Bioinformatics Publications

Bhatti UF, Remmer H, Williams AM, Biesterveld BE, Russo R, Wakam G…Tagett R…et al. Assessment of the Cytoprotective Effects of High-Dose Valproic Acid Compared to a  Clinically Used Lower Dose. J Surg Res. 2021 May;266:125–41.  Available from:

Burton JB, Carruthers NJ, Stemmer PM. Enriching extracellular vesicles for mass spectrometry. Mass Spectrom Rev. 2021 Oct; Available from:

Carruthers NJ, Strieder-Barboza C, Caruso JA, Flesher CG, Baker NA, Kerk SA, et al. The human type 2 diabetes-specific visceral adipose tissue proteome and  transcriptome in obesity. Sci Rep. 2021 Aug;11(1):17394. Available from:

Dekker SE, Biesterveld BE, Bambakidis T, Williams AM, Tagett R, Johnson CN, et al. Modulation of Brain Transcriptome by Combined Histone Deacetylase Inhibition and  Plasma Treatment Following Traumatic Brain Injury and Hemorrhagic Shock. Shock. 2021 Jan;55(1):110–20. Available from:

Delorme J, Wang L, Kuhn FR, Kodoth V, Ma J, Martinez JD, et al. Sleep loss drives acetylcholine- and somatostatin interneuron-mediated gating of  hippocampal activity to inhibit memory consolidation. Proc Natl Acad Sci U S A. 2021 Aug;118(32). Available from:

Delorme J, Wang L, Kodoth V, Wang Y, Ma J, Jiang S, et al. Hippocampal neurons’ cytosolic and membrane-bound ribosomal transcript profiles are  differentially regulated by learning and subsequent sleep. Proc Natl Acad Sci U S A. 2021 Nov;118(48). Available from:

Fortier SM, Penke LR, King DM, Pham TX, Ligresti G, Peters-Golden M. Myofibroblast de-differentiation proceeds via distinct transcriptomic and phenotypic  transitions. JCI insight. 2021 Feb; Available from:

Weber SR, Zhao Y, Gates C, Ma J, da Veiga Leprevost F, Basrur V, et al. Proteomic Analyses of Vitreous in Proliferative Diabetic Retinopathy: Prior Studies  and Future Outlook. J Clin Med. 2021 May;10(11). Available from:

Weber SR, Zhao Y, Ma J, Gates C, da Veiga Leprevost F, Basrur V, et al. A validated analysis pipeline for mass spectrometry-based vitreous proteomics: new  insights into proliferative diabetic retinopathy. Clin Proteomics. 2021 Dec;18(1):28. Available from:

Wu W, Lovett JL, Shedden K, Strassmann BI, Vincenz C. Targeted RNA-seq improves efficiency, resolution, and accuracy of allele specific expression for human term placentas. G3 (Bethesda). 2021 May; Available from:

Alghamri MS, Thalla R, Avvari R, Dabaja A, Taher A, Zhao L, Ulintz PJ, et al. Tumor mutational burden predicts survival in patients with low grade gliomas expressing mutated idh1. Neuro-Oncology Adv. 2020;2(March):1–13. Available from:

Atchison DK, O’Connor CL, Menon R, Otto EA, Ganesh SK, Wiggins RC, et al. Hypertension Induces Glomerulosclerosis in Phospholipase C Epsilon 1 Deficiency. Am J Physiol Renal Physiol. 2020 Mar;318(5):F1177‐F1187. Available from:

Aw Yong KM, Ulintz PJ, Caceres S, Cheng X, Bao L, Wu Z, et al. Heterogeneity at the invasion front of triple negative breast cancer cells. Sci Rep. 2020 Apr;10(1):5781. Available from:

Dragon JA, Gates C, Sui SH, Hutchinson JN, Karuturi RKM, Kucukural A, et al. Bioinformatics Core Survey Highlights the Challenges Facing Data Analysis  Facilities. J Biomol Tech. 2020 Apr;31(2):66–73. Available from:

Guo NL, Bello D, Ye Q, Tagett R, Chanetsa L, Singh D, et al. Pilot deep RNA sequencing of worker blood samples