Shaw GD, Whitmore AC, West A, Morrison CR, Noll KE, Plante KS, Cockrell AS, Threadgill DW, Pardo-Manuel de Villena F, Baric RS, Heise MT, Valdar W. Bayesian Diallel Analysis Reveals Mx1-Dependent and Mx1-Independent Effects on Response to Influenza A Virus in Mice. G3 (Bethesda) 2018 02 8:427-445 PMID: 29187420 DOI: 10.1534/g3.117.300438

Turner SD, Maurizio PL, Valdar W, Yandell BS, Simon PW. Dissecting the Genetic Architecture of Shoot Growth in Carrot (Daucus carota L.) Using a Diallel Mating Design. G3 (Bethesda) 2018 02 8:411-426 PMID: 29187419 DOI: 10.1534/g3.117.300235

Weiser M, Simon JM, Kochar B, Tovar A, Israel JW, Robinson A, Gipson GR, Schaner MS, Herfarth HH, Sartor RB, McGovern DPB, Rahbar R, Sadiq TS, Koruda MJ, Furey TS, Sheikh SZ. Molecular classification of Crohn’s disease reveals two clinically relevant subtypes. Gut 2018 01 67:36-42 PMID: 27742763 DOI: 10.1136/gutjnl-2016-312518

2017

Haggerty RA, Purvis JE. Natural language processing: put your model where your mouth is. Mol Syst Biol 2017 12 13:958 PMID: 29254950 (erratum 29175850) DOI: 10.15252/msb.20178077

Richard MA, Huan T, Ligthart S, Gondalia R, Jhun MA, Brody JA, Irvin MR, Marioni R, Shen J, Tsai PC, Montasser ME, Jia Y, Syme C, Salfati EL, Boerwinkle E, Guan W, Mosley TH, Bressler J, Morrison AC, Liu C, Mendelson MM, Uitterlinden AG, van Meurs JB, Franco OH, Zhang G, Li Y, Stewart JD, Bis JC, Psaty BM, Chen YI, Kardia SLR, Zhao W, Turner ST, Absher D, Aslibekyan S, Starr JM, McRae AF, Hou L, Just AC, Schwartz JD, Vokonas PS, Menni C, Spector TD, Shuldiner A, Damcott CM, Rotter JI, Palmas W, Liu Y, Paus T, Horvath S, O’Connell JR, Guo X, Pausova Z, Assimes TL, Sotoodehnia N, Smith JA, Arnett DK, Deary IJ, Baccarelli AA, Bell JT, Whitsel E, Dehghan A, Levy D, Fornage M, Heijmans BT, ‘t Hoen PAC, van Meurs J, Isaacs A, Jansen R, Franke L, Boomsma DI, Pool R, van Dongen J, Hottenga JJ, van Greevenbroek MMJ, Stehouwer CDA, van der Kallen CJH, Schalkwijk CG, Wijmenga C, Zhernakova A, Tigchelaar EF, Slagboom PE, Beekman M, Deelen J, van Heemst D, Veldink JH, van den Berg LH, van Duijn CM, Hofman A, Uitterlinden AG, Jhamai PM, Verbiest M, Suchiman HED, Verkerk M, van der Breggen R, van Rooij J, Lakenberg N, Mei H, van Iterson M, van Galen M, Bot J, van ‘t Hof P, Deelen P, Nooren I, Moed M, Vermaat M, Zhernakova DV, Luijk R, Bonder MJ, van Dijk F, Arindrarto W, Kielbasa SM, Swertz MA, van Zwet EW. DNA Methylation Analysis Identifies Loci for Blood Pressure Regulation. Am J Hum Genet 2017 Dec 101:888-902 PMID: 29198723 DOI: 10.1016/j.ajhg.2017.09.028

Corley M, Solem A, Phillips G, Lackey L, Ziehr B, Vincent HA, Mustoe AM, Ramos SBV, Weeks KM, Moorman NJ, Laederach A. An RNA structure-mediated, posttranscriptional model of human α-1-antitrypsin expression. Proc Natl Acad Sci U S A 2017 11 114:E10244-E10253 PMID: 29109288 DOI: 10.1073/pnas.1706539114

Chao HX, Poovey CE, Privette AA, Grant GD, Chao HY, Cook JG, Purvis JE. Orchestration of DNA Damage Checkpoint Dynamics across the Human Cell Cycle. Cell Syst 2017 11 5:445-459.e5 PMID: 29102360 (erratum 29169017) DOI: 10.1016/j.cels.2017.09.015

Rosshart SP, Vassallo BG, Angeletti D, Hutchinson DS, Morgan AP, Takeda K, Hickman HD, McCulloch JA, Badger JH, Ajami NJ, Trinchieri G, Pardo-Manuel de Villena F, Yewdell JW, Rehermann B. Wild Mouse Gut Microbiota Promotes Host Fitness and Improves Disease Resistance. Cell 2017 Nov 171:1015-1028.e13 PMID: 29056339 (erratum 29192675) DOI: 10.1016/j.cell.2017.09.016

