Kim MC, Borcherding N, Ahmed KK, Voigt AP, Vishwakarma A, Kolb R, Kluz PN, Pandey G, De U, Drashansky T, Helm EY, Zhang X, Gibson-Corley KN, Klesney-Tait J, Zhu Y, Lu J, Lu J, Huang X, Xiang H, Cheng J, Wang D, Wang Z, Tang J, Hu J, Wang Z, Liu H, Li M, Zhuang H, Avram D, Zhou D, Bacher R, Zheng SG, Wu X, Zakharia Y, Zhang W. CD177 modulates the function and homeostasis of tumor-infiltrating regulatory T cells. Nat Commun. 2021 10 01; 12(1):5764.

El-Sheikh Ali H, Loux SC, Kennedy L, Scoggin KE, Dini P, Fedorka CE, Kalbfleisch TS, Esteller-Vico A, Horohov DW, Erol E, Carter CN, Smith JL, Ball BA. Transcriptomic analysis of equine chorioallantois reveals immune networks and molecular mechanisms involved in nocardioform placentitis. Vet Res. 2021 Jul 08; 52(1):103.

Pasetto A, Lu YC. Single-Cell TCR and Transcriptome Analysis: An Indispensable Tool for Studying T-Cell Biology and Cancer Immunotherapy. Front Immunol. 2021; 12:689091.

Kunadirek P, Ariyachet C, Sriphoosanaphan S, Pinjaroen N, Sirichindakul P, Nookaew I, Chuaypen N, Tangkijvanich P. Identification of BHLHE40 expression in peripheral blood mononuclear cells as a novel biomarker for diagnosis and prognosis of hepatocellular carcinoma. Sci Rep. 2021 05 27; 11(1):11201.

Rhone ET, Bardhi E, Bontha SV, Walker PD, Almenara JA, Dumur CI, Cathro H, Maluf D, Mas V. An Integrated Transcriptomic Approach to Identify Molecular Markers of Calcineurin Inhibitor Nephrotoxicity in Pediatric Kidney Transplant Recipients. Int J Mol Sci. 2021 May 21; 22(11).

Fan H, Guo Y, Tsai YH, Storey AJ, Kim A, Gong W, Edmondson RD, Mackintosh SG, Li H, Byrum SD, Tackett AJ, Cai L, Wang GG. A conserved BAH module within mammalian BAHD1 connects H3K27me3 to Polycomb gene silencing. Nucleic Acids Res. 2021 05 07; 49(8):4441-4455.

Scheid JF, Barnes CO, Eraslan B, Hudak A, Keeffe JR, Cosimi LA, Brown EM, Muecksch F, Weisblum Y, Zhang S, Delorey T, Woolley AE, Ghantous F, Park SM, Phillips D, Tusi B, Huey-Tubman KE, Cohen AA, Gnanapragasam PNP, Rzasa K, Hatziioanno T, Durney MA, Gu X, Tada T, Landau NR, West AP, Rozenblatt-Rosen O, Seaman MS, Baden LR, Graham DB, Deguine J, Bieniasz PD, Regev A, Hung D, Bjorkman PJ, Xavier RJ. B cell genomics behind cross-neutralization of SARS-CoV-2 variants and SARS-CoV. Cell. 2021 06 10; 184(12):3205-3221.e24.

Manjang K, Tripathi S, Yli-Harja O, Dehmer M, Glazko G, Emmert-Streib F. Prognostic gene expression signatures of breast cancer are lacking a sensible biological meaning. Sci Rep. 2021 01 08; 11(1):156.

Mohan M, Yarlagadda N, Szabo A, Singh A, Pina Oviedo S, Schinke C. Clinical characteristics of testicular extramedullary involvement in multiple myeloma. Am J Hematol. 2021 03 01; 96(3):E77-E81.

Wang R, Dang M, Harada K, Han G, Wang F, Pool Pizzi M, Zhao M, Tatlonghari G, Zhang S, Hao D, Lu Y, Zhao S, Badgwell BD, Blum Murphy M, Shanbhag N, Estrella JS, Roy-Chowdhuri S, Abdelhakeem AAF, Wang Y, Peng G, Hanash S, Calin GA, Song X, Chu Y, Zhang J, Li M, Chen K, Lazar AJ, Futreal A, Song S, Ajani JA, Wang L. Single-cell dissection of intratumoral heterogeneity and lineage diversity in metastatic gastric adenocarcinoma. Nat Med. 2021 01; 27(1):141-151.

Chen J, Goyal N, Dai L, Lin Z, Del Valle L, Zabaleta J, Liu J, Post SR, Foroozesh M, Qin Z. Developing new ceramide analogs and identifying novel sphingolipid-controlled genes against a virus-associated lymphoma. Blood. 2020 11 05; 136(19):2175-2187.

Boyd DF, Allen EK, Randolph AG, Guo XJ, Weng Y, Sanders CJ, Bajracharya R, Lee NK, Guy CS, Vogel P, Guan W, Li Y, Liu X, Novak T, Newhams MM, Fabrizio TP, Wohlgemuth N, Mourani PM, Wight TN, Schultz-Cherry S, Cormier SA, Shaw-Saliba K, Pekosz A, Rothman RE, Chen KF, Yang Z, Webby RJ, Zhong N, Crawford JC, Thomas PG. Exuberant fibroblast activity compromises lung function via ADAMTS4. Nature. 2020 11; 587(7834):466-471.

Kulkarni AS, Peck BD, Walton RG, Kern PA, Mar JC, Windham ST, Bamman MM, Barzilai N, Peterson CA. Metformin alters skeletal muscle transcriptome adaptations to resistance training in older adults. Aging (Albany NY). 2020 10 18; 12(20):19852-19866.

Åsenius F, Gorrie-Stone TJ, Brew A, Panchbhaya Y, Williamson E, Schalkwyk LC, Rakyan VK, Holland ML, Marzi SJ, Williams DJ. The DNA methylome of human sperm is distinct from blood with little evidence for tissue-consistent obesity associations. PLoS Genet. 2020 10; 16(10):e1009035.

Berglund A, Amankwah EK, Kim YC, Spiess PE, Sexton WJ, Manley B, Park HY, Wang L, Chahoud J, Chakrabarti R, Yeo CD, Luu HN, Pietro GD, Parker A, Park JY. Influence of gene expression on survival of clear cell renal cell carcinoma. Cancer Med. 2020 11; 9(22):8662-8675.

Batteiger TA, Spencer N, Washam CL, Byrum S, Eledge M, Batteiger BE, Rank RG, Yeruva L. Endocervical miRNA Expression Profiles in Women Positive for Chlamydia trachomatis with Clinical Signs and/or Symptoms Are Distinct from Those in Women Positive for Chlamydia trachomatis without Signs and Symptoms. Infect Immun. 2020 09 18; 88(10).

de Conti A, Tryndyak V, Heidor R, Jimenez L, Moreno FS, Beland FA, Rusyn I, Pogribny IP. Butyrate-containing structured lipids inhibit RAC1 and epithelial-to-mesenchymal transition markers: a chemopreventive mechanism against hepatocarcinogenesis. J Nutr Biochem. 2020 12; 86:108496.

Choudhury SR, Ashby C, Tytarenko R, Bauer M, Wang Y, Deshpande S, Den J, Schinke C, Zangari M, Thanendrarajan S, Davies FE, van Rhee F, Morgan GJ, Walker BA. The functional epigenetic landscape of aberrant gene expression in molecular subgroups of newly diagnosed multiple myeloma. J Hematol Oncol. 2020 08 06; 13(1):108.

Geistlinger L, Oh S, Ramos M, Schiffer L, LaRue RS, Henzler CM, Munro SA, Daughters C, Nelson AC, Winterhoff BJ, Chang Z, Talukdar S, Shetty M, Mullany SA, Morgan M, Parmigiani G, Birrer MJ, Qin LX, Riester M, Starr TK, Waldron L. Multiomic Analysis of Subtype Evolution and Heterogeneity in High-Grade Serous Ovarian Carcinoma. Cancer Res. 2020 10 15; 80(20):4335-4345.

Richard MA, Sok P, Canon S, Nembhard WN, Brown AL, Peckham-Gregory EC, Ton M, Ehli EA, Kallsen NA, Peyton SA, Davies GE, Patel A, Zamilpa I, Hobbs CA, Scheurer ME, Lupo PJ. Altered mechanisms of genital development identified through integration of DNA methylation and genomic measures in hypospadias. Sci Rep. 2020 07 29; 10(1):12715.

Kathuria A, Lopez-Lengowski K, Jagtap SS, McPhie D, Perlis RH, Cohen BM, Karmacharya R. Transcriptomic Landscape and Functional Characterization of Induced Pluripotent Stem Cell-Derived Cerebral Organoids in Schizophrenia. JAMA Psychiatry. 2020 07 01; 77(7):745-754.

Schinke C, Boyle EM, Ashby C, Wang Y, Lyzogubov V, Wardell C, Qu P, Hoering A, Deshpande S, Ryan K, Thanendrarajan S, Mohan M, Yarlagadda N, Khan M, Choudhury SR, Zangari M, van Rhee F, Davies F, Barlogie B, Morgan G, Walker BA. Genomic analysis of primary plasma cell leukemia reveals complex structural alterations and high-risk mutational patterns. Blood Cancer J. 2020 06 19; 10(6):70.

Zhao Y, Kang X, Barsegian A, He J, Guzman A, Lau RP, Biniwale R, Wadhra M, Reemtsen B, Garg M, Halnon N, Quintero-Rivera F, Grody WW, Van Arsdell G, Nelson SF, Touma M. Gene-environment regulation of chamber-specific maturation during hypoxemic perinatal circulatory transition. J Mol Med (Berl). 2020 07; 98(7):1009-1020.

Mazzu YZ, Armenia J, Nandakumar S, Chakraborty G, Yoshikawa Y, Jehane LE, Lee GM, Atiq M, Khan N, Schultz N, Kantoff PW. Ribonucleotide reductase small subunit M2 is a master driver of aggressive prostate cancer. Mol Oncol. 2020 08; 14(8):1881-1897.

Seidman JS, Troutman TD, Sakai M, Gola A, Spann NJ, Bennett H, Bruni CM, Ouyang Z, Li RZ, Sun X, Vu BT, Pasillas MP, Ego KM, Gosselin D, Link VM, Chong LW, Evans RM, Thompson BM, McDonald JG, Hosseini M, Witztum JL, Germain RN, Glass CK. Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis. Immunity. 2020 06 16; 52(6):1057-1074.e7.

Williams AE, Watt J, Robertson LW, Gadupudi G, Osborn ML, Soares MJ, Iqbal K, Pedersen KB, Shankar K, Littleton S, Maimone C, Eti NA, Suva LJ, Ronis MJJ. Skeletal Toxicity of Coplanar Polychlorinated Biphenyl Congener 126 in the Rat Is Aryl Hydrocarbon Receptor Dependent. Toxicol Sci. 2020 05 01; 175(1):113-125.

Fuscoe JC, Vijay V, Hanig JP, Han T, Ren L, Greenhaw JJ, Beger RD, Pence LM, Shi Q. Hepatic Transcript Profiles of Cytochrome P450 Genes Predict Sex Differences in Drug Metabolism. Drug Metab Dispos. 2020 06; 48(6):447-458.

Shah V, Sherborne AL, Johnson DC, Ellis S, Price A, Chowdhury F, Kendall J, Jenner MW, Drayson MT, Owen RG, Gregory WM, Morgan GJ, Davies FE, Cook G, Cairns DA, Houlston RS, Jackson G, Kaiser MF. Predicting ultrahigh risk multiple myeloma by molecular profiling: an analysis of newly diagnosed transplant eligible myeloma XI trial patients. Leukemia. 2020 11; 34(11):3091-3096.

Zhao X, Du W, Zhang M, Atiq ZO, Xia F. Sirt2-associated transcriptome modifications in cisplatin-induced neuronal injury. BMC Genomics. 2020 Mar 02; 21(1):192.

Gomez-Acevedo H, Dai Y, Strub G, Shawber C, Wu JK, Richter GT. Identification of putative biomarkers for Infantile Hemangiomas and Propranolol treatment via data integration. Sci Rep. 2020 02 24; 10(1):3261.

Sittikankaew K, Pootakham W, Sonthirod C, Sangsrakru D, Yoocha T, Khudet J, Nookaew I, Uawisetwathana U, Rungrassamee W, Karoonuthaisiri N. Transcriptome analyses reveal the synergistic effects of feeding and eyestalk ablation on ovarian maturation in black tiger shrimp. Sci Rep. 2020 02 24; 10(1):3239.

Bushel PR, Caiment F, Wu H, O'Lone R, Day F, Calley J, Smith A, Li J, Harrill AH. RATEmiRs: the rat atlas of tissue-specific and enriched miRNAs for discerning baseline expression exclusivity of candidate biomarkers. RNA Biol. 2020 05; 17(5):630-636.

Zhang Q. Testing Differential Gene Networks under Nonparanormal Graphical Models with False Discovery Rate Control. Genes (Basel). 2020 02 05; 11(2).

Ling L, Ren X, Cao X, Hassan ABM, Mah S, Sathiyanathan P, Smith RAA, Tan CLL, Eio M, Samsonraj RM, van Wijnen AJ, Raghunath M, Nurcombe V, Hui JH, Cool SM. Enhancing the Efficacy of Stem Cell Therapy with Glycosaminoglycans. Stem Cell Reports. 2020 01 14; 14(1):105-121.

Schwede M, Waldron L, Mok SC, Wei W, Basunia A, Merritt MA, Mitsiades CS, Parmigiani G, Harrington DP, Quackenbush J, Birrer MJ, Culhane AC. The Impact of Stroma Admixture on Molecular Subtypes and Prognostic Gene Signatures in Serous Ovarian Cancer. Cancer Epidemiol Biomarkers Prev. 2020 02; 29(2):509-519.

Woo CC, Liu W, Lin XY, Dorajoo R, Lee KW, Richards AM, Lee CN, Wongsurawat T, Nookaew I, Sorokin V. The interaction between 30b-5p miRNA and MBNL1 mRNA is involved in vascular smooth muscle cell differentiation in patients with coronary atherosclerosis. Int J Mol Sci. 2019 Dec 18; 21(1).

Zhao Y, Kang X, Gao F, Guzman A, Lau RP, Biniwale R, Wadehra M, Reemtsen B, Garg M, Halnon N, Quintero-Rivera F, Van Arsdell G, Coppola G, Nelson SF, Touma M. Gene-environment regulatory circuits of right ventricular pathology in tetralogy of fallot. J Mol Med (Berl). 2019 12; 97(12):1711-1722.