Weir WH, Emmons S, Gibson R, Taylor D, Mucha PJ. Post-Processing Partitions to Identify Domains of Modularity Optimization. Algorithms 2017 Sep 10: PMID: 29046743 DOI: 10.3390/a10030093

Morgan AP, Pardo-Manuel de Villena F. Sequence and Structural Diversity of Mouse Y Chromosomes. Mol Biol Evol 2017 Dec 34:3186-3204 PMID: 29029271 DOI: 10.1093/molbev/msx250

Buchkovich ML, Brown CC, Robasky K, Chai S, Westfall S, Vincent BG, Weimer ET, Powers JG. HLAProfiler utilizes k-mer profiles to improve HLA calling accuracy for rare and common alleles in RNA-seq data. Genome Med 2017 09 9:86 PMID: 28954626 DOI: 10.1186/s13073-017-0473-6

Hui D, Fang Z, Lin J, Duan Q, Li Y, Hu M, Chen W. LAIT: a local ancestry inference toolkit. BMC Genet 2017 09 18:83 PMID: 28877673 DOI: 10.1186/s12863-017-0546-y

Makhanova N, Morgan AP, Kayashima Y, Makhanov A, Hiller S, Zhilicheva S, Xu L, Pardo-Manuel de Villena F, Maeda N. Genetic architecture of atherosclerosis dissected by QTL analyses in three F2 intercrosses of apolipoprotein E-null mice on C57BL6/J, DBA/2J and 129S6/SvEvTac backgrounds. PLoS One 2017 12:e0182882 PMID: 28837567 DOI: 10.1371/journal.pone.0182882

Finkel OM, Castrillo G, Herrera Paredes S, Salas González I, Dangl JL. Understanding and exploiting plant beneficial microbes. Curr Opin Plant Biol 2017 08 38:155-163 PMID: 28622659 DOI: 10.1016/j.pbi.2017.04.018

Gralinski LE, Menachery VD, Morgan AP, Totura AL, Beall A, Kocher J, Plante J, Harrison-Shostak DC, Schäfer A, Pardo-Manuel de Villena F, Ferris MT, Baric RS. Allelic Variation in the Toll-Like Receptor Adaptor Protein Ticam2 Contributes to SARS-Coronavirus Pathogenesis in Mice. G3 (Bethesda) 2017 06 7:1653-1663 PMID: 28592648 DOI: 10.1534/g3.117.041434

Oreper D, Cai Y, Tarantino LM, de Villena FP, Valdar W. Inbred Strain Variant Database (ISVdb): A Repository for Probabilistically Informed Sequence Differences Among the Collaborative Cross Strains and Their Founders. G3 (Bethesda) 2017 06 7:1623-1630 PMID: 28592645 DOI: 10.1534/g3.117.041491

Morgan AP, Gatti DM, Najarian ML, Keane TM, Galante RJ, Pack AI, Mott R, Churchill GA, de Villena FP. Structural Variation Shapes the Landscape of Recombination in Mouse. Genetics 2017 06 206:603-619 PMID: 28592499 DOI: 10.1534/genetics.116.197988

Srivastava A, Morgan AP, Najarian ML, Sarsani VK, Sigmon JS, Shorter JR, Kashfeen A, McMullan RC, Williams LH, Giusti-Rodríguez P, Ferris MT, Sullivan P, Hock P, Miller DR, Bell TA, McMillan L, Churchill GA, de Villena FP. Genomes of the Mouse Collaborative Cross. Genetics 2017 06 206:537-556 PMID: 28592495 DOI: 10.1534/genetics.116.198838

Jacob RB, Michaels KC, Anderson CJ, Fay JM, Dokholyan NV. Corrigendum: Harnessing Nature’s Diversity: Discovering organophosphate bioscavenger characteristics among low molecular weight proteins. Sci Rep 2017 04 7:46727 PMID: 28452359 (erratum 27845442) DOI: 10.1038/srep46727

Silva GO, Siegel MB, Mose LE, Parker JS, Sun W, Perou CM, Chen M. SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling. Genome Biol 2017 04 18:66 PMID: 28390427 DOI: 10.1186/s13059-017-1193-3

Walsh DM, McCullough SD, Yourstone S, Jones SW, Cairns BA, Jones CD, Jaspers I, Diaz-Sanchez D. Alterations in airway microbiota in patients with PaO2/FiO2 ratio ≤ 300 after burn and inhalation injury. PLoS One 2017 12:e0173848 PMID: 28358811 DOI: 10.1371/journal.pone.0173848

Dinh TA, Vitucci EC, Wauthier E, Graham RP, Pitman WA, Oikawa T, Chen M, Silva GO, Greene KG, Torbenson MS, Reid LM, Sethupathy P. Comprehensive analysis of The Cancer Genome Atlas reveals a unique gene and non-coding RNA signature of fibrolamellar carcinoma. Sci Rep 2017 03 7:44653 PMID: 28304380 DOI: 10.1038/srep44653

Castrillo G, Teixeira PJ, Paredes SH, Law TF, de Lorenzo L, Feltcher ME, Finkel OM, Breakfield NW, Mieczkowski P, Jones CD, Paz-Ares J, Dangl JL. Root microbiota drive direct integration of phosphate stress and immunity. Nature 2017 03 543:513-518 PMID: 28297714 (erratum 28399400) DOI: 10.1038/nature21417

Civelek M, Wu Y, Pan C, Raulerson CK, Ko A, He A, Tilford C, Saleem NK, Stančáková A, Scott LJ, Fuchsberger C, Stringham HM, Jackson AU, Narisu N, Chines PS, Small KS, Kuusisto J, Parks BW, Pajukanta P, Kirchgessner T, Collins FS, Gargalovic PS, Boehnke M, Laakso M, Mohlke KL, Lusis AJ. Genetic Regulation of Adipose Gene Expression and Cardio-Metabolic Traits. Am J Hum Genet 2017 Mar 100:428-443 PMID: 28257690 DOI: 10.1016/j.ajhg.2017.01.027

Jacob RB, Michaels KC, Anderson CJ, Fay JM, Dokholyan NV. Corrigendum: Harnessing Nature’s Diversity: Discovering organophosphate bioscavenger characteristics among low molecular weight proteins. Sci Rep 2017 02 7:42832 PMID: 28211477 (erratum 27845442) DOI: 10.1038/srep42832

Lakhani V, Elston TC. Testing the limits of gradient sensing. PLoS Comput Biol 2017 02 13:e1005386 PMID: 28207738 DOI: 10.1371/journal.pcbi.1005386

Yamane D, Selitsky SR, Shimakami T, Li Y, Zhou M, Honda M, Sethupathy P, Lemon SM. Differential hepatitis C virus RNA target site selection and host factor activities of naturally occurring miR-122 3΄ variants. Nucleic Acids Res 2017 05 45:4743-4755 PMID: 28082397 DOI: 10.1093/nar/gkw1332

Quach B, Furey TS. DeFCoM: analysis and modeling of transcription factor binding sites using a motif-centric genomic footprinter. Bioinformatics 2017 04 33:956-963 PMID: 27993786 DOI: 10.1093/bioinformatics/btw740

Kutchko KM, Laederach A. Transcending the prediction paradigm: novel applications of SHAPE to RNA function and evolution. Wiley Interdiscip Rev RNA 2017 01 8: PMID: 27396578 DOI: 10.1002/wrna.1374

2016

Stanley N, Shai S, Taylor D, Mucha PJ. Clustering network layers with the strata multilayer stochastic block model. IEEE Trans Netw Sci Eng 2016 Apr 3:95-105 PMID: 28435844 DOI: 10.1109/TNSE.2016.2537545

Jones SK, Yun YJ, Hedrick TL, Griffith BE, Miller LA. Bristles reduce the force required to ‘fling’ wings apart in the smallest insects. J Exp Biol 2016 12 219:3759-3772 PMID: 27903629 DOI:

Jacob RB, Michaels KC, Anderson CJ, Fay JM, Dokholyan NV. Harnessing Nature’s Diversity: Discovering organophosphate bioscavenger characteristics among low molecular weight proteins. Sci Rep 2016 11 6:37175 PMID: 27845442 (erratum 28211477) DOI: 10.1038/srep37175

Schoenrock SA, Oreper D, Young N, Ervin RB, Bogue MA, Valdar W, Tarantino LM. Ovariectomy results in inbred strain-specific increases in anxiety-like behavior in mice. Physiol Behav 2016 12 167:404-412 PMID: 27693591 DOI: 10.1016/j.physbeh.2016.09.026

Morgan AP, Didion JP, Doran AG, Holt JM, McMillan L, Keane TM, de Villena FP. Whole Genome Sequence of Two Wild-Derived Mus musculus domesticus Inbred Strains, LEWES/EiJ and ZALENDE/EiJ, with Different Diploid Numbers. G3 (Bethesda) 2016 12 6:4211-4216 PMID: 27765810 DOI: 10.1534/g3.116.034751

Kardos J, Chai S, Mose LE, Selitsky SR, Krishnan B, Saito R, Iglesia MD, Milowsky MI, Parker JS, Kim WY, Vincent BG. Claudin-low bladder tumors are immune infiltrated and actively immune suppressed. JCI Insight 2016 03 1:e85902 PMID: 27699256 (erratum 29539894) DOI: 85902

Mose LE, Selitsky SR, Bixby LM, Marron DL, Iglesia MD, Serody JS, Perou CM, Vincent BG, Parker JS. Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V’DJer. Bioinformatics 2016 12 32:3729-3734 PMID: 27559159 DOI:

Baran-Gale J, Purvis JE, Sethupathy P. An integrative transcriptomics approach identifies miR-503 as a candidate master regulator of the estrogen response in MCF-7 breast cancer cells. RNA 2016 10 22:1592-603 PMID: 27539783 DOI: 10.1261/rna.056895.116