Smith JL, Ries RE, Hylkema T, Alonzo TA, Gerbing RB, Santaguida MT, Eidenschink Brodersen L, Pardo L, Cummings CL, Loeb KR, Le Q, Imren S, Leonti AR, Gamis AS, Aplenc R, Kolb EA, Farrar JE, Triche TJ, Nguyen C, Meerzaman D, Loken MR, Oehler VG, Bolouri H, Meshinchi S. Comprehensive Transcriptome Profiling of Cryptic CBFA2T3-GLIS2 Fusion-Positive AML Defines Novel Therapeutic Options: A COG and TARGET Pediatric AML Study. Clin Cancer Res. 2020 02 01; 26(3):726-737.

Lu YC, Jia L, Zheng Z, Tran E, Robbins PF, Rosenberg SA. Single-Cell Transcriptome Analysis Reveals Gene Signatures Associated with T-cell Persistence Following Adoptive Cell Therapy. Cancer Immunol Res. 2019 Nov; 7(11):1824-1836.

Byrum SD, Washam CL, Patterson JD, Vyas KK, Gilbert KM, Blossom SJ. Continuous Developmental and Early Life Trichloroethylene Exposure Promoted DNA Methylation Alterations in Polycomb Protein Binding Sites in Effector/Memory CD4+ T Cells. Front Immunol. 2019; 10:2016.

Went M, Kinnersley B, Sud A, Johnson DC, Weinhold N, Försti A, van Duin M, Orlando G, Mitchell JS, Kuiper R, Walker BA, Gregory WM, Hoffmann P, Jackson GH, Nöthen MM, da Silva Filho MI, Thomsen H, Broyl A, Davies FE, Thorsteinsdottir U, Hansson M, Kaiser M, Sonneveld P, Goldschmidt H, Stefansson K, Hemminki K, Nilsson B, Morgan GJ, Houlston RS. Transcriptome-wide association study of multiple myeloma identifies candidate susceptibility genes. Hum Genomics. 2019 08 20; 13(1):37.

Wang H, Diaz AK, Shaw TI, Li Y, Niu M, Cho JH, Paugh BS, Zhang Y, Sifford J, Bai B, Wu Z, Tan H, Zhou S, Hover LD, Tillman HS, Shirinifard A, Thiagarajan S, Sablauer A, Pagala V, High AA, Wang X, Li C, Baker SJ, Peng J. Deep multiomics profiling of brain tumors identifies signaling networks downstream of cancer driver genes. Nat Commun. 2019 08 16; 10(1):3718.

Li J, Rozwadowska N, Clark A, Fil D, Napierala JS, Napierala M. Excision of the expanded GAA repeats corrects cardiomyopathy phenotypes of iPSC-derived Friedreich's ataxia cardiomyocytes. Stem Cell Res. 2019 10; 40:101529.

Mousavian Z, Nowzari-Dalini A, Rahmatallah Y, Masoudi-Nejad A. Differential network analysis and protein-protein interaction study reveals active protein modules in glucocorticoid resistance for infant acute lymphoblastic leukemia. Mol Med. 2019 08 01; 25(1):36.

Munawar U, Rasche L, Müller N, Vogt C, Da-Via M, Haertle L, Arampatzi P, Dietrich S, Roth M, Garitano-Trojaola A, Steinhardt MJ, Strifler S, Gallardo M, Martinez-Lopez J, Bargou RC, Heckel T, Einsele H, Stühmer T, Kortüm KM, Barrio S. Hierarchy of mono- and biallelic TP53 alterations in multiple myeloma cell fitness. Blood. 2019 09 05; 134(10):836-840.

Wang R, Song S, Harada K, Ghazanfari Amlashi F, Badgwell B, Pizzi MP, Xu Y, Zhao W, Dong X, Jin J, Wang Y, Scott A, Ma L, Huo L, Vicente D, Blum Murphy M, Shanbhag N, Tatlonghari G, Thomas I, Rogers J, Kobayashi M, Vykoukal J, Estrella JS, Roy-Chowdhuri S, Han G, Zhang S, Mao X, Song X, Zhang J, Gu J, Johnson RL, Calin GA, Peng G, Lee JS, Hanash SM, Futreal A, Wang Z, Wang L, Ajani JA. Multiplex profiling of peritoneal metastases from gastric adenocarcinoma identified novel targets and molecular subtypes that predict treatment response. Gut. 2020 01; 69(1):18-31.

Maguire A, Chen X, Wisner L, Malasi S, Ramsower C, Kendrick S, Barrett MT, Glinsmann-Gibson B, McGrath M, Rimsza LM. Enhanced DNA repair and genomic stability identify a novel HIV-related diffuse large B-cell lymphoma signature. Int J Cancer. 2019 12 01; 145(11):3078-3088.

Thomas J, Kim HR, Rahmatallah Y, Wiggins G, Yang Q, Singh R, Glazko G, Mukherjee A. RNA-seq reveals differentially expressed genes in rice (Oryza sativa) roots during interactions with plant-growth promoting bacteria, Azospirillum brasilense. PLoS One. 2019; 14(5):e0217309.

Der E, Suryawanshi H, Morozov P, Kustagi M, Goilav B, Ranabothu S, Izmirly P, Clancy R, Belmont HM, Koenigsberg M, Mokrzycki M, Rominieki H, Graham JA, Rocca JP, Bornkamp N, Jordan N, Schulte E, Wu M, Pullman J, Slowikowski K, Raychaudhuri S, Guthridge J, James J, Buyon J, Tuschl T, Putterman C. Tubular cell and keratinocyte single-cell transcriptomics applied to lupus nephritis reveal type I IFN and fibrosis relevant pathways. Nat Immunol. 2019 07; 20(7):915-927.

Morris EM, Meers GME, Ruegsegger GN, Wankhade UD, Robinson T, Koch LG, Britton SL, Rector RS, Shankar K, Thyfault JP. Intrinsic High Aerobic Capacity in Male Rats Protects Against Diet-Induced Insulin Resistance. Endocrinology. 2019 05 01; 160(5):1179-1192.

Ewing LE, Skinner CM, Quick CM, Kennon-McGill S, McGill MR, Walker LA, ElSohly MA, Gurley BJ, Koturbash I. Hepatotoxicity of a Cannabidiol-Rich Cannabis Extract in the Mouse Model. Molecules. 2019 Apr 30; 24(9).

Shao L, Sottoriva K, Palasiewicz K, Zhang J, Hyun J, Soni SS, Paik NY, Gao X, Cuervo H, Malik AB, Rehman J, Lucas D, Pajcini KV. A Tie2-Notch1 signaling axis regulates regeneration of the endothelial bone marrow niche. Haematologica. 2019 11; 104(11):2164-2177.

West KL, Byrum SD, Mackintosh SG, Edmondson RD, Taverna SD, Tackett AJ. Proteomic characterization of the arsenic response locus in S. cerevisiae. Epigenetics. 2019 02; 14(2):130-145.

Stephens KE, Zhou W, Ji Z, Chen Z, He S, Ji H, Guan Y, Taverna SD. Sex differences in gene regulation in the dorsal root ganglion after nerve injury. BMC Genomics. 2019 Feb 19; 20(1):147.

Jones JR, Weinhold N, Ashby C, Walker BA, Wardell C, Pawlyn C, Rasche L, Melchor L, Cairns DA, Gregory WM, Johnson D, Begum DB, Ellis S, Sherborne AL, Cook G, Kaiser MF, Drayson MT, Owen RG, Jackson GH, Davies FE, Greaves M, Morgan GJ. Clonal evolution in myeloma: the impact of maintenance lenalidomide and depth of response on the genetics and sub-clonal structure of relapsed disease in uniformly treated newly diagnosed patients. Haematologica. 2019 07; 104(7):1440-1450.

Boyle WK, Groshong AM, Drecktrah D, Boylan JA, Gherardini FC, Blevins JS, Samuels DS, Bourret TJ. DksA Controls the Response of the Lyme Disease Spirochete Borrelia burgdorferi to Starvation. J Bacteriol. 2019 02 15; 201(4).

Cao M, Bandyopadhyay S, Zhu H, You H, Hermonat PL. The HPV16 E1 Carboxyl Domain Provides a Helper Function for Adeno-Associated Virus Replication. Intervirology. 2018; 61(4):185-192.

Joffre E, Nicklasson M, Álvarez-Carretero S, Xiao X, Sun L, Nookaew I, Zhu B, Sjöling Å. The bile salt glycocholate induces global changes in gene and protein expression and activates virulence in enterotoxigenic Escherichia coli. Sci Rep. 2019 01 14; 9(1):108.

Gu C, Jing X, Holman C, Sompallae R, Zhan F, Tricot G, Yang Y, Janz S. Upregulation of FOXM1 leads to diminished drug sensitivity in myeloma. BMC Cancer. 2018 Nov 21; 18(1):1152.

Stephens KE, Chen Z, Sivanesan E, Raja SN, Linderoth B, Taverna SD, Guan Y. RNA-seq of spinal cord from nerve-injured rats after spinal cord stimulation. Mol Pain. 2018 Jan-Dec; 14:1744806918817429.

Elias KM, Tsantoulis P, Tille JC, Vitonis A, Doyle LA, Hornick JL, Kaya G, Barnes L, Cramer DW, Puppa G, Stuckelberger S, Hooda J, Dietrich PY, Goggins M, Kerr CL, Birrer M, Hirsch MS, Drapkin R, Labidi-Galy SI. Primordial germ cells as a potential shared cell of origin for mucinous cystic neoplasms of the pancreas and mucinous ovarian tumors. J Pathol. 2018 12; 246(4):459-469.

Hao M, Barlogie B, Tricot G, Liu L, Qiu L, Shaughnessy JD, Zhan F. Gene Expression Profiling Reveals Aberrant T-cell Marker Expression on Tumor Cells of Waldenström's Macroglobulinemia. Clin Cancer Res. 2019 01 01; 25(1):201-209.

Skinner CM, Miousse IR, Ewing LE, Sridharan V, Cao M, Lin H, Williams DK, Avula B, Haider S, Chittiboyina AG, Khan IA, ElSohly MA, Boerma M, Gurley BJ, Koturbash I. Impact of obesity on the toxicity of a multi-ingredient dietary supplement, OxyELITE Pro™ (New Formula), using the novel NZO/HILtJ obese mouse model: Physiological and mechanistic assessments. Food Chem Toxicol. 2018 Dec; 122:21-32.

Bødker JS, Brøndum RF, Schmitz A, Schönherz AA, Jespersen DS, Sønderkær M, Vesteghem C, Due H, Nørgaard CH, Perez-Andres M, Samur MK, Davies F, Walker B, Pawlyn C, Kaiser M, Johnson D, Bertsch U, Broyl A, van Duin M, Shah R, Johansen P, Nørgaard MA, Samworth RJ, Sonneveld P, Goldschmidt H, Morgan GJ, Orfao A, Munshi N, Johnson HE, El-Galaly T, Dybkær K, Bøgsted M. A multiple myeloma classification system that associates normal B-cell subset phenotypes with prognosis. Blood Adv. 2018 09 25; 2(18):2400-2411.

Gomez-Acevedo H, Dornhoffer JR, Stone A, Dai Y, Richter GT. Gene Expression Differences in Pediatric Lymphatic Malformations: Size Really Matters. Lymphat Res Biol. 2018 08; 16(4):347-352.

Lu Y, Beeghly-Fadiel A, Wu L, Guo X, Li B, Schildkraut JM, Im HK, Chen YA, Permuth JB, Reid BM, Teer JK, Moysich KB, Andrulis IL, Anton-Culver H, Arun BK, Bandera EV, Barkardottir RB, Barnes DR, Benitez J, Bjorge L, Brenton J, Butzow R, Caldes T, Caligo MA, Campbell I, Chang-Claude J, Claes KBM, Couch FJ, Cramer DW, Daly MB, deFazio A, Dennis J, Diez O, Domchek SM, Dörk T, Easton DF, Eccles DM, Fasching PA, Fortner RT, Fountzilas G, Friedman E, Ganz PA, Garber J, Giles GG, Godwin AK, Goldgar DE, Goodman MT, Greene MH, Gronwald J, Hamann U, Heitz F, Hildebrandt MAT, Høgdall CK, Hollestelle A, Hulick PJ, Huntsman DG, Imyanitov EN, Isaacs C, Jakubowska A, James P, Karlan BY, Kelemen LE, Kiemeney LA, Kjaer SK, Kwong A, Le ND, Leslie G, Lesueur F, Levine DA, Mattiello A, May T, McGuffog L, McNeish IA, Merritt MA, Modugno F, Montagna M, Neuhausen SL, Nevanlinna H, Nielsen FC, Nikitina-Zake L, Nussbaum RL, Offit K, Olah E, Olopade OI, Olson SH, Olsson H, Osorio A, Park SK, Parsons MT, Peeters PHM, Pejovic T, Peterlongo P, Phelan CM, Pujana MA, Ramus SJ, Rennert G, Risch H, Rodriguez GC, Rodríguez-Antona C, Romieu I, Rookus MA, Rossing MA, Rzepecka IK, Sandler DP, Schmutzler RK, Setiawan VW, Sharma P, Sieh W, Simard J, Singer CF, Song H, Southey MC, Spurdle AB, Sutphen R, Swerdlow AJ, Teixeira MR, Teo SH, Thomassen M, Tischkowitz M, Toland AE, Trichopoulou A, Tung N, Tworoger SS, van Rensburg EJ, Vanderstichele A, Vega A, Edwards DV, Webb PM, Weitzel JN, Wentzensen N, White E, Wolk A, Wu AH, Yannoukakos D, Zorn KK, Gayther SA, Antoniou AC, Berchuck A, Goode EL, Chenevix-Trench G, Sellers TA, Pharoah PDP, Zheng W, Long J. A Transcriptome-Wide Association Study Among 97,898 Women to Identify Candidate Susceptibility Genes for Epithelial Ovarian Cancer Risk. Cancer Res. 2018 09 15; 78(18):5419-5430.

Hovelson DH, Udager AM, McDaniel AS, Grivas P, Palmbos P, Tamura S, Lazo de la Vega L, Palapattu G, Veeneman B, El-Sawy L, Sadis SE, Morgan TM, Montgomery JS, Weizer AZ, Day KC, Neamati N, Liebert M, Keller ET, Day ML, Mehra R, Tomlins SA. Targeted DNA and RNA Sequencing of Paired Urothelial and Squamous Bladder Cancers Reveals Discordant Genomic and Transcriptomic Events and Unique Therapeutic Implications. Eur Urol. 2018 12; 74(6):741-753.

Chen GM, Kannan L, Geistlinger L, Kofia V, Safikhani Z, Gendoo DMA, Parmigiani G, Birrer M, Haibe-Kains B, Waldron L. Consensus on Molecular Subtypes of High-Grade Serous Ovarian Carcinoma. Clin Cancer Res. 2018 10 15; 24(20):5037-5047.