Morgan AP, Holt JM, McMullan RC, Bell TA, Clayshulte AM, Didion JP, Yadgary L, Thybert D, Odom DT, Flicek P, McMillan L, de Villena FP. The Evolutionary Fates of a Large Segmental Duplication in Mouse. Genetics 2016 Sep 204:267-85 PMID: 27371833 DOI: 10.1534/genetics.116.191007

Dominguez D, Tsai YH, Gomez N, Jha DK, Davis I, Wang Z. A high-resolution transcriptome map of cell cycle reveals novel connections between periodic genes and cancer. Cell Res 2016 08 26:946-62 PMID: 27364684 DOI: 10.1038/cr.2016.84

Taylor D, Shai S, Stanley N, Mucha PJ. Enhanced Detectability of Community Structure in Multilayer Networks through Layer Aggregation. Phys Rev Lett 2016 Jun 116:228301 PMID: 27314740 DOI: 10.1103/PhysRevLett.116.228301

Simon JM, Davis JP, Lee SE, Schaner MR, Gipson GR, Weiser M, Sartor RB, Herfarth HH, Rahbar R, Sadiq TS, Koruda MJ, McGovern DP, Lieb JD, Mohlke KL, Furey TS, Sheikh SZ. Alterations to chromatin in intestinal macrophages link IL-10 deficiency to inappropriate inflammatory responses. Eur J Immunol 2016 08 46:1912-25 PMID: 27159132 (erratum 27518699) DOI: 10.1002/eji.201546237

Xu Z, Zhang G, Wu C, Li Y, Hu M. FastHiC: a fast and accurate algorithm to detect long-range chromosomal interactions from Hi-C data. Bioinformatics 2016 09 32:2692-5 PMID: 27153668 DOI: 10.1093/bioinformatics/btw240

Zhang G, Huang KC, Xu Z, Tzeng JY, Conneely KN, Guan W, Kang J, Li Y. Across-Platform Imputation of DNA Methylation Levels Incorporating Nonlocal Information Using Penalized Functional Regression. Genet Epidemiol 2016 May 40:333-40 PMID: 27061717 DOI: 10.1002/gepi.21969

Dominguez D, Tsai YH, Weatheritt R, Wang Y, Blencowe BJ, Wang Z. An extensive program of periodic alternative splicing linked to cell cycle progression. Elife 2016 03 5: PMID: 27015110 DOI: e10288

Xu Z, Zhang G, Duan Q, Chai S, Zhang B, Wu C, Jin F, Yue F, Li Y, Hu M. HiView: an integrative genome browser to leverage Hi-C results for the interpretation of GWAS variants. BMC Res Notes 2016 Mar 9:159 PMID: 26969411 DOI: 10.1186/s13104-016-1947-0

Zhao W, Hoadley KA, Parker JS, Perou CM. Identification of mRNA isoform switching in breast cancer. BMC Genomics 2016 Mar 17:181 PMID: 26939613 DOI: 10.1186/s12864-016-2521-9

Didion JP, Morgan AP, Yadgary L, Bell TA, McMullan RC, Ortiz de Solorzano L, Britton-Davidian J, Bult CJ, Campbell KJ, Castiglia R, Ching YH, Chunco AJ, Crowley JJ, Chesler EJ, Förster DW, French JE, Gabriel SI, Gatti DM, Garland T, Giagia-Athanasopoulou EB, Giménez MD, Grize SA, Gündüz İ, Holmes A, Hauffe HC, Herman JS, Holt JM, Hua K, Jolley WJ, Lindholm AK, López-Fuster MJ, Mitsainas G, da Luz Mathias M, McMillan L, Ramalhinho Mda G, Rehermann B, Rosshart SP, Searle JB, Shiao MS, Solano E, Svenson KL, Thomas-Laemont P, Threadgill DW, Ventura J, Weinstock GM, Pomp D, Churchill GA, Pardo-Manuel de Villena F. R2d2 Drives Selfish Sweeps in the House Mouse. Mol Biol Evol 2016 06 33:1381-95 PMID: 26882987 DOI: 10.1093/molbev/msw036

Chappell G, Silva GO, Uehara T, Pogribny IP, Rusyn I. Characterization of copy number alterations in a mouse model of fibrosis-associated hepatocellular carcinoma reveals concordance with human disease. Cancer Med 2016 Mar 5:574-85 PMID: 26778414 DOI: 10.1002/cam4.606

Swahari V, Nakamura A, Baran-Gale J, Garcia I, Crowther AJ, Sons R, Gershon TR, Hammond S, Sethupathy P, Deshmukh M. Essential Function of Dicer in Resolving DNA Damage in the Rapidly Dividing Cells of the Developing and Malignant Cerebellum. Cell Rep 2016 Jan 14:216-24 PMID: 26748703 DOI: S2211-1247(15)01461-8