Kuppa SS, Jia W, Liu S, Nguyen H, Smyth SS, Mills GB, Dobbin KK, Hardman WJ, Murph MM. Autotaxin exacerbates tumor progression by enhancing MEK1 and overriding the function of miR-489-3p. Cancer Lett. 2018 09 28; 432:84-92.

Derda AA, Woo CC, Wongsurawat T, Richards M, Lee CN, Kofidis T, Kuznetsov VA, Sorokin VA. Gene expression profile analysis of aortic vascular smooth muscle cells reveals upregulation of cadherin genes in myocardial infarction patients. Physiol Genomics. 2018 08 01; 50(8):648-657.

Zhang Q. A powerful nonparametric method for detecting differentially co-expressed genes: distance correlation screening and edge-count test. BMC Syst Biol. 2018 05 16; 12(1):58.

Musa A, Ghoraie LS, Zhang SD, Glazko G, Yli-Harja O, Dehmer M, Haibe-Kains B, Emmert-Streib F. A review of connectivity map and computational approaches in pharmacogenomics. Brief Bioinform. 2018 05 01; 19(3):506-523.

Ali M, Ajore R, Wihlborg AK, Niroula A, Swaminathan B, Johnsson E, Stephens OW, Morgan G, Meissner T, Turesson I, Goldschmidt H, Mellqvist UH, Gullberg U, Hansson M, Hemminki K, Nahi H, Waage A, Weinhold N, Nilsson B. The multiple myeloma risk allele at 5q15 lowers ELL2 expression and increases ribosomal gene expression. Nat Commun. 2018 04 25; 9(1):1649.

Berger AC, Korkut A, Kanchi RS, Hegde AM, Lenoir W, Liu W, Liu Y, Fan H, Shen H, Ravikumar V, Rao A, Schultz A, Li X, Sumazin P, Williams C, Mestdagh P, Gunaratne PH, Yau C, Bowlby R, Robertson AG, Tiezzi DG, Wang C, Cherniack AD, Godwin AK, Kuderer NM, Rader JS, Zuna RE, Sood AK, Lazar AJ, Ojesina AI, Adebamowo C, Adebamowo SN, Baggerly KA, Chen TW, Chiu HS, Lefever S, Liu L, MacKenzie K, Orsulic S, Roszik J, Shelley CS, Song Q, Vellano CP, Wentzensen N, Weinstein JN, Mills GB, Levine DA, Akbani R. A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers. Cancer Cell. 2018 04 09; 33(4):690-705.e9.

Schinke C, Qu P, Mehdi SJ, Hoering A, Epstein J, Johnson SK, van Rhee F, Zangari M, Thanendrarajan S, Barlogie B, Davies FE, Yaccoby S, Morgan GJ. The Pattern of Mesenchymal Stem Cell Expression Is an Independent Marker of Outcome in Multiple Myeloma. Clin Cancer Res. 2018 06 15; 24(12):2913-2919.

Kiffer F, Howe AK, Carr H, Wang J, Alexander T, Anderson JE, Groves T, Seawright JW, Sridharan V, Carter G, Boerma M, Allen AR. Late effects of 1H irradiation on hippocampal physiology. Life Sci Space Res (Amst). 2018 May; 17:51-62.

Roberts BS, Hardigan AA, Moore DE, Ramaker RC, Jones AL, Fitz-Gerald MB, Cooper GM, Wilcox CM, Kimberly RP, Myers RM. Discovery and Validation of Circulating Biomarkers of Colorectal Adenoma by High-Depth Small RNA Sequencing. Clin Cancer Res. 2018 05 01; 24(9):2092-2099.

Fok JHL, Hedayat S, Zhang L, Aronson LI, Mirabella F, Pawlyn C, Bright MD, Wardell CP, Keats JJ, De Billy E, Rye CS, Chessum NEA, Jones K, Morgan GJ, Eccles SA, Workman P, Davies FE. HSF1 Is Essential for Myeloma Cell Survival and A Promising Therapeutic Target. Clin Cancer Res. 2018 05 15; 24(10):2395-2407.

Mirkovic J, McFarland M, Garcia E, Sholl LM, Lindeman N, MacConaill L, Dong F, Hirsch M, Nucci MR, Quick CM, Crum CP, McCluggage WG, Howitt BE. Targeted Genomic Profiling Reveals Recurrent KRAS Mutations in Mesonephric-like Adenocarcinomas of the Female Genital Tract. Am J Surg Pathol. 2018 02; 42(2):227-233.

Wongsurawat T, Woo CC, Giannakakis A, Lin XY, Cheow ESH, Lee CN, Richards M, Sze SK, Nookaew I, Kuznetsov VA, Sorokin V. Distinctive molecular signature and activated signaling pathways in aortic smooth muscle cells of patients with myocardial infarction. Atherosclerosis. 2018 04; 271:237-244.

Nattkemper LA, Tey HL, Valdes-Rodriguez R, Lee H, Mollanazar NK, Albornoz C, Sanders KM, Yosipovitch G. The Genetics of Chronic Itch: Gene Expression in the Skin of Patients with Atopic Dermatitis and Psoriasis with Severe Itch. J Invest Dermatol. 2018 06; 138(6):1311-1317.

Leung CS, Yeung TL, Yip KP, Wong KK, Ho SY, Mangala LS, Sood AK, Lopez-Berestein G, Sheng J, Wong ST, Birrer MJ, Mok SC. Cancer-associated fibroblasts regulate endothelial adhesion protein LPP to promote ovarian cancer chemoresistance. J Clin Invest. 2018 02 01; 128(2):589-606.

Wei W, Giulia F, Luffer S, Kumar R, Wu B, Tavallai M, Bekele RT, Birrer MJ. How can molecular abnormalities influence our clinical approach. Ann Oncol. 2017 Nov 01; 28(suppl_8):viii16-viii24.

Saad AG, Balik V, Parvez A, El Jamal SM. Multifocal Supra and Infratentorial Medulloblastoma in an Adult: Histologic, Immunohistochemical, and Molecular Evaluation of a Rare Case and Review of the Literature. Appl Immunohistochem Mol Morphol. 2017 Nov/Dec; 25(10):e89-e94.

Lin H, Ewing LE, Koturbash I, Gurley BJ, Miousse IR. MicroRNAs as biomarkers for liver injury: Current knowledge, challenges and future prospects. Food Chem Toxicol. 2017 Dec; 110:229-239.

Wang J, Jenjaroenpun P, Bhinge A, Angarica VE, Del Sol A, Nookaew I, Kuznetsov VA, Stanton LW. Single-cell gene expression analysis reveals regulators of distinct cell subpopulations among developing human neurons. Genome Res. 2017 11; 27(11):1783-1794.

Ramaker RC, Savic D, Hardigan AA, Newberry K, Cooper GM, Myers RM, Cooper SJ. A genome-wide interactome of DNA-associated proteins in the human liver. Genome Res. 2017 11; 27(11):1950-1960.

Bagla S, Cukovic D, Asano E, Sood S, Luat A, Chugani HT, Chugani DC, Dombkowski AA. A distinct microRNA expression profile is associated with a[11C]-methyl-L-tryptophan (AMT) PET uptake in epileptogenic cortical tubers resected from patients with tuberous sclerosis complex. Neurobiol Dis. 2018 Jan; 109(Pt A):76-87.

Thorell K, Bengtsson-Palme J, Liu OH, Palacios Gonzales RV, Nookaew I, Rabeneck L, Paszat L, Graham DY, Nielsen J, Lundin SB, Sjöling Å. In Vivo Analysis of the Viable Microbiota and Helicobacter pylori Transcriptome in Gastric Infection and Early Stages of Carcinogenesis. Infect Immun. 2017 10; 85(10).

Phillips CM, Zatarain JR, Nicholls ME, Porter C, Widen SG, Thanki K, Johnson P, Jawad MU, Moyer MP, Randall JW, Hellmich JL, Maskey M, Qiu S, Wood TG, Druzhyna N, Szczesny B, Módis K, Szabo C, Chao C, Hellmich MR. Upregulation of Cystathionine-ß-Synthase in Colonic Epithelia Reprograms Metabolism and Promotes Carcinogenesis. Cancer Res. 2017 11 01; 77(21):5741-5754.

Moncrieffe H, Bennett MF, Tsoras M, Luyrink LK, Johnson AL, Xu H, Dare J, Becker ML, Prahalad S, Rosenkranz M, O'Neil KM, Nigrovic PA, Griffin TA, Lovell DJ, Grom AA, Medvedovic M, Thompson SD. Transcriptional profiles of JIA patient blood with subsequent poor response to methotrexate. Rheumatology (Oxford). 2017 09 01; 56(9):1542-1551.

Palatnik A, Ye S, Kendziorski C, Iden M, Zigman JS, Hessner MJ, Rader JS. Identification of a serum-induced transcriptional signature associated with metastatic cervical cancer. PLoS One. 2017; 12(8):e0181242.

Leung W, Shaffer CD, Chen EJ, Quisenberry TJ, Ko K, Braverman JM, Giarla TC, Mortimer NT, Reed LK, Smith ST, Robic S, McCartha SR, Perry DR, Prescod LM, Sheppard ZA, Saville KJ, McClish A, Morlock EA, Sochor VR, Stanton B, Veysey-White IC, Revie D, Jimenez LA, Palomino JJ, Patao MD, Patao SM, Himelblau ET, Campbell JD, Hertz AL, McEvilly MF, Wagner AR, Youngblom J, Bedi B, Bettincourt J, Duso E, Her M, Hilton W, House S, Karimi M, Kumimoto K, Lee R, Lopez D, Odisho G, Prasad R, Robbins HL, Sandhu T, Selfridge T, Tsukashima K, Yosif H, Kokan NP, Britt L, Zoellner A, Spana EP, Chlebina BT, Chong I, Friedman H, Mammo DA, Ng CL, Nikam VS, Schwartz NU, Xu TQ, Burg MG, Batten SM, Corbeill LM, Enoch E, Ensign JJ, Franks ME, Haiker B, Ingles JA, Kirkland LD, Lorenz-Guertin JM, Matthews J, Mittig CM, Monsma N, Olson KJ, Perez-Aragon G, Ramic A, Ramirez JR, Scheiber C, Schneider PA, Schultz DE, Simon M, Spencer E, Wernette AC, Wykle ME, Zavala-Arellano E, McDonald MJ, Ostby K, Wendland P, DiAngelo JR, Ceasrine AM, Cox AH, Docherty JEB, Gingras RM, Grieb SM, Pavia MJ, Personius CL, Polak GL, Beach DL, Cerritos HL, Horansky EA, Sharif KA, Moran R, Parrish S, Bickford K, Bland J, Broussard J, Campbell K, Deibel KE, Forka R, Lemke MC, Nelson MB, O'Keeffe C, Ramey SM, Schmidt L, Villegas P, Jones CJ, Christ SL, Mamari S, Rinaldi AS, Stity G, Hark AT, Scheuerman M, Silver Key SC, McRae BD, Haberman AS, Asinof S, Carrington H, Drumm K, Embry T, McGuire R, Miller-Foreman D, Rosen S, Safa N, Schultz D, Segal M, Shevin Y, Svoronos P, Vuong T, Skuse G, Paetkau DW, Bridgman RK, Brown CM, Carroll AR, Gifford FM, Gillespie JB, Herman SE, Holtcamp KL, Host MA, Hussey G, Kramer DM, Lawrence JQ, Martin MM, Niemiec EN, O'Reilly AP, Pahl OA, Quintana G, Rettie EAS, Richardson TL, Rodriguez AE, Rodriguez MO, Schiraldi L, Smith JJ, Sugrue KF, Suriano LJ, Takach KE, Vasquez AM, Velez X, Villafuerte EJ, Vives LT, Zellmer VR, Hauke J, Hauser CR, Barker K, Cannon L, Parsamian P, Parsons S, Wichman Z, Bazinet CW, Johnson DE, Bangura A, Black JA, Chevee V, Einsteen SA, Hilton SK, Kollmer M, Nadendla R, Stamm J, Fafara-Thompson AE, Gygi AM, Ogawa EE, Van Camp M, Kocsisova Z, Leatherman JL, Modahl CM, Rubin MR, Apiz-Saab SS, Arias-Mejias SM, Carrion-Ortiz CF, Claudio-Vazquez PN, Espada-Green DM, Feliciano-Camacho M, Gonzalez-Bonilla KM, Taboas-Arroyo M, Vargas-Franco D, Montañez-Gonzalez R, Perez-Otero J, Rivera-Burgos M, Rivera-Rosario FJ, Eisler HL, Alexander J, Begley SK, Gabbard D, Allen RJ, Aung WY, Barshop WD, Boozalis A, Chu VP, Davis JS, Duggal RN, Franklin R, Gavinski K, Gebreyesus H, Gong HZ, Greenstein RA, Guo AD, Hanson C, Homa KE, Hsu SC, Huang Y, Huo L, Jacobs S, Jia S, Jung KL, Wai-Chee Kong S, Kroll MR, Lee BM, Lee PF, Levine KM, Li AS, Liu C, Liu MM, Lousararian AP, Lowery PB, Mallya AP, Marcus JE, Ng PC, Nguyen HP, Patel R, Precht H, Rastogi S, Sarezky JM, Schefkind A, Schultz MB, Shen D, Skorupa T, Spies NC, Stancu G, Vivian Tsang HM, Turski AL, Venkat R, Waldman LE, Wang K, Wang T, Wei JW, Wu DY, Xiong DD, Yu J, Zhou K, McNeil GP, Fernandez RW, Menzies PG, Gu T, Buhler J, Mardis ER, Elgin SCR. Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element. G3 (Bethesda). 2017 08 07; 7(8):2439-2460.

Nagarajan R, Upreti M. An ensemble predictive modeling framework for breast cancer classification. Methods. 2017 12 01; 131:128-134.

Cavalli FMG, Remke M, Rampasek L, Peacock J, Shih DJH, Luu B, Garzia L, Torchia J, Nor C, Morrissy AS, Agnihotri S, Thompson YY, Kuzan-Fischer CM, Farooq H, Isaev K, Daniels C, Cho BK, Kim SK, Wang KC, Lee JY, Grajkowska WA, Perek-Polnik M, Vasiljevic A, Faure-Conter C, Jouvet A, Giannini C, Nageswara Rao AA, Li KKW, Ng HK, Eberhart CG, Pollack IF, Hamilton RL, Gillespie GY, Olson JM, Leary S, Weiss WA, Lach B, Chambless LB, Thompson RC, Cooper MK, Vibhakar R, Hauser P, van Veelen MC, Kros JM, French PJ, Ra YS, Kumabe T, López-Aguilar E, Zitterbart K, Sterba J, Finocchiaro G, Massimino M, Van Meir EG, Osuka S, Shofuda T, Klekner A, Zollo M, Leonard JR, Rubin JB, Jabado N, Albrecht S, Mora J, Van Meter TE, Jung S, Moore AS, Hallahan AR, Chan JA, Tirapelli DPC, Carlotti CG, Fouladi M, Pimentel J, Faria CC, Saad AG, Massimi L, Liau LM, Wheeler H, Nakamura H, Elbabaa SK, Perezpeña-Diazconti M, Chico Ponce de León F, Robinson S, Zapotocky M, Lassaletta A, Huang A, Hawkins CE, Tabori U, Bouffet E, Bartels U, Dirks PB, Rutka JT, Bader GD, Reimand J, Goldenberg A, Ramaswamy V, Taylor MD. Intertumoral Heterogeneity within Medulloblastoma Subgroups. Cancer Cell. 2017 06 12; 31(6):737-754.e6.

Ruebel ML, Cotter M, Sims CR, Moutos DM, Badger TM, Cleves MA, Shankar K, Andres A. Obesity Modulates Inflammation and Lipid Metabolism Oocyte Gene Expression: A Single-Cell Transcriptome Perspective. J Clin Endocrinol Metab. 2017 06 01; 102(6):2029-2038.

Dai L, Cao Y, Jiang W, Zabaleta J, Liu Z, Qiao J, Qin Z. KSHV co-infection down-regulates HPV16 E6 and E7 from cervical cancer cells. Oncotarget. 2017 May 30; 8(22):35792-35803.

Matsui S, Noma H, Qu P, Sakai Y, Matsui K, Heuck C, Crowley J. Multi-subgroup gene screening using semi-parametric hierarchical mixture models and the optimal discovery procedure: Application to a randomized clinical trial in multiple myeloma. Biometrics. 2018 03; 74(1):313-320.

Atrash S, Zhang Q, Papanikolaou X, Stein C, Abdallah AO, Barlogie B. Clinical Presentation and Gene Expression Profiling of Immunoglobulin M Multiple Myeloma Compared With Other Myeloma Subtypes and Waldenström Macroglobulinemia. J Glob Oncol. 2018 09; 4:1-8.

Stein CK, Pawlyn C, Chavan S, Rasche L, Weinhold N, Corken A, Buros A, Sonneveld P, Jackson GH, Landgren O, Mughal T, He J, Barlogie B, Bergsagel PL, Davies FE, Walker BA, Morgan GJ. The varied distribution and impact of RAS codon and other key DNA alterations across the translocation cyclin D subgroups in multiple myeloma. Oncotarget. 2017 Apr 25; 8(17):27854-27867.

Tao Y, Yang G, Yang H, Song D, Hu L, Xie B, Wang H, Gao L, Gao M, Xu H, Xu Z, Wu X, Zhang Y, Zhu W, Zhan F, Shi J. TRIP13 impairs mitotic checkpoint surveillance and is associated with poor prognosis in multiple myeloma. Oncotarget. 2017 Apr 18; 8(16):26718-26731.

Wankhade UD, Zhong Y, Kang P, Alfaro M, Chintapalli SV, Thakali KM, Shankar K. Enhanced offspring predisposition to steatohepatitis with maternal high-fat diet is associated with epigenetic and microbiome alterations. PLoS One. 2017; 12(4):e0175675.

Pawlyn C, Bright MD, Buros AF, Stein CK, Walters Z, Aronson LI, Mirabella F, Jones JR, Kaiser MF, Walker BA, Jackson GH, Clarke PA, Bergsagel PL, Workman P, Chesi M, Morgan GJ, Davies FE. Overexpression of EZH2 in multiple myeloma is associated with poor prognosis and dysregulation of cell cycle control. Blood Cancer J. 2017 03 31; 7(3):e549.

Chen L, Jenjaroenpun P, Pillai AM, Ivshina AV, Ow GS, Efthimios M, Zhiqun T, Tan TZ, Lee SC, Rogers K, Ward JM, Mori S, Adams DJ, Jenkins NA, Copeland NG, Ban KH, Kuznetsov VA, Thiery JP. Transposon insertional mutagenesis in mice identifies human breast cancer susceptibility genes and signatures for stratification. Proc Natl Acad Sci U S A. 2017 03 14; 114(11):E2215-E2224.

Jin HY, Oda H, Chen P, Yang C, Zhou X, Kang SG, Valentine E, Kefauver JM, Liao L, Zhang Y, Gonzalez-Martin A, Shepherd J, Morgan GJ, Mondala TS, Head SR, Kim PH, Xiao N, Fu G, Liu WH, Han J, Williamson JR, Xiao C. Differential Sensitivity of Target Genes to Translational Repression by miR-17~92. PLoS Genet. 2017 02; 13(2):e1006623.

Lo CL, Choudhury SR, Irudayaraj J, Zhou FC. Epigenetic Editing of Ascl1 Gene in Neural Stem Cells by Optogenetics. Sci Rep. 2017 02 09; 7:42047.

McDaniel JM, Varley KE, Gertz J, Savic DS, Roberts BS, Bailey SK, Shevde LA, Ramaker RC, Lasseigne BN, Kirby MK, Newberry KM, Partridge EC, Jones AL, Boone B, Levy SE, Oliver PG, Sexton KC, Grizzle WE, Forero A, Buchsbaum DJ, Cooper SJ, Myers RM. Genomic regulation of invasion by STAT3 in triple negative breast cancer. Oncotarget. 2017 Jan 31; 8(5):8226-8238.

Adams R, Burnley RJ, Valenzano CR, Qureshi O, Doyle C, Lumb S, Del Carmen Lopez M, Griffin R, McMillan D, Taylor RD, Meier C, Mori P, Griffin LM, Wernery U, Kinne J, Rapecki S, Baker TS, Lawson AD, Wright M, Ettorre A. Discovery of a junctional epitope antibody that stabilizes IL-6 and gp80 protein:protein interaction and modulates its downstream signaling. Sci Rep. 2017 01 30; 7:37716.

Rahmatallah Y, Zybailov B, Emmert-Streib F, Glazko G. GSAR: Bioconductor package for Gene Set analysis in R. BMC Bioinformatics. 2017 Jan 24; 18(1):61.

Buckberry S, Bianco-Miotto T, Bent SJ, Clifton V, Shoubridge C, Shankar K, Roberts CT. Placental transcriptome co-expression analysis reveals conserved regulatory programs across gestation. BMC Genomics. 2017 01 03; 18(1):10.

Glazko G, Rahmatallah Y, Zybailov B, Emmert-Streib F. Extracting the Strongest Signals from Omics Data: Differentially Expressed Pathways and Beyond. Methods Mol Biol. 2017; 1613:125-159.

Yeruva L, Pouncey DL, Eledge MR, Bhattacharya S, Luo C, Weatherford EW, Ojcius DM, Rank RG. MicroRNAs Modulate Pathogenesis Resulting from Chlamydial Infection in Mice. Infect Immun. 2017 Jan; 85(1).

Williams K, Valencia L, Gokulan K, Trbojevich R, Khare S. Assessment of antimicrobial effects of food contact materials containing silver on growth of Salmonella Typhimurium. Food Chem Toxicol. 2017 Feb; 100:197-206.

Coleman CM, Sisk JM, Halasz G, Zhong J, Beck SE, Matthews KL, Venkataraman T, Rajagopalan S, Kyratsous CA, Frieman MB. CD8+ T Cells and Macrophages Regulate Pathogenesis in a Mouse Model of Middle East Respiratory Syndrome. J Virol. 2017 Jan 01; 91(1).

Olafsdottir TA, Lindqvist M, Nookaew I, Andersen P, Maertzdorf J, Persson J, Christensen D, Zhang Y, Anderson J, Khoomrung S, Sen P, Agger EM, Coler R, Carter D, Meinke A, Rappuoli R, Kaufmann SH, Reed SG, Harandi AM. Comparative Systems Analyses Reveal Molecular Signatures of Clinically tested Vaccine Adjuvants. Sci Rep. 2016 12 13; 6:39097.

Walworth NG, Lee MD, Fu FX, Hutchins DA, Webb EA. Molecular and physiological evidence of genetic assimilation to high CO2 in the marine nitrogen fixer Trichodesmium. Proc Natl Acad Sci U S A. 2016 11 22; 113(47):E7367-E7374.

Allen JC, Nault JC, Zhu G, Khor AYK, Liu J, Lim TKH, Zucman-Rossi J, Chow PKH. The transcriptomic G1-G6 signature of hepatocellular carcinoma in an Asian population: Association of G3 with microvascular invasion. Medicine (Baltimore). 2016 Nov; 95(47):e5263.

Mousavian Z, Nowzari-Dalini A, Stam RW, Rahmatallah Y, Masoudi-Nejad A. Network-based expression analysis reveals key genes related to glucocorticoid resistance in infant acute lymphoblastic leukemia. Cell Oncol (Dordr). 2017 Feb; 40(1):33-45.

Kosoy R, Agashe C, Grishin A, Leung DY, Wood RA, Sicherer SH, Jones SM, Burks AW, Davidson WF, Lindblad RW, Dawson P, Merad M, Kidd BA, Dudley JT, Sampson HA, Berin MC. Transcriptional Profiling of Egg Allergy and Relationship to Disease Phenotype. PLoS One. 2016; 11(10):e0163831.

Ashouri A, Sayin VI, Van den Eynden J, Singh SX, Papagiannakopoulos T, Larsson E. Pan-cancer transcriptomic analysis associates long non-coding RNAs with key mutational driver events. Nat Commun. 2016 10 25; 7:13197.

Asakura M, Karaki F, Fujii H, Atsuda K, Itoh T, Fujiwara R. Vildagliptin and its metabolite M20.7 induce the expression of S100A8 and S100A9 in human hepatoma HepG2 and leukemia HL-60 cells. Sci Rep. 2016 10 19; 6:35633.

Koyanagi S, Kusunose N, Taniguchi M, Akamine T, Kanado Y, Ozono Y, Masuda T, Kohro Y, Matsunaga N, Tsuda M, Salter MW, Inoue K, Ohdo S. Glucocorticoid regulation of ATP release from spinal astrocytes underlies diurnal exacerbation of neuropathic mechanical allodynia. Nat Commun. 2016 10 14; 7:13102.

Soni NK, Ross AB, Scheers N, Savolainen OI, Nookaew I, Gabrielsson BG, Sandberg AS. Eicosapentaenoic and Docosahexaenoic Acid-Enriched High Fat Diet Delays Skeletal Muscle Degradation in Mice. Nutrients. 2016 Sep 03; 8(9).

Touma M, Kang X, Zhao Y, Cass AA, Gao F, Biniwale R, Coppola G, Xiao X, Reemtsen B, Wang Y. Decoding the Long Noncoding RNA During Cardiac Maturation: A Roadmap for Functional Discovery. Circ Cardiovasc Genet. 2016 Oct; 9(5):395-407.

Ghatalia P, Yang ES, Lasseigne BN, Ramaker RC, Cooper SJ, Chen D, Sudarshan S, Wei S, Guru AS, Zhao A, Cooper T, Della Manna DL, Naik G, Myers RM, Sonpavde G. Kinase Gene Expression Profiling of Metastatic Clear Cell Renal Cell Carcinoma Tissue Identifies Potential New Therapeutic Targets. PLoS One. 2016; 11(8):e0160924.

Gilbert KM, Blossom SJ, Erickson SW, Broadfoot B, West K, Bai S, Li J, Cooney CA. Chronic exposure to trichloroethylene increases DNA methylation of the Ifng promoter in CD4+ T cells. Toxicol Lett. 2016 Oct 17; 260:1-7.

Zhou S, Liu X, Zhou C, Zhou Q, Zhao Y, Li G, Zhou DX. Cooperation between the H3K27me3 Chromatin Mark and Non-CG Methylation in Epigenetic Regulation. Plant Physiol. 2016 10; 172(2):1131-1141.

Zhang J, Chen LL, Xing F, Kudrna DA, Yao W, Copetti D, Mu T, Li W, Song JM, Xie W, Lee S, Talag J, Shao L, An Y, Zhang CL, Ouyang Y, Sun S, Jiao WB, Lv F, Du B, Luo M, Maldonado CE, Goicoechea JL, Xiong L, Wu C, Xing Y, Zhou DX, Yu S, Zhao Y, Wang G, Yu Y, Luo Y, Zhou ZW, Hurtado BE, Danowitz A, Wing RA, Zhang Q. Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63. Proc Natl Acad Sci U S A. 2016 08 30; 113(35):E5163-71.

Weinhold N, Ashby C, Rasche L, Chavan SS, Stein C, Stephens OW, Tytarenko R, Bauer MA, Meissner T, Deshpande S, Patel PH, Buzder T, Molnar G, Peterson EA, van Rhee F, Zangari M, Thanendrarajan S, Schinke C, Tian E, Epstein J, Barlogie B, Davies FE, Heuck CJ, Walker BA, Morgan GJ. Clonal selection and double-hit events involving tumor suppressor genes underlie relapse in myeloma. Blood. 2016 09 29; 128(13):1735-44.

Jethava Y, Mitchell A, Zangari M, Waheed S, Schinke C, Thanendrarajan S, Sawyer J, Alapat D, Tian E, Stein C, Khan R, Heuck CJ, Petty N, Avery D, Steward D, Smith R, Bailey C, Epstein J, Yaccoby S, Hoering A, Crowley J, Morgan G, Barlogie B, van Rhee F. Dose-dense and less dose-intense Total Therapy 5 for gene expression profiling-defined high-risk multiple myeloma. Blood Cancer J. 2016 07 29; 6(7):e453.

Nagarajan R, Upreti M. An approach for deciphering patient-specific variations with application to breast cancer molecular expression profiles. J Biomed Inform. 2016 10; 63:120-130.

Dai L, Bai L, Lin Z, Qiao J, Yang L, Flemington EK, Zabaleta J, Qin Z. Transcriptomic analysis of KSHV-infected primary oral fibroblasts: The role of interferon-induced genes in the latency of oncogenic virus. Oncotarget. 2016 Jul 26; 7(30):47052-47060.

Tryndyak V, de Conti A, Doerge DR, Olson GR, Beland FA, Pogribny IP. Furan-induced transcriptomic and gene-specific DNA methylation changes in the livers of Fischer 344 rats in a 2-year carcinogenicity study. Arch Toxicol. 2017 Mar; 91(3):1233-1243.

Waldron L, Riester M, Ramos M, Parmigiani G, Birrer M. The Doppelgänger Effect: Hidden Duplicates in Databases of Transcriptome Profiles. J Natl Cancer Inst. 2016 11; 108(11).

Pelham CJ, Drews EM, Agrawal DK. Vitamin D controls resistance artery function through regulation of perivascular adipose tissue hypoxia and inflammation. J Mol Cell Cardiol. 2016 09; 98:1-10.

Govindarajan R, Posey J, Chao CY, Lu R, Jadhav T, Javed AY, Javed A, Mahmoud FA, Osarogiagbon RU, Manne U. A comparison of 12-gene colon cancer assay gene expression in African American and Caucasian patients with stage II colon cancer. BMC Cancer. 2016 06 18; 16:368.

Kirby MK, Ramaker RC, Gertz J, Davis NS, Johnston BE, Oliver PG, Sexton KC, Greeno EW, Christein JD, Heslin MJ, Posey JA, Grizzle WE, Vickers SM, Buchsbaum DJ, Cooper SJ, Myers RM. RNA sequencing of pancreatic adenocarcinoma tumors yields novel expression patterns associated with long-term survival and reveals a role for ANGPTL4. Mol Oncol. 2016 10; 10(8):1169-82.

Chepelev NL, Long AS, Bowers WJ, Gagné R, Williams A, Kuo B, Phillips DH, Arlt VM, White PA, Yauk CL. Transcriptional profiling of the mouse hippocampus supports an NMDAR-mediated neurotoxic mode of action for benzo[a]pyrene. Environ Mol Mutagen. 2016 06; 57(5):350-63.

Svahn SL, Väremo L, Gabrielsson BG, Peris E, Nookaew I, Grahnemo L, Sandberg AS, Wernstedt Asterholm I, Jansson JO, Nielsen J, Johansson ME. Six Tissue Transcriptomics Reveals Specific Immune Suppression in Spleen by Dietary Polyunsaturated Fatty Acids. PLoS One. 2016; 11(5):e0155099.

Zhang XD, Baladandayuthapani V, Lin H, Mulligan G, Li B, Esseltine DW, Qi L, Xu J, Hunziker W, Barlogie B, Usmani SZ, Zhang Q, Crowley J, Hoering A, Shah JJ, Weber DM, Manasanch EE, Thomas SK, Li BZ, Wang HH, Zhang J, Kuiatse I, Tang JL, Wang H, He J, Yang J, Milan E, Cenci S, Ma WC, Wang ZQ, Davis RE, Yang L, Orlowski RZ. Tight Junction Protein 1 Modulates Proteasome Capacity and Proteasome Inhibitor Sensitivity in Multiple Myeloma via EGFR/JAK1/STAT3 Signaling. Cancer Cell. 2016 05 09; 29(5):639-652.

Wei T, Zhang H, Cetin N, Miller E, Moak T, Suen JY, Richter GT. Elevated Expression of Matrix Metalloproteinase-9 not Matrix Metalloproteinase-2 Contributes to Progression of Extracranial Arteriovenous Malformation. Sci Rep. 2016 Apr 14; 6:24378.

Hao M, Zang M, Zhao L, Deng S, Xu Y, Qi F, An G, Qin Y, Sui W, Li F, Yang W, Li Z, Yi S, Zou D, Zhan F, Qiu L. Serum high expression of miR-214 and miR-135b as novel predictor for myeloma bone disease development and prognosis. Oncotarget. 2016 Apr 12; 7(15):19589-600.

Liu M, Chen S, Yueh MF, Fujiwara R, Konopnicki C, Hao H, Tukey RH. Cadmium and arsenic override NF-?B developmental regulation of the intestinal UGT1A1 gene and control of hyperbilirubinemia. Biochem Pharmacol. 2016 06 15; 110-111:37-46.

Kovalchuk A, Rodriguez-Juarez R, Ilnytskyy Y, Byeon B, Shpyleva S, Melnyk S, Pogribny I, Kolb B, Kovalchuk O. Sex-specific effects of cytotoxic chemotherapy agents cyclophosphamide and mitomycin C on gene expression, oxidative DNA damage, and epigenetic alterations in the prefrontal cortex and hippocampus - an aging connection. Aging (Albany NY). 2016 04; 8(4):697-711.

Farrar JE, Schuback HL, Ries RE, Wai D, Hampton OA, Trevino LR, Alonzo TA, Guidry Auvil JM, Davidsen TM, Gesuwan P, Hermida L, Muzny DM, Dewal N, Rustagi N, Lewis LR, Gamis AS, Wheeler DA, Smith MA, Gerhard DS, Meshinchi S. Genomic Profiling of Pediatric Acute Myeloid Leukemia Reveals a Changing Mutational Landscape from Disease Diagnosis to Relapse. Cancer Res. 2016 04 15; 76(8):2197-205.

Wu SP, Pfeiffer RM, Ahn IE, Mailankody S, Sonneveld P, van Duin M, Munshi NC, Walker BA, Morgan G, Landgren O. Impact of Genes Highly Correlated with MMSET Myeloma on the Survival of Non-MMSET Myeloma Patients. Clin Cancer Res. 2016 Aug 15; 22(16):4039-44.

El Bissati K, Suvorova ES, Xiao H, Lucas O, Upadhya R, Ma Y, Angeletti RH, White MW, Weiss LM, Kim K. Toxoplasma gondii Arginine Methyltransferase 1 (PRMT1) Is Necessary for Centrosome Dynamics during Tachyzoite Cell Division. mBio. 2016 Feb 02; 7(1):e02094-15.

Dai L, Trillo-Tinoco J, Chen Y, Bonstaff K, Del Valle L, Parsons C, Ochoa AC, Zabaleta J, Toole BP, Qin Z. CD147 and downstream ADAMTSs promote the tumorigenicity of Kaposi's sarcoma-associated herpesvirus infected endothelial cells. Oncotarget. 2016 Jan 26; 7(4):3806-18.

Calura E, Bisognin A, Manzoni M, Todoerti K, Taiana E, Sales G, Morgan GJ, Tonon G, Amodio N, Tassone P, Neri A, Agnelli L, Romualdi C, Bortoluzzi S. Disentangling the microRNA regulatory milieu in multiple myeloma: integrative genomics analysis outlines mixed miRNA-TF circuits and pathway-derived networks modulated in t(4;14) patients. Oncotarget. 2016 Jan 19; 7(3):2367-78.

Paiva B, Corchete LA, Vidriales MB, Puig N, Maiso P, Rodriguez I, Alignani D, Burgos L, Sanchez ML, Barcena P, Echeveste MA, Hernandez MT, García-Sanz R, Ocio EM, Oriol A, Gironella M, Palomera L, De Arriba F, Gonzalez Y, Johnson SK, Epstein J, Barlogie B, Lahuerta JJ, Blade J, Orfao A, Mateos MV, San Miguel JF. Phenotypic and genomic analysis of multiple myeloma minimal residual disease tumor cells: a new model to understand chemoresistance. Blood. 2016 Apr 14; 127(15):1896-906.

Zheng Y, Ding Y, Sun X, Xie S, Wang D, Liu X, Su L, Wei W, Pan L, Zhou DX. Histone deacetylase HDA9 negatively regulates salt and drought stress responsiveness in Arabidopsis. J Exp Bot. 2016 Mar; 67(6):1703-13.

Meißner T, Seckinger A, Hemminki K, Bertsch U, Foersti A, Haenel M, Duering J, Salwender H, Goldschmidt H, Morgan GJ, Hose D, Weinhold N. Profound impact of sample processing delay on gene expression of multiple myeloma plasma cells. BMC Med Genomics. 2015 Dec 30; 8:85.

Duarte-Rojo A, Fischer SE, Adeyi O, Zita D, Deneke MG, Selzner N, Chen L, Malespin M, Cotler SJ, McGilvray ID, Feld JJ. Protease inhibitors partially overcome the interferon nonresponse phenotype in patients with chronic hepatitis C. J Viral Hepat. 2016 May; 23(5):340-7.

Moran-Jones K, Gloss BS, Murali R, Chang DK, Colvin EK, Jones MD, Yuen S, Howell VM, Brown LM, Wong CW, Spong SM, Scarlett CJ, Hacker NF, Ghosh S, Mok SC, Birrer MJ, Samimi G. Connective tissue growth factor as a novel therapeutic target in high grade serous ovarian cancer. Oncotarget. 2015 Dec 29; 6(42):44551-62.

Kirby TJ, Walton RG, Finlin B, Zhu B, Unal R, Rasouli N, Peterson CA, Kern PA. Integrative mRNA-microRNA analyses reveal novel interactions related to insulin sensitivity in human adipose tissue. Physiol Genomics. 2016 Feb; 48(2):145-53.

Grinchuk OV, Motakis E, Yenamandra SP, Ow GS, Jenjaroenpun P, Tang Z, Yarmishyn AA, Ivshina AV, Kuznetsov VA. Sense-antisense gene-pairs in breast cancer and associated pathological pathways. Oncotarget. 2015 Dec 08; 6(39):42197-221.

Kelly KR, Espitia CM, Zhao W, Wendlandt E, Tricot G, Zhan F, Carew JS, Nawrocki ST. Junctional adhesion molecule-A is overexpressed in advanced multiple myeloma and determines response to oncolytic reovirus. Oncotarget. 2015 Dec 01; 6(38):41275-89.

Govindarajah V, Leung YK, Ying J, Gear R, Bornschein RL, Medvedovic M, Ho SM. In utero exposure of rats to high-fat diets perturbs gene expression profiles and cancer susceptibility of prepubertal mammary glands. J Nutr Biochem. 2016 Mar; 29:73-82.

Khattak S, Brimble E, Zhang W, Zaslavsky K, Strong E, Ross PJ, Hendry J, Mital S, Salter MW, Osborne LR, Ellis J. Human induced pluripotent stem cell derived neurons as a model for Williams-Beuren syndrome. Mol Brain. 2015 Nov 24; 8(1):77.

Zheng J, Wang J, Pouliot M, Authier S, Zhou D, Loose DS, Hauer-Jensen M. Gene expression profiling in non-human primate jejunum, ileum and colon after total-body irradiation: a comparative study of segment-specific molecular and cellular responses. BMC Genomics. 2015 Nov 21; 16:984.

Weinhold N, Heuck CJ, Rosenthal A, Thanendrarajan S, Stein CK, Van Rhee F, Zangari M, Hoering A, Tian E, Davies FE, Barlogie B, Morgan GJ. Clinical value of molecular subtyping multiple myeloma using gene expression profiling. Leukemia. 2016 Feb; 30(2):423-30.

Chepelev NL, Long AS, Williams A, Kuo B, Gagné R, Kennedy DA, Phillips DH, Arlt VM, White PA, Yauk CL. Transcriptional Profiling of Dibenzo[def,p]chrysene-induced Spleen Atrophy Provides Mechanistic Insights into its Immunotoxicity in MutaMouse. Toxicol Sci. 2016 Jan; 149(1):251-68.

Lam HM, Ho SM, Chen J, Medvedovic M, Tam NN. Bisphenol A Disrupts HNF4a-Regulated Gene Networks Linking to Prostate Preneoplasia and Immune Disruption in Noble Rats. Endocrinology. 2016 Jan; 157(1):207-19.

Stasulli NM, Eichelberger KR, Price PA, Pechous RD, Montgomery SA, Parker JS, Goldman WE. Spatially distinct neutrophil responses within the inflammatory lesions of pneumonic plague. mBio. 2015 Oct 13; 6(5):e01530-15.

Kendrick S, Tus K, Wright G, Jaffe ES, Rosenwald A, Campo E, Chan WC, Connors JM, Braziel RM, Ott G, Delabie J, Cook JR, Weisenburger DD, Greiner TC, Fu K, Staudt LM, Gascoyne RD, Scott DW, Rimsza LM. Diffuse large B-cell lymphoma cell-of-origin classification using the Lymph2Cx assay in the context of BCL2 and MYC expression status. Leuk Lymphoma. 2016; 57(3):717-20.

Rahmatallah Y, Emmert-Streib F, Glazko G. Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline. Brief Bioinform. 2016 05; 17(3):393-407.

Kuiper R, van Duin M, van Vliet MH, Broijl A, van der Holt B, El Jarari L, van Beers EH, Mulligan G, Avet-Loiseau H, Gregory WM, Morgan G, Goldschmidt H, Lokhorst HM, Sonneveld P. Prediction of high- and low-risk multiple myeloma based on gene expression and the International Staging System. Blood. 2015 Oct 22; 126(17):1996-2004.

Kogan V, Molodtsov I, Menshikov LI, Shmookler Reis RJ, Fedichev P. Stability analysis of a model gene network links aging, stress resistance, and negligible senescence. Sci Rep. 2015 Aug 28; 5:13589.

Weng DY, Chen J, Taslim C, Hsu PC, Marian C, David SP, Loffredo CA, Shields PG. Persistent alterations of gene expression profiling of human peripheral blood mononuclear cells from smokers. Mol Carcinog. 2016 10; 55(10):1424-37.

Usmani SZ, Rodriguez-Otero P, Bhutani M, Mateos MV, Miguel JS. Defining and treating high-risk multiple myeloma. Leukemia. 2015 Nov; 29(11):2119-25.

Stolarz AJ, Farris RA, Wiley CA, O'Brien CE, Price ET. Fenofibrate Attenuates Neutrophilic Inflammation in Airway Epithelia: Potential Drug Repurposing for Cystic Fibrosis. Clin Transl Sci. 2015 Dec; 8(6):696-701.

Stupnikov A, Glazko GV, Emmert-Streib F. Effects of subsampling on characteristics of RNA-seq data from triple-negative breast cancer patients. Chin J Cancer. 2015 Aug 08; 34(10):427-38.

Huang J, Zhou Y, Thomas GS, Gu Z, Yang Y, Xu H, Tricot G, Zhan F. NEDD8 Inhibition Overcomes CKS1B-Induced Drug Resistance by Upregulation of p21 in Multiple Myeloma. Clin Cancer Res. 2015 Dec 15; 21(24):5532-42.

Miousse IR, Currie R, Datta K, Ellinger-Ziegelbauer H, French JE, Harrill AH, Koturbash I, Lawton M, Mann D, Meehan RR, Moggs JG, O'Lone R, Rasoulpour RJ, Pera RA, Thompson K. Importance of investigating epigenetic alterations for industry and regulators: An appraisal of current efforts by the Health and Environmental Sciences Institute. Toxicology. 2015 Sep 01; 335:11-9.

Giannakakis A, Zhang J, Jenjaroenpun P, Nama S, Zainolabidin N, Aau MY, Yarmishyn AA, Vaz C, Ivshina AV, Grinchuk OV, Voorhoeve M, Vardy LA, Sampath P, Kuznetsov VA, Kurochkin IV, Guccione E. Contrasting expression patterns of coding and noncoding parts of the human genome upon oxidative stress. Sci Rep. 2015 May 29; 5:9737.

Vathipadiekal V, Wang V, Wei W, Waldron L, Drapkin R, Gillette M, Skates S, Birrer M. Creation of a Human Secretome: A Novel Composite Library of Human Secreted Proteins: Validation Using Ovarian Cancer Gene Expression Data and a Virtual Secretome Array. Clin Cancer Res. 2015 Nov 01; 21(21):4960-9.

Tyekucheva S, Martin NE, Stack EC, Wei W, Vathipadiekal V, Waldron L, Fiorentino M, Lis RT, Stampfer MJ, Loda M, Parmigiani G, Mucci LA, Birrer M. Comparing Platforms for Messenger RNA Expression Profiling of Archival Formalin-Fixed, Paraffin-Embedded Tissues. J Mol Diagn. 2015 Jul; 17(4):374-81.

Walker BA, Wardell CP, Murison A, Boyle EM, Begum DB, Dahir NM, Proszek PZ, Melchor L, Pawlyn C, Kaiser MF, Johnson DC, Qiang YW, Jones JR, Cairns DA, Gregory WM, Owen RG, Cook G, Drayson MT, Jackson GH, Davies FE, Morgan GJ. APOBEC family mutational signatures are associated with poor prognosis translocations in multiple myeloma. Nat Commun. 2015 Apr 23; 6:6997.

Goossens KV, Ielasi FS, Nookaew I, Stals I, Alonso-Sarduy L, Daenen L, Van Mulders SE, Stassen C, van Eijsden RG, Siewers V, Delvaux FR, Kasas S, Nielsen J, Devreese B, Willaert RG. Molecular mechanism of flocculation self-recognition in yeast and its role in mating and survival. mBio. 2015 Apr 14; 6(2).

Marrone AK, Shpyleva S, Chappell G, Tryndyak V, Uehara T, Tsuchiya M, Beland FA, Rusyn I, Pogribny IP. Differentially expressed MicroRNAs provide mechanistic insight into fibrosis-associated liver carcinogenesis in mice. Mol Carcinog. 2016 May; 55(5):808-17.

Telli ML, Jensen KC, Vinayak S, Kurian AW, Lipson JA, Flaherty PJ, Timms K, Abkevich V, Schackmann EA, Wapnir IL, Carlson RW, Chang PJ, Sparano JA, Head B, Goldstein LJ, Haley B, Dakhil SR, Reid JE, Hartman AR, Manola J, Ford JM. Phase II Study of Gemcitabine, Carboplatin, and Iniparib As Neoadjuvant Therapy for Triple-Negative and BRCA1/2 Mutation-Associated Breast Cancer With Assessment of a Tumor-Based Measure of Genomic Instability: PrECOG 0105. J Clin Oncol. 2015 Jun 10; 33(17):1895-901.

Yan S, Tsurumi A, Que YA, Ryan CM, Bandyopadhaya A, Morgan AA, Flaherty PJ, Tompkins RG, Rahme LG. Prediction of multiple infections after severe burn trauma: a prospective cohort study. Ann Surg. 2015 Apr; 261(4):781-92.

Schinke C, Giricz O, Li W, Shastri A, Gordon S, Barreyro L, Barreryo L, Bhagat T, Bhattacharyya S, Ramachandra N, Bartenstein M, Pellagatti A, Boultwood J, Wickrema A, Yu Y, Will B, Wei S, Steidl U, Verma A. IL8-CXCR2 pathway inhibition as a therapeutic strategy against MDS and AML stem cells. Blood. 2015 May 14; 125(20):3144-52.

Ma S, Johnson D, Ashby C, Xiong D, Cramer CL, Moore JH, Zhang S, Huang X. SPARCoC: a new framework for molecular pattern discovery and cancer gene identification. PLoS One. 2015; 10(3):e0117135.

Papanikolaou X, Alapat D, Rosenthal A, Stein C, Epstein J, Owens R, Yaccoby S, Johnson S, Bailey C, Heuck C, Tian E, Joiner A, van Rhee F, Khan R, Zangari M, Jethava Y, Waheed S, Davies F, Morgan G, Barlogie B. The flow cytometry-defined light chain cytoplasmic immunoglobulin index and an associated 12-gene expression signature are independent prognostic factors in multiple myeloma. Leukemia. 2015 Aug; 29(8):1713-20.

Saulnier Sholler GL, Bond JP, Bergendahl G, Dutta A, Dragon J, Neville K, Ferguson W, Roberts W, Eslin D, Kraveka J, Kaplan J, Mitchell D, Parikh N, Merchant M, Ashikaga T, Hanna G, Lescault PJ, Siniard A, Corneveaux J, Huentelman M, Trent J. Feasibility of implementing molecular-guided therapy for the treatment of patients with relapsed or refractory neuroblastoma. Cancer Med. 2015 Jun; 4(6):871-86.

Stein CK, Qu P, Epstein J, Buros A, Rosenthal A, Crowley J, Morgan G, Barlogie B. Removing batch effects from purified plasma cell gene expression microarrays with modified ComBat. BMC Bioinformatics. 2015 Feb 25; 16:63.

Pechous RD, Broberg CA, Stasulli NM, Miller VL, Goldman WE. In vivo transcriptional profiling of Yersinia pestis reveals a novel bacterial mediator of pulmonary inflammation. mBio. 2015 Feb 17; 6(1):e02302-14.

Chang Z, Li G, Liu J, Zhang Y, Ashby C, Liu D, Cramer CL, Huang X. Bridger: a new framework for de novo transcriptome assembly using RNA-seq data. Genome Biol. 2015 Feb 11; 16:30.

Bhutani M, Landgren O, Usmani SZ. Multiple myeloma: is it time for biomarker-driven therapy? Am Soc Clin Oncol Educ Book. 2015; e493-503.

Philchenkov AA, Zavelevich MP, Tryndyak VP, Kuiava LM, Blokhin DY, Miura K, Silvestri R, Pogribny IP. Antiproliferative and proapoptotic effects of a pyrrole containing arylthioindole in human Jurkat leukemia cell line and multidrug-resistant Jurkat/A4 cells. . 2015; 16(12):1820-9.

de Conti A, Kobets T, Tryndyak V, Burnett SD, Han T, Fuscoe JC, Beland FA, Doerge DR, Pogribny IP. Persistence of furan-induced epigenetic aberrations in the livers of F344 rats. Toxicol Sci. 2015 Apr; 144(2):217-26.

Wali S, Gupta R, Veselenak RL, Li Y, Yu JJ, Murthy AK, Cap AP, Guentzel MN, Chambers JP, Zhong G, Rank RG, Pyles RB, Arulanandam BP. Use of a Guinea pig-specific transcriptome array for evaluation of protective immunity against genital chlamydial infection following intranasal vaccination in Guinea pigs. PLoS One. 2014; 9(12):e114261.

Rahmatallah Y, Emmert-Streib F, Glazko G. Comparative evaluation of gene set analysis approaches for RNA-Seq data. BMC Bioinformatics. 2014 Dec 05; 15:397.

De Silva TM, Ketsawatsomkron P, Pelham C, Sigmund CD, Faraci FM. Genetic interference with peroxisome proliferator-activated receptor ? in smooth muscle enhances myogenic tone in the cerebrovasculature via A Rho kinase-dependent mechanism. Hypertension. 2015 Feb; 65(2):345-51.

Bauer MA, Chavan SS, Peterson EA, Heuck CJ, Johann DJ. Leveraging the new with the old: providing a framework for the integration of historic microarray studies with next generation sequencing. BMC Bioinformatics. 2014; 15 Suppl 11:S3.

Lam HM, Ouyang B, Chen J, Ying J, Wang J, Wu CL, Jia L, Medvedovic M, Vessella RL, Ho SM. Targeting GPR30 with G-1: a new therapeutic target for castration-resistant prostate cancer. Endocr Relat Cancer. 2014; 21(6):903-14.

Saben J, Kang P, Zhong Y, Thakali KM, Gomez-Acevedo H, Borengasser SJ, Andres A, Badger TM, Shankar K. RNA-seq analysis of the rat placentation site reveals maternal obesity-associated changes in placental and offspring thyroid hormone signaling. Placenta. 2014 Dec; 35(12):1013-20.

Saddiki H, McAuliffe J, Flaherty P. GLAD: a mixed-membership model for heterogeneous tumor subtype classification. Bioinformatics. 2015 Jan 15; 31(2):225-32.

Portilla D. Apoptosis, fibrosis and senescence. Nephron Clin Pract. 2014; 127(1-4):65-9.

Ryu S, Lee Y, Hyun MY, Choi SY, Jeong KH, Park YM, Kang H, Park KY, Armstrong CA, Johnson A, Song PI, Kim BJ. Mycophenolate antagonizes IFN-?-induced catagen-like changes via ß-catenin activation in human dermal papilla cells and hair follicles. Int J Mol Sci. 2014 Sep 22; 15(9):16800-15.

Krais AM, Mühlbauer KR, Kucab JE, Chinbuah H, Cornelius MG, Wei QX, Hollstein M, Phillips DH, Arlt VM, Schmeiser HH. Comparison of the metabolic activation of environmental carcinogens in mouse embryonic stem cells and mouse embryonic fibroblasts. Toxicol In Vitro. 2015 Feb; 29(1):34-43.

Ronis MJ, Miousse IR, Mason AZ, Sharma N, Blackburn ML, Badger TM. Trace element status and zinc homeostasis differ in breast and formula-fed piglets. Exp Biol Med (Maywood). 2015 Jan; 240(1):58-66.

Wu P, Walker BA, Broyl A, Kaiser M, Johnson DC, Kuiper R, van Duin M, Gregory WM, Davies FE, Brewer D, Hose D, Sonneveld P, Morgan GJ. A gene expression based predictor for high risk myeloma treated with intensive therapy and autologous stem cell rescue. Leuk Lymphoma. 2015 Mar; 56(3):594-601.

de Conti A, Tryndyak V, Churchwell MI, Melnyk S, Latendresse JR, Muskhelishvili L, Beland FA, Pogribny IP. Genotoxic, epigenetic, and transcriptomic effects of tamoxifen in mouse liver. Toxicology. 2014 Nov 05; 325:12-20.

Salama ME, Du S, Efimova O, Heikal NM, Wendlandt E, Toydemir RM, South S, Perkins SL, Hussong JW, Zhan F. Neoplastic plasma cell aberrant antigen expression patterns and their association with genetic abnormalities. Leuk Lymphoma. 2015 Feb; 56(2):426-33.

Heuck CJ, Qu P, van Rhee F, Waheed S, Usmani SZ, Epstein J, Zhang Q, Edmondson R, Hoering A, Crowley J, Barlogie B. Five gene probes carry most of the discriminatory power of the 70-gene risk model in multiple myeloma. Leukemia. 2014 Dec; 28(12):2410-3.

Zubenko GS, Hughes HB, Jordan RM, Lyons-Weiler J, Cohen BM. Differential hippocampal gene expression and pathway analysis in an etiology-based mouse model of major depressive disorder. Am J Med Genet B Neuropsychiatr Genet. 2014 Sep; 165B(6):457-66.

Croken MM, Qiu W, White MW, Kim K. Gene Set Enrichment Analysis (GSEA) of Toxoplasma gondii expression datasets links cell cycle progression and the bradyzoite developmental program. BMC Genomics. 2014 Jun 24; 15:515.

Dunlop BW, Rothbaum BO, Binder EB, Duncan E, Harvey PD, Jovanovic T, Kelley ME, Kinkead B, Kutner M, Iosifescu DV, Mathew SJ, Neylan TC, Kilts CD, Nemeroff CB, Mayberg HS. Evaluation of a corticotropin releasing hormone type 1 receptor antagonist in women with posttraumatic stress disorder: study protocol for a randomized controlled trial. Trials. 2014 Jun 21; 15:240.

Saben J, Thakali KM, Lindsey FE, Zhong Y, Badger TM, Andres A, Shankar K. Distinct adipogenic differentiation phenotypes of human umbilical cord mesenchymal cells dependent on adipogenic conditions. Exp Biol Med (Maywood). 2014 Oct; 239(10):1340-51.

Das KC, Wasnick JD. Biphasic response of checkpoint control proteins in hyperoxia: exposure to lower levels of oxygen induces genome maintenance genes in experimental baboon BPD. Mol Cell Biochem. 2014 Oct; 395(1-2):187-98.

Chiang KC, Yeh CN, Lin KJ, Su LJ, Yen TC, Pang JH, Kittaka A, Sun CC, Chen MF, Jan YY, Chen TC, Juang HH, Yeh TS. Chemopreventive and chemotherapeutic effect of dietary supplementation of vitamin D on cholangiocarcinoma in a Chemical-Induced animal model. Oncotarget. 2014 Jun 15; 5(11):3849-61.

Chauss D, Basu S, Rajakaruna S, Ma Z, Gau V, Anastas S, Brennan LA, Hejtmancik JF, Menko AS, Kantorow M. Differentiation state-specific mitochondrial dynamic regulatory networks are revealed by global transcriptional analysis of the developing chicken lens. G3 (Bethesda). 2014 Jun 13; 4(8):1515-27.

Gao M, Gao L, Yang G, Tao Y, Hou J, Xu H, Hu X, Han Y, Zhang Q, Zhan F, Wu X, Shi J. Myeloma cells resistance to NK cell lysis mainly involves an HLA class I-dependent mechanism. Acta Biochim Biophys Sin (Shanghai). 2014 Jul; 46(7):597-604.

van Laar R, Flinchum R, Brown N, Ramsey J, Riccitelli S, Heuck C, Barlogie B, Shaughnessy JD. Translating a gene expression signature for multiple myeloma prognosis into a robust high-throughput assay for clinical use. BMC Med Genomics. 2014 May 17; 7:25.

Emmert-Streib F, de Matos Simoes R, Glazko G, McDade S, Haibe-Kains B, Holzinger A, Dehmer M, Campbell F. Functional and genetic analysis of the colon cancer network. BMC Bioinformatics. 2014; 15 Suppl 6:S6.

Thakali KM, Saben J, Faske JB, Lindsey F, Gomez-Acevedo H, Lowery CL, Badger TM, Andres A, Shankar K. Maternal pregravid obesity changes gene expression profiles toward greater inflammation and reduced insulin sensitivity in umbilical cord. Pediatr Res. 2014 Aug; 76(2):202-10.

Garcia-Albornoz M, Thankaswamy-Kosalai S, Nilsson A, Väremo L, Nookaew I, Nielsen J. BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data. Nucleic Acids Res. 2014 Jul; 42(Web Server issue):W175-81.

Ochs MF, Farrar JE, Considine M, Wei Y, Meshinchi S, Arceci RJ. Outlier Analysis and Top Scoring Pair for Integrated Data Analysis and Biomarker Discovery. IEEE/ACM Trans Comput Biol Bioinform. 2014 May-Jun; 11(3):520-32.

Tian E, Sawyer JR, Heuck CJ, Zhang Q, van Rhee F, Barlogie B, Epstein J. In multiple myeloma, 14q32 translocations are nonrandom chromosomal fusions driving high expression levels of the respective partner genes. Genes Chromosomes Cancer. 2014 Jul; 53(7):549-57.

Kendrick S, Kang HJ, Alam MP, Madathil MM, Agrawal P, Gokhale V, Yang D, Hecht SM, Hurley LH. The dynamic character of the BCL2 promoter i-motif provides a mechanism for modulation of gene expression by compounds that bind selectively to the alternative DNA hairpin structure. J Am Chem Soc. 2014 Mar 19; 136(11):4161-71.

Kang HJ, Kendrick S, Hecht SM, Hurley LH. The transcriptional complex between the BCL2 i-motif and hnRNP LL is a molecular switch for control of gene expression that can be modulated by small molecules. J Am Chem Soc. 2014 Mar 19; 136(11):4172-85.

Gatto F, Nookaew I, Nielsen J. Chromosome 3p loss of heterozygosity is associated with a unique metabolic network in clear cell renal carcinoma. Proc Natl Acad Sci U S A. 2014 Mar 04; 111(9):E866-75.

Delker DA, McGettigan BM, Kanth P, Pop S, Neklason DW, Bronner MP, Burt RW, Hagedorn CH. RNA sequencing of sessile serrated colon polyps identifies differentially expressed genes and immunohistochemical markers. PLoS One. 2014; 9(2):e88367.

Choi HY, Moon SJ, Ratliff BB, Ahn SH, Jung A, Lee M, Lee S, Lim BJ, Kim BS, Plotkin MD, Ha SK, Park HC. Microparticles from kidney-derived mesenchymal stem cells act as carriers of proangiogenic signals and contribute to recovery from acute kidney injury. PLoS One. 2014; 9(2):e87853.

Shih DJ, Northcott PA, Remke M, Korshunov A, Ramaswamy V, Kool M, Luu B, Yao Y, Wang X, Dubuc AM, Garzia L, Peacock J, Mack SC, Wu X, Rolider A, Morrissy AS, Cavalli FM, Jones DT, Zitterbart K, Faria CC, Schüller U, Kren L, Kumabe T, Tominaga T, Shin Ra Y, Garami M, Hauser P, Chan JA, Robinson S, Bognár L, Klekner A, Saad AG, Liau LM, Albrecht S, Fontebasso A, Cinalli G, De Antonellis P, Zollo M, Cooper MK, Thompson RC, Bailey S, Lindsey JC, Di Rocco C, Massimi L, Michiels EM, Scherer SW, Phillips JJ, Gupta N, Fan X, Muraszko KM, Vibhakar R, Eberhart CG, Fouladi M, Lach B, Jung S, Wechsler-Reya RJ, Fèvre-Montange M, Jouvet A, Jabado N, Pollack IF, Weiss WA, Lee JY, Cho BK, Kim SK, Wang KC, Leonard JR, Rubin JB, de Torres C, Lavarino C, Mora J, Cho YJ, Tabori U, Olson JM, Gajjar A, Packer RJ, Rutkowski S, Pomeroy SL, French PJ, Kloosterhof NK, Kros JM, Van Meir EG, Clifford SC, Bourdeaut F, Delattre O, Doz FF, Hawkins CE, Malkin D, Grajkowska WA, Perek-Polnik M, Bouffet E, Rutka JT, Pfister SM, Taylor MD. Cytogenetic prognostication within medulloblastoma subgroups. J Clin Oncol. 2014 Mar 20; 32(9):886-96.

Jeong W, Kim SB, Sohn BH, Park YY, Park ES, Kim SC, Kim SS, Johnson RL, Birrer M, Bowtell DSL, Mills GB, Sood A, Lee JS. Activation of YAP1 is associated with poor prognosis and response to taxanes in ovarian cancer. Anticancer Res. 2014 Feb; 34(2):811-817.

Knuf C, Nookaew I, Remmers I, Khoomrung S, Brown S, Berry A, Nielsen J. Physiological characterization of the high malic acid-producing Aspergillus oryzae strain 2103a-68. Appl Microbiol Biotechnol. 2014 Apr; 98(8):3517-27.

Weinkopff T, de Oliveira CI, de Carvalho AM, Hauyon-La Torre Y, Muniz AC, Miranda JC, Barral A, Tacchini-Cottier F. Repeated exposure to Lutzomyia intermedia sand fly saliva induces local expression of interferon-inducible genes both at the site of injection in mice and in human blood. PLoS Negl Trop Dis. 2014; 8(1):e2627.

Bøgsted M, Bilgrau AE, Wardell CP, Bertsch U, Schmitz A, Bødker JS, Kjeldsen MK, Goldschmidt H, Morgan GJ, Dybkaer K, Johnsen HE. Proof of the concept to use a malignant B cell line drug screen strategy for identification and weight of melphalan resistance genes in multiple myeloma. PLoS One. 2013; 8(12):e83252.

Nagarajan R, Scutari M. Impact of noise on molecular network inference. PLoS One. 2013; 8(12):e80735.

Rahmatallah Y, Emmert-Streib F, Glazko G. Gene Sets Net Correlations Analysis (GSNCA): a multivariate differential coexpression test for gene sets. Bioinformatics. 2014 Feb 01; 30(3):360-8.

Przybyla BD, Shafirstein G, Vishal SJ, Dennis RA, Griffin RJ. Molecular changes in bone marrow, tumor and serum after conductive ablation of murine 4T1 breast carcinoma. Int J Oncol. 2014 Feb; 44(2):600-8.

Jewett MC, Workman CT, Nookaew I, Pizarro FA, Agosin E, Hellgren LI, Nielsen J. Mapping condition-dependent regulation of lipid metabolism in Saccharomyces cerevisiae. G3 (Bethesda). 2013 Nov 06; 3(11):1979-95.

Remke M, Ramaswamy V, Peacock J, Shih DJ, Koelsche C, Northcott PA, Hill N, Cavalli FM, Kool M, Wang X, Mack SC, Barszczyk M, Morrissy AS, Wu X, Agnihotri S, Luu B, Jones DT, Garzia L, Dubuc AM, Zhukova N, Vanner R, Kros JM, French PJ, Van Meir EG, Vibhakar R, Zitterbart K, Chan JA, Bognár L, Klekner A, Lach B, Jung S, Saad AG, Liau LM, Albrecht S, Zollo M, Cooper MK, Thompson RC, Delattre OO, Bourdeaut F, Doz FF, Garami M, Hauser P, Carlotti CG, Van Meter TE, Massimi L, Fults D, Pomeroy SL, Kumabe T, Ra YS, Leonard JR, Elbabaa SK, Mora J, Rubin JB, Cho YJ, McLendon RE, Bigner DD, Eberhart CG, Fouladi M, Wechsler-Reya RJ, Faria CC, Croul SE, Huang A, Bouffet E, Hawkins CE, Dirks PB, Weiss WA, Schüller U, Pollack IF, Rutkowski S, Meyronet D, Jouvet A, Fèvre-Montange M, Jabado N, Perek-Polnik M, Grajkowska WA, Kim SK, Rutka JT, Malkin D, Tabori U, Pfister SM, Korshunov A, von Deimling A, Taylor MD. TERT promoter mutations are highly recurrent in SHH subgroup medulloblastoma. Acta Neuropathol. 2013 Dec; 126(6):917-29.

Moura LI, Dias AM, Leal EC, Carvalho L, de Sousa HC, Carvalho E. Chitosan-based dressings loaded with neurotensin--an efficient strategy to improve early diabetic wound healing. Acta Biomater. 2014 Feb; 10(2):843-57.

Chavan SS, Bauer MA, Peterson EA, Heuck CJ, Johann DJ. Towards the integration, annotation and association of historical microarray experiments with RNA-seq. BMC Bioinformatics. 2013; 14 Suppl 14:S4.

Levanon K, Sapoznik S, Bahar-Shany K, Brand H, Shapira-Frommer R, Korach J, Hirsch MS, Roh MH, Miron A, Liu JF, Vena N, Ligon AH, Fotheringham S, Bailey D, Flavin RJ, Birrer MJ, Drapkin RI. FOXO3a loss is a frequent early event in high-grade pelvic serous carcinogenesis. Oncogene. 2014 Aug 28; 33(35):4424-32.

Puvvada S, Kendrick S, Rimsza L. Molecular classification, pathway addiction, and therapeutic targeting in diffuse large B cell lymphoma. Cancer Genet. 2013 Jul-Aug; 206(7-8):257-65.

Wiggs JL, Hauser MA, Abdrabou W, Allingham RR, Budenz DL, Delbono E, Friedman DS, Kang JH, Gaasterland D, Gaasterland T, Lee RK, Lichter PR, Loomis S, Liu Y, McCarty C, Medeiros FA, Moroi SE, Olson LM, Realini A, Richards JE, Rozsa FW, Schuman JS, Singh K, Stein JD, Vollrath D, Weinreb RN, Wollstein G, Yaspan BL, Yoneyama S, Zack D, Zhang K, Pericak-Vance M, Pasquale LR, Haines JL. The NEIGHBOR consortium primary open-angle glaucoma genome-wide association study: rationale, study design, and clinical variables. J Glaucoma. 2013 Sep; 22(7):517-25.

Mercado CP, Byrum S, Beggs ML, Ziu E, Singh P, Raj VR, Haun RS, Kilic F. Impact of elevated plasma serotonin on global gene expression of murine megakaryocytes. PLoS One. 2013; 8(8):e72580.

Miousse IR, Gomez-Acevedo H, Sharma N, Vantrease J, Hennings L, Shankar K, Cleves MA, Badger TM, Ronis MJ. Mammary gland morphology and gene expression signature of weanling male and female rats following exposure to exogenous estradiol. Exp Biol Med (Maywood). 2013 Sep; 238(9):1033-46.

Gonzalo DH, Lai KK, Shadrach B, Goldblum JR, Bennett AE, Downs-Kelly E, Liu X, Henricks W, Patil DT, Carver P, Na J, Gopalan B, Rybicki L, Pai RK. Gene expression profiling of serrated polyps identifies annexin A10 as a marker of a sessile serrated adenoma/polyp. J Pathol. 2013 Aug; 230(4):420-9.

Knecht KR, MacLeod SL, Hobbs CA, Li M, Morrow WR. Gene expression profiling in pediatric heart transplant rejection. Int J Cardiol. 2013 Oct 12; 168(5):5052-3.

Jernås M, Malmeström C, Axelsson M, Nookaew I, Wadenvik H, Lycke J, Olsson B. MicroRNA regulate immune pathways in T-cells in multiple sclerosis (MS). BMC Immunol. 2013 Jul 29; 14:32.

Knuf C, Nookaew I, Brown SH, McCulloch M, Berry A, Nielsen J. Investigation of malic acid production in Aspergillus oryzae under nitrogen starvation conditions. Appl Environ Microbiol. 2013 Oct; 79(19):6050-8.

Jernås M, Hou Y, Strömberg Célind F, Shao L, Nookaew I, Wang Q, Ju X, Mellgren K, Wadenvik H, Hou M, Olsson B. Differences in gene expression and cytokine levels between newly diagnosed and chronic pediatric ITP. Blood. 2013 Sep 05; 122(10):1789-92.

Yang Y, Shi J, Tolomelli G, Xu H, Xia J, Wang H, Zhou W, Zhou Y, Das S, Gu Z, Levasseur D, Zhan F, Tricot G. RARa2 expression confers myeloma stem cell features. Blood. 2013 Aug 22; 122(8):1437-47.

Smalling RV, Delker DA, Zhang Y, Nieto N, McGuiness MS, Liu S, Friedman SL, Hagedorn CH, Wang L. Genome-wide transcriptome analysis identifies novel gene signatures implicated in human chronic liver disease. Am J Physiol Gastrointest Liver Physiol. 2013 09 01; 305(5):G364-74.

Walker BA, Wardell CP, Ross FM, Morgan GJ. Identification of a novel t(7;14) translocation in multiple myeloma resulting in overexpression of EGFR. Genes Chromosomes Cancer. 2013 Sep; 52(9):817-22.

Zhang C, Kodell RL. Subpopulation-specific confidence designation for more informative biomedical classification. Artif Intell Med. 2013 Jul; 58(3):155-63.

Wu P, Agnelli L, Walker BA, Todoerti K, Lionetti M, Johnson DC, Kaiser M, Mirabella F, Wardell C, Gregory WM, Davies FE, Brewer D, Neri A, Morgan GJ. Improved risk stratification in myeloma using a microRNA-based classifier. Br J Haematol. 2013 Aug; 162(3):348-59.

Kaiser MF, Johnson DC, Wu P, Walker BA, Brioli A, Mirabella F, Wardell CP, Melchor L, Davies FE, Morgan GJ. Global methylation analysis identifies prognostically important epigenetically inactivated tumor suppressor genes in multiple myeloma. Blood. 2013 Jul 11; 122(2):219-26.

Stessman HA, Baughn LB, Sarver A, Xia T, Deshpande R, Mansoor A, Walsh SA, Sunderland JJ, Dolloff NG, Linden MA, Zhan F, Janz S, Myers CL, Van Ness BG. Profiling bortezomib resistance identifies secondary therapies in a mouse myeloma model. Mol Cancer Ther. 2013 Jun; 12(6):1140-50.

Brown CO, Schibler J, Fitzgerald MP, Singh N, Salem K, Zhan F, Goel A. Scavenger receptor class A member 3 (SCARA3) in disease progression and therapy resistance in multiple myeloma. Leuk Res. 2013 Aug; 37(8):963-9.

Väremo L, Nielsen J, Nookaew I. Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods. Nucleic Acids Res. 2013 Apr; 41(8):4378-91.

Delgado-Calle J, Arozamena J, Pérez-López J, Bolado-Carrancio A, Sañudo C, Agudo G, de la Vega R, Alonso MA, Rodríguez-Rey JC, Riancho JA. Role of BMPs in the regulation of sclerostin as revealed by an epigenetic modifier of human bone cells. Mol Cell Endocrinol. 2013 Apr 30; 369(1-2):27-34.

Tripathi S, Glazko GV, Emmert-Streib F. Ensuring the statistical soundness of competitive gene set approaches: gene filtering and genome-scale coverage are essential. Nucleic Acids Res. 2013 Apr; 41(7):e82.

Zaid TM, Yeung TL, Thompson MS, Leung CS, Harding T, Co NN, Schmandt RS, Kwan SY, Rodriguez-Aguay C, Lopez-Berestein G, Sood AK, Wong KK, Birrer MJ, Mok SC. Identification of FGFR4 as a potential therapeutic target for advanced-stage, high-grade serous ovarian cancer. Clin Cancer Res. 2013 Feb 15; 19(4):809-20.

Zhou W, Yang Y, Xia J, Wang H, Salama ME, Xiong W, Xu H, Shetty S, Chen T, Zeng Z, Shi L, Zangari M, Miles R, Bearss D, Tricot G, Zhan F. NEK2 induces drug resistance mainly through activation of efflux drug pumps and is associated with poor prognosis in myeloma and other cancers. Cancer Cell. 2013 Jan 14; 23(1):48-62.

Usmani SZ, Mitchell A, Waheed S, Crowley J, Hoering A, Petty N, Brown T, Bartel T, Anaissie E, van Rhee F, Barlogie B. Prognostic implications of serial 18-fluoro-deoxyglucose emission tomography in multiple myeloma treated with total therapy 3. Blood. 2013 Mar 07; 121(10):1819-23.

Jernås M, Nookaew I, Wadenvik H, Olsson B. MicroRNA regulate immunological pathways in T-cells in immune thrombocytopenia (ITP). Blood. 2013 Mar 14; 121(11):2095-8.

Delgado-Calle J, Fernández AF, Sainz J, Zarrabeitia MT, Sañudo C, García-Renedo R, Pérez-Núñez MI, García-Ibarbia C, Fraga MF, Riancho JA. Genome-wide profiling of bone reveals differentially methylated regions in osteoporosis and osteoarthritis. Arthritis Rheum. 2013 Jan; 65(1):197-205.

Verhaak RG, Tamayo P, Yang JY, Hubbard D, Zhang H, Creighton CJ, Fereday S, Lawrence M, Carter SL, Mermel CH, Kostic AD, Etemadmoghadam D, Saksena G, Cibulskis K, Duraisamy S, Levanon K, Sougnez C, Tsherniak A, Gomez S, Onofrio R, Gabriel S, Chin L, Zhang N, Spellman PT, Zhang Y, Akbani R, Hoadley KA, Kahn A, Köbel M, Huntsman D, Soslow RA, Defazio A, Birrer MJ, Gray JW, Weinstein JN, Bowtell DD, Drapkin R, Mesirov JP, Getz G, Levine DA, Meyerson M. Prognostically relevant gene signatures of high-grade serous ovarian carcinoma. J Clin Invest. 2013 Jan; 123(1):517-25.

Jin C, Chen J, Meng Q, Carreira V, Tam NN, Geh E, Karyala S, Ho SM, Zhou X, Medvedovic M, Xia Y. Deciphering gene expression program of MAP3K1 in mouse eyelid morphogenesis. Dev Biol. 2013 Feb 01; 374(1):96-107.

Ounpraseuth S, Lensing SY, Spencer HJ, Kodell RL. Estimating misclassification error: a closer look at cross-validation based methods. BMC Res Notes. 2012 Nov 28; 5:656.

Todorova VK, Beggs ML, Delongchamp RR, Dhakal I, Makhoul I, Wei JY, Klimberg VS. Transcriptome profiling of peripheral blood cells identifies potential biomarkers for doxorubicin cardiotoxicity in a rat model. PLoS One. 2012; 7(11):e48398.

Jernås M, Nookaew I, Wadenvik H, Olsson B. Differential expression of T-cell genes in blood and bone marrow between ITP patients and controls. Thromb Haemost. 2013 Jan; 109(1):112-7.

Qin Z, Dai L, Defee M, Findlay VJ, Watson DK, Toole BP, Cameron J, Peruzzi F, Kirkwood K, Parsons C. Kaposi's sarcoma-associated herpesvirus suppression of DUSP1 facilitates cellular pathogenesis following de novo infection. J Virol. 2013 Jan; 87(1):621-35.

Bawa-Khalfe T, Lu LS, Zuo Y, Huang C, Dere R, Lin FM, Yeh ET. Differential expression of SUMO-specific protease 7 variants regulates epithelial-mesenchymal transition. Proc Natl Acad Sci U S A. 2012 Oct 23; 109(43):17466-71.

Rahmatallah Y, Emmert-Streib F, Glazko G. Gene set analysis for self-contained tests: complex null and specific alternative hypotheses. Bioinformatics. 2012 Dec 01; 28(23):3073-80.

Pitroda SP, Zhou T, Sweis RF, Filippo M, Labay E, Beckett MA, Mauceri HJ, Liang H, Darga TE, Perakis S, Khan SA, Sutton HG, Zhang W, Khodarev NN, Garcia JG, Weichselbaum RR. Tumor endothelial inflammation predicts clinical outcome in diverse human cancers. PLoS One. 2012; 7(10):e46104.

Hall AO, Beiting DP, Tato C, John B, Oldenhove G, Lombana CG, Pritchard GH, Silver JS, Bouladoux N, Stumhofer JS, Harris TH, Grainger J, Wojno ED, Wagage S, Roos DS, Scott P, Turka LA, Cherry S, Reiner SL, Cua D, Belkaid Y, Elloso MM, Hunter CA. The cytokines interleukin 27 and interferon-? promote distinct Treg cell populations required to limit infection-induced pathology. Immunity. 2012 Sep 21; 37(3):511-23.

Nookaew I, Papini M, Pornputtapong N, Scalcinati G, Fagerberg L, Uhlén M, Nielsen J. A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae. Nucleic Acids Res. 2012 Nov 01; 40(20):10084-97.

Ketsawatsomkron P, Lorca RA, Keen HL, Weatherford ET, Liu X, Pelham CJ, Grobe JL, Faraci FM, England SK, Sigmund CD. PPAR? regulates resistance vessel tone through a mechanism involving RGS5-mediated control of protein kinase C and BKCa channel activity. Circ Res. 2012 Nov 09; 111(11):1446-58.

Feng L, Li XQ, Li XN, Li J, Meng XM, Zhang HY, Liang JJ, Li H, Sun SK, Cai XB, Su LJ, Yin S, Li YS, Luo TR. In vitro infection with classical swine fever virus inhibits the transcription of immune response genes. Virol J. 2012 Aug 28; 9:175.

Badve S, Goswami C, Gökmen-Polar Y, Nelson RP, Henley J, Miller N, Zaheer NA, Sledge GW, Li L, Kesler KA, Loehrer PJ. Molecular analysis of thymoma. PLoS One. 2012; 7(8):e42669.

Chen T, Berno T, Zangari M. Low-risk identification in multiple myeloma using a new 14-gene model. Eur J Haematol. 2012 Jul; 89(1):28-36.

Waheed S, Mitchell A, Usmani S, Epstein J, Yaccoby S, Nair B, van Hemert R, Angtuaco E, Brown T, Bartel T, McDonald J, Anaissie E, van Rhee F, Crowley J, Barlogie B. Standard and novel imaging methods for multiple myeloma: correlates with prognostic laboratory variables including gene expression profiling data. Haematologica. 2013 Jan; 98(1):71-8.

Gray WL. The simian varicella virus ORF A is expressed in infected cells but is non-essential for replication in cell culture. Arch Virol. 2012 Sep; 157(9):1803-6.

Finlin BS, Bodles-Brakhop AM, Yao-Borengasser A, Zhu B, Starnes CP, McGehee RE, Peterson CA, Kern PA, Rasouli N. Regulation of small ubiquitin-like modifier-1, nuclear receptor coreceptor, histone deacetylase 3, and peroxisome proliferator-activated receptor-? in human adipose tissue. Metab Syndr Relat Disord. 2012 Aug; 10(4):312-7.

Walker BA, Wardell CP, Melchor L, Hulkki S, Potter NE, Johnson DC, Fenwick K, Kozarewa I, Gonzalez D, Lord CJ, Ashworth A, Davies FE, Morgan GJ. Intraclonal heterogeneity and distinct molecular mechanisms characterize the development of t(4;14) and t(11;14) myeloma. Blood. 2012 Aug 02; 120(5):1077-86.

McBurney RN, Hines WM, VonTungeln LS, Schnackenberg LK, Beger RD, Moland CL, Han T, Fuscoe JC, Chang CW, Chen JJ, Su Z, Fan XH, Tong W, Booth SA, Balasubramanian R, Courchesne PL, Campbell JM, Graber A, Guo Y, Juhasz P, Li TY, Lynch MD, Morel NM, Plasterer TN, Takach EJ, Zeng C, Beland FA. The liver toxicity biomarker study phase I: markers for the effects of tolcapone or entacapone. Toxicol Pathol. 2012 Aug; 40(6):951-64.

Zhang J, Lazarenko OP, Wu X, Tong Y, Blackburn ML, Gomez-Acevedo H, Shankar K, Badger TM, Ronis MJ, Chen JR. Differential effects of short term feeding of a soy protein isolate diet and estrogen treatment on bone in the pre-pubertal rat. PLoS One. 2012; 7(4):e35736.

Zhang X, Azhar G, Wei JY. The expression of microRNA and microRNA clusters in the aging heart. PLoS One. 2012; 7(4):e34688.

Usmani SZ, Nair B, Qu P, Hansen E, Zhang Q, Petty N, Waheed S, Shaughnessy JD, Alsayed Y, Heuck CJ, van Rhee F, Milner T, Hoering A, Szymonifka J, Sexton R, Sawyer J, Singh Z, Crowley J, Barlogie B. Primary plasma cell leukemia: clinical and laboratory presentation, gene-expression profiling and clinical outcome with Total Therapy protocols. Leukemia. 2012 Nov; 26(11):2398-405.

Papic N, Maxwell CI, Delker DA, Liu S, Heale BS, Hagedorn CH. RNA-sequencing analysis of 5' capped RNAs identifies many new differentially expressed genes in acute hepatitis C virus infection. Viruses. 2012 04; 4(4):581-612.

Aboud O, Mrak RE, Boop F, Griffin ST. Apolipoprotein epsilon 3 alleles are associated with indicators of neuronal resilience. BMC Med. 2012 Apr 13; 10:35.

Zhou Y, Zhang Q, Stephens O, Heuck CJ, Tian E, Sawyer JR, Cartron-Mizeracki MA, Qu P, Keller J, Epstein J, Barlogie B, Shaughnessy JD. Prediction of cytogenetic abnormalities with gene expression profiles. Blood. 2012 May 24; 119(21):e148-50.

Rangani G, Khodakovskaya M, Alimohammadi M, Hoecker U, Srivastava V. Site-specific methylation in gene coding region underlies transcriptional silencing of the Phytochrome A epiallele in Arabidopsis thaliana. Plant Mol Biol. 2012 May; 79(1-2):191-202.

Deffenbacher KE, Iqbal J, Sanger W, Shen Y, Lachel C, Liu Z, Liu Y, Lim MS, Perkins SL, Fu K, Smith L, Lynch J, Staudt LM, Rimsza LM, Jaffe E, Rosenwald A, Ott GK, Delabie J, Campo E, Gascoyne RD, Cairo MS, Weisenburger DD, Greiner TC, Gross TG, Chan WC. Molecular distinctions between pediatric and adult mature B-cell non-Hodgkin lymphomas identified through genomic profiling. Blood. 2012 Apr 19; 119(16):3757-66.

Shankar K, Zhong Y, Kang P, Blackburn ML, Soares MJ, Badger TM, Gomez-Acevedo H. RNA-seq analysis of the functional compartments within the rat placentation site. Endocrinology. 2012 Apr; 153(4):1999-2011.

Engler DA, Gupta S, Growdon WB, Drapkin RI, Nitta M, Sergent PA, Allred SF, Gross J, Deavers MT, Kuo WL, Karlan BY, Rueda BR, Orsulic S, Gershenson DM, Birrer MJ, Gray JW, Mohapatra G. Genome wide DNA copy number analysis of serous type ovarian carcinomas identifies genetic markers predictive of clinical outcome. PLoS One. 2012; 7(2):e30996.

Ferriss JS, Kim Y, Duska L, Birrer M, Levine DA, Moskaluk C, Theodorescu D, Lee JK. Multi-gene expression predictors of single drug responses to adjuvant chemotherapy in ovarian carcinoma: predicting platinum resistance. PLoS One. 2012; 7(2):e30550.

Cheng BY, Zhi J, Santana A, Khan S, Salinas E, Forrest JC, Zheng Y, Jaggi S, Leatherwood J, Krug LT. Tiled microarray identification of novel viral transcript structures and distinct transcriptional profiles during two modes of productive murine gammaherpesvirus 68 infection. J Virol. 2012 Apr; 86(8):4340-57.

Tomita-Mitchell A, Mahnke DK, Struble CA, Tuffnell ME, Stamm KD, Hidestrand M, Harris SE, Goetsch MA, Simpson PM, Bick DP, Broeckel U, Pelech AN, Tweddell JS, Mitchell ME. Human gene copy number spectra analysis in congenital heart malformations. Physiol Genomics. 2012 May 01; 44(9):518-41.

Fang Z, Du R, Cui X. Uniform approximation is more appropriate for Wilcoxon Rank-Sum Test in gene set analysis. PLoS One. 2012; 7(2):e31505.

Ashida S, Orloff MS, Bebek G, Zhang L, Zheng P, Peehl DM, Eng C. Integrated analysis reveals critical genomic regions in prostate tumor microenvironment associated with clinicopathologic phenotypes. Clin Cancer Res. 2012 Mar 15; 18(6):1578-87.

Vathipadiekal V, Saxena D, Mok SC, Hauschka PV, Ozbun L, Birrer MJ. Identification of a potential ovarian cancer stem cell gene expression profile from advanced stage papillary serous ovarian cancer. PLoS One. 2012; 7(1):e29079.

Schwarz JK, Payton JE, Rashmi R, Xiang T, Jia Y, Huettner P, Rogers BE, Yang Q, Watson M, Rader JS, Grigsby PW. Pathway-specific analysis of gene expression data identifies the PI3K/Akt pathway as a novel therapeutic target in cervical cancer. Clin Cancer Res. 2012 Mar 01; 18(5):1464-71.

Alapat D, Coviello-Malle J, Owens R, Qu P, Barlogie B, Shaughnessy JD, Lorsbach RB. Diagnostic usefulness and prognostic impact of CD200 expression in lymphoid malignancies and plasma cell myeloma. Am J Clin Pathol. 2012 Jan; 137(1):93-100.

Lussier YA, Xing HR, Salama JK, Khodarev NN, Huang Y, Zhang Q, Khan SA, Yang X, Hasselle MD, Darga TE, Malik R, Fan H, Perakis S, Filippo M, Corbin K, Lee Y, Posner MC, Chmura SJ, Hellman S, Weichselbaum RR. MicroRNA expression characterizes oligometastasis(es). PLoS One. 2011; 6(12):e28650.