Proctor EA, Fee L, Tao Y, Redler RL, Fay JM, Zhang Y, Lv Z, Mercer IP, Deshmukh M, Lyubchenko YL, Dokholyan NV. Nonnative SOD1 trimer is toxic to motor neurons in a model of amyotrophic lateral sclerosis. Proc Natl Acad Sci U S A 2016 Jan 113:614-9 PMID: 26719414 DOI: 10.1073/pnas.1516725113

Xu Z, Zhang G, Jin F, Chen M, Furey TS, Sullivan PF, Qin Z, Hu M, Li Y. A hidden Markov random field-based Bayesian method for the detection of long-range chromosomal interactions in Hi-C data. Bioinformatics 2016 03 32:650-6 PMID: 26543175 DOI: 10.1093/bioinformatics/btv650

2015

Baran-Gale J, Kurtz CL, Erdos MR, Sison C, Young A, Fannin EE, Chines PS, Sethupathy P. Addressing Bias in Small RNA Library Preparation for Sequencing: A New Protocol Recovers MicroRNAs that Evade Capture by Current Methods. Front Genet 2015 6:352 PMID: 26734062 DOI: 10.3389/fgene.2015.00352

Morgan AP, Fu CP, Kao CY, Welsh CE, Didion JP, Yadgary L, Hyacinth L, Ferris MT, Bell TA, Miller DR, Giusti-Rodriguez P, Nonneman RJ, Cook KD, Whitmire JK, Gralinski LE, Keller M, Attie AD, Churchill GA, Petkov P, Sullivan PF, Brennan JR, McMillan L, Pardo-Manuel de Villena F. The Mouse Universal Genotyping Array: From Substrains to Subspecies. G3 (Bethesda) 2015 Dec 6:263-79 PMID: 26684931 DOI: 10.1534/g3.115.022087

Selitsky SR, Dinh TA, Toth CL, Kurtz CL, Honda M, Struck BR, Kaneko S, Vickers KC, Lemon SM, Sethupathy P. Transcriptomic Analysis of Chronic Hepatitis B and C and Liver Cancer Reveals MicroRNA-Mediated Control of Cholesterol Synthesis Programs. mBio 2015 Dec 6:e01500-15 PMID: 26646011 DOI: e01500-15

Roman TS, Marvelle AF, Fogarty MP, Vadlamudi S, Gonzalez AJ, Buchkovich ML, Huyghe JR, Fuchsberger C, Jackson AU, Wu Y, Civelek M, Lusis AJ, Gaulton KJ, Sethupathy P, Kangas AJ, Soininen P, Ala-Korpela M, Kuusisto J, Collins FS, Laakso M, Boehnke M, Mohlke KL. Multiple Hepatic Regulatory Variants at the GALNT2 GWAS Locus Associated with High-Density Lipoprotein Cholesterol. Am J Hum Genet 2015 Dec 97:801-15 PMID: 26637976 DOI: S0002-9297(15)00442-5

Lakhani VV, Hinde E, Gratton E, Elston TC. Spatio-Temporal Regulation of Rac1 Mobility by Actin Islands. PLoS One 2015 10:e0143753 PMID: 26606145 DOI: 10.1371/journal.pone.0143753

Selitsky SR, Sethupathy P. tDRmapper: challenges and solutions to mapping, naming, and quantifying tRNA-derived RNAs from human small RNA-sequencing data. BMC Bioinformatics 2015 Nov 16:354 PMID: 26530785 DOI: 10.1186/s12859-015-0800-0

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 142:4288-98 PMID: 26493402 DOI: 10.1242/dev.115006

Oikawa T, Wauthier E, Dinh TA, Selitsky SR, Reyna-Neyra A, Carpino G, Levine R, Cardinale V, Klimstra D, Gaudio E, Alvaro D, Carrasco N, Sethupathy P, Reid LM. Model of fibrolamellar hepatocellular carcinomas reveals striking enrichment in cancer stem cells. Nat Commun 2015 Oct 6:8070 PMID: 26437858 (erratum 26503883) DOI: 10.1038/ncomms9070

Simon JM, Parker JS, Liu F, Rothbart SB, Ait-Si-Ali S, Strahl BD, Jin J, Davis IJ, Mosley AL, Pattenden SG. A Role for Widely Interspaced Zinc Finger (WIZ) in Retention of the G9a Methyltransferase on Chromatin. J Biol Chem 2015 Oct 290:26088-102 PMID: 26338712 DOI: 10.1074/jbc.M115.654459

Venkatapurapu SP, Kelley JB, Dixit G, Pena M, Errede B, Dohlman HG, Elston TC. Modulation of receptor dynamics by the regulator of G protein signaling Sst2. Mol Biol Cell 2015 Nov 26:4124-34 PMID: 26310439 DOI: 10.1091/mbc.E14-12-1635

Rutledge H, Baran-Gale J, de Villena FP, Chesler EJ, Churchill GA, Sethupathy P, Kelada SN. Identification of microRNAs associated with allergic airway disease using a genetically diverse mouse population. BMC Genomics 2015 Aug 16:633 PMID: 26303911 DOI: 10.1186/s12864-015-1732-9

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 Dev 2015 Aug 29:1734-46 PMID: 26272819 DOI: 10.1101/gad.263731.115

Lebeis SL, Paredes SH, Lundberg DS, Breakfield N, Gehring J, McDonald M, Malfatti S, Glavina del Rio T, Jones CD, Tringe SG, Dangl JL. PLANT MICROBIOME. Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Science 2015 Aug 349:860-4 PMID: 26184915 (erratum 26293938) DOI: 10.1126/science.aaa8764

Peck BC, Weiser M, Lee SE, Gipson GR, Iyer VB, Sartor RB, Herfarth HH, Long MD, Hansen JJ, Isaacs KL, Trembath DG, Rahbar R, Sadiq TS, Furey TS, Sethupathy P, Sheikh SZ. MicroRNAs Classify Different Disease Behavior Phenotypes of Crohn’s Disease and May Have Prognostic Utility. Inflamm Bowel Dis 2015 Sep 21:2178-87 PMID: 26164662 DOI: 10.1097/MIB.0000000000000478

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 Jun 47:690 PMID: 26018903 (erratum 25730764) DOI: 10.1038/ng0615-690a

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 21:1274-85 PMID: 25999316 DOI: 10.1261/rna.049221.114

Xu Z, Duan Q, Yan S, Chen W, Li M, Lange E, Li Y. DISSCO: direct imputation of summary statistics allowing covariates. Bioinformatics 2015 Aug 31:2434-42 PMID: 25810429 DOI: 10.1093/bioinformatics/btv168

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 16:113 PMID: 25765044 DOI: 10.1186/s12864-015-1227-8

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 47:353-60 PMID: 25730764 (erratum 26018903) DOI: 10.1038/ng.3222

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 6:1237-1246 PMID: 25685315 DOI:

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, 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 11:e1004850 PMID: 25679959 DOI: 10.1371/journal.pgen.1004850

Chandler RL, Damrauer JS, Raab JR, Schisler JC, Wilkerson MD, Didion JP, Starmer J, Serber D, Yee D, Xiong J, Darr DB, Pardo-Manuel de Villena F, Kim WY, Magnuson T. Coexistent ARID1A-PIK3CA mutations promote ovarian clear-cell tumorigenesis through pro-tumorigenic inflammatory cytokine signalling. Nat Commun 2015 Jan 6:6118 PMID: 25625625 DOI: 10.1038/ncomms7118

Corley M, Solem A, Qu K, Chang HY, Laederach A. Detecting riboSNitches with RNA folding algorithms: a genome-wide benchmark. Nucleic Acids Res 2015 Feb 43:1859-68 PMID: 25618847 DOI: 10.1093/nar/gkv010

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 Aug 28:1031-7 PMID: 25618516 DOI: 10.1093/ajh/hpu263

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 25:275-285 PMID: 25601550 DOI: 10.1016/j.cub.2014.11.047

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 8:ra5 PMID: 25587192 DOI: 10.1126/scisignal.2005774

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 5:7675 PMID: 25567797 DOI: 10.1038/srep07675

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 9:e115225 PMID: 25506936 DOI: 10.1371/journal.pone.0115225

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 107:1620-8 PMID: 25296314 DOI: S0006-3495(14)00840-6

Weiser M, Mukherjee S, Furey TS. Novel distal eQTL analysis demonstrates effect of population genetic architecture on detecting and interpreting associations. Genetics 2014 Nov 198:879-93 PMID: 25230953 DOI: 10.1534/genetics.114.167791

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 46:1051-9 PMID: 25151356 DOI: 10.1038/ng.3073

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

Mellnik J, Vasquez PA, McKinley SA, Witten J, Hill DB, Forest MG. Micro-heterogeneity metrics for diffusion in soft matter. Soft Matter 2014 Oct 10:7781-96 PMID: 25144347 DOI: 10.1039/c4sm00676c

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 74:6486-6498 PMID: 25115300 DOI: 10.1158/0008-5472.CAN-14-0061

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 426:4112-4124 PMID: 25083917 DOI: 10.1016/j.jmb.2014.07.016

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 15:419 PMID: 24888378 DOI: 10.1186/1471-2164-15-419

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 197:91-106 PMID: 24578350 DOI: 10.1534/genetics.114.161653

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 25:95-108 PMID: 24487921 DOI: 10.1007/s00335-013-9499-2

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:e1003807 PMID: 24391493 DOI: 10.1371/journal.ppat.1003807

2013

Kutchko KM, Fröhlich F. Emergence of metastable state dynamics in interconnected cortical networks with propagation delays. PLoS Comput Biol 2013 Oct 9:e1003304 PMID: 24204238 DOI: 10.1371/journal.pcbi.1003304

Calaway JD, Lenarcic AB, Didion JP, Wang JR, Searle JB, McMillan L, Valdar W, Pardo-Manuel de Villena F. Genetic architecture of skewed X inactivation in the laboratory mouse. PLoS Genet 2013 9:e1003853 PMID: 24098153 DOI: 10.1371/journal.pgen.1003853

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 8:e73240 PMID: 24039891 DOI: 10.1371/journal.pone.0073240

Proctor EA, Kota P, Demarest SJ, Caravella JA, Dokholyan NV. Highly covarying residues have a functional role in antibody constant domains. Proteins 2013 May 81:884-95 PMID: 23280585 DOI: 10.1002/prot.24247

Prat A, Cheang MC, Martín M, Parker JS, Carrasco E, Caballero R, Tyldesley S, Gelmon K, Bernard PS, Nielsen TO, Perou CM. Prognostic significance of progesterone receptor-positive tumor cells within immunohistochemically defined luminal A breast cancer. J Clin Oncol 2013 Jan 31:203-9 PMID: 23233704 (erratum 23690409) DOI: 10.1200/JCO.2012.43.4134

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 425:475-8 PMID: 23219465 DOI: S0022-2836(12)00903-5

Paredes SH, Melgar MF, Sethupathy P. Promoter-proximal CCCTC-factor binding is associated with an increase in the transcriptional pausing index. Bioinformatics 2013 Jun 29:1485-7 PMID: 23047559 DOI: 10.1093/bioinformatics/bts596

2012

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:e51719 PMID: 23284754 DOI: 10.1371/journal.pone.0051719

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 489:75-82 PMID: 22955617 (erratum 22955793) DOI: 10.1038/nature11232

Cabanski CR, Cavin K, Bizon C, Wilkerson MD, Parker JS, Wilhelmsen KC, Perou CM, Marron JS, Hayes DN. ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data. BMC Bioinformatics 2012 Sep 13:221 PMID: 22946927 DOI:

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 488:86-90 PMID: 22859206 DOI: 10.1038/nature11237

Chia SK, Bramwell VH, Tu D, Shepherd LE, Jiang S, Vickery T, Mardis E, Leung S, Ung K, Pritchard KI, Parker JS, Bernard PS, Perou CM, Ellis MJ, Nielsen TO. A 50-gene intrinsic subtype classifier for prognosis and prediction of benefit from adjuvant tamoxifen. Clin Cancer Res 2012 Aug 18:4465-72 PMID: 22711706 DOI:

Cheang MC, Voduc KD, Tu D, Jiang S, Leung S, Chia SK, Shepherd LE, Levine MN, Pritchard KI, Davies S, Stijleman IJ, Davis C, Ebbert MT, Parker JS, Ellis MJ, Bernard PS, Perou CM, Nielsen TO. Responsiveness of intrinsic subtypes to adjuvant anthracycline substitution in the NCIC.CTG MA.5 randomized trial. Clin Cancer Res 2012 Apr 18:2402-12 PMID: 22351696 DOI: 10.1158/1078-0432.CCR-11-2956

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

Proctor EA, Yin S, Tropsha A, Dokholyan NV. Discrete molecular dynamics distinguishes nativelike binding poses from decoys in difficult targets. Biophys J 2012 Jan 102:144-51 PMID: 22225808 DOI: 10.1016/j.bpj.2011.11.4008

Weigman VJ, Chao HH, Shabalin AA, He X, Parker JS, Nordgard SH, Grushko T, Huo D, Nwachukwu C, Nobel A, Kristensen VN, Børresen-Dale AL, Olopade OI, Perou CM. Basal-like Breast cancer DNA copy number losses identify genes involved in genomic instability, response to therapy, and patient survival. Breast Cancer Res Treat 2012 Jun 133:865-80 PMID: 22048815 DOI: 10.1007/s10549-011-1846-y

Harrell JC, Prat A, Parker JS, Fan C, He X, Carey L, Anders C, Ewend M, Perou CM. Genomic analysis identifies unique signatures predictive of brain, lung, and liver relapse. Breast Cancer Res Treat 2012 Apr 132:523-35 PMID: 21671017 DOI: 10.1007/s10549-011-1619-7

2011

Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, Lee BK, Sheffield NC, Gräf S, Huss M, Keefe D, Liu Z, London D, McDaniell RM, Shibata Y, Showers KA, Simon JM, Vales T, Wang T, Winter D, Zhang Z, Clarke ND, Birney E, Iyer VR, Crawford GE, Lieb JD, Furey TS. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res 2011 Oct 21:1757-67 PMID: 21750106 DOI: 10.1101/gr.121541.111

Dunbier AK, Anderson H, Ghazoui Z, Salter J, Parker JS, Perou CM, Smith IE, Dowsett M. Association between breast cancer subtypes and response to neoadjuvant anastrozole. Steroids 2011 Jul 76:736-40 PMID: 21447351 DOI: 10.1016/j.steroids.2011.02.025

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

Fan C, Prat A, Parker JS, Liu Y, Carey LA, Troester MA, Perou CM. Building prognostic models for breast cancer patients using clinical variables and hundreds of gene expression signatures. BMC Med Genomics 2011 Jan 4:3 PMID: 21214954 DOI: 10.1186/1755-8794-4-3

Anders CK, Fan C, Parker JS, Carey LA, Blackwell KL, Klauber-DeMore N, Perou CM. Breast carcinomas arising at a young age: unique biology or a surrogate for aggressive intrinsic subtypes? J Clin Oncol 2011 Jan 29:e18-20 PMID: 21115855 DOI: 10.1200/JCO.2010.28.9199

2010

Thorner AR, Parker JS, Hoadley KA, Perou CM. Potential tumor suppressor role for the c-Myb oncogene in luminal breast cancer. PLoS One 2010 Oct 5:e13073 PMID: 20949095 DOI: e13073

Nielsen TO, Parker JS, Leung S, Voduc D, Ebbert M, Vickery T, Davies SR, Snider J, Stijleman IJ, Reed J, Cheang MC, Mardis ER, Perou CM, Bernard PS, Ellis MJ. A comparison of PAM50 intrinsic subtyping with immunohistochemistry and clinical prognostic factors in tamoxifen-treated estrogen receptor-positive breast cancer. Clin Cancer Res 2010 Nov 16:5222-32 PMID: 20837693 DOI: 10.1158/1078-0432.CCR-10-1282

Prat A, Parker JS, Karginova O, Fan C, Livasy C, Herschkowitz JI, He X, Perou CM. Phenotypic and molecular characterization of the claudin-low intrinsic subtype of breast cancer. Breast Cancer Res 2010 12:R68 PMID: 20813035 DOI: 10.1186/bcr2635

Perou CM, Parker JS, Prat A, Ellis MJ, Bernard PS. Clinical implementation of the intrinsic subtypes of breast cancer. Lancet Oncol 2010 Aug 11:718-9; author reply 720-1 PMID: 20688274 (erratum 20181526) DOI: 10.1016/S1470-2045(10)70176-5

Doolittle JM, Gomez SM. Structural similarity-based predictions of protein interactions between HIV-1 and Homo sapiens. Virol J 2010 Apr 7:82 PMID: 20426868 DOI: 10.1186/1743-422X-7-82

Dunbier AK, Anderson H, Ghazoui Z, Folkerd EJ, A’hern R, Crowder RJ, Hoog J, Smith IE, Osin P, Nerurkar A, Parker JS, Perou CM, Ellis MJ, Dowsett M. Relationship between plasma estradiol levels and estrogen-responsive gene expression in estrogen receptor-positive breast cancer in postmenopausal women. J Clin Oncol 2010 Mar 28:1161-7 PMID: 20124184 DOI: 10.1200/JCO.2009.23.9616

2009

Bild AH, Parker JS, Gustafson AM, Acharya CR, Hoadley KA, Anders C, Marcom PK, Carey LA, Potti A, Nevins JR, Perou CM. An integration of complementary strategies for gene-expression analysis to reveal novel therapeutic opportunities for breast cancer. Breast Cancer Res 2009 11:R55 PMID: 19638211 DOI: 10.1186/bcr2344

Cheang MC, Chia SK, Voduc D, Gao D, Leung S, Snider J, Watson M, Davies S, Bernard PS, Parker JS, Perou CM, Ellis MJ, Nielsen TO. Ki67 index, HER2 status, and prognosis of patients with luminal B breast cancer. J Natl Cancer Inst 2009 May 101:736-50 PMID: 19436038 (erratum 19893007) DOI: 10.1093/jnci/djp082

Crowder RJ, Phommaly C, Tao Y, Hoog J, Luo J, Perou CM, Parker JS, Miller MA, Huntsman DG, Lin L, Snider J, Davies SR, Olson JA, Watson MA, Saporita A, Weber JD, Ellis MJ. PIK3CA and PIK3CB inhibition produce synthetic lethality when combined with estrogen deprivation in estrogen receptor-positive breast cancer. Cancer Res 2009 May 69:3955-62 PMID: 19366795 DOI: 10.1158/0008-5472.CAN-08-4450

Parker JS, Mullins M, Cheang MC, Leung S, Voduc D, Vickery T, Davies S, Fauron C, He X, Hu Z, Quackenbush JF, Stijleman IJ, Palazzo J, Marron JS, Nobel AB, Mardis E, Nielsen TO, Ellis MJ, Perou CM, Bernard PS. Supervised risk predictor of breast cancer based on intrinsic subtypes. J Clin Oncol 2009 Mar 27:1160-7 PMID: 19204204 (erratum 19204193) DOI: 10.1200/JCO.2008.18.1370

2007

Mullins M, Perreard L, Quackenbush JF, Gauthier N, Bayer S, Ellis M, Parker J, Perou CM, Szabo A, Bernard PS. Agreement in breast cancer classification between microarray and quantitative reverse transcription PCR from fresh-frozen and formalin-fixed, paraffin-embedded tissues. Clin Chem 2007 Jul 53:1273-9 PMID: 17525107 DOI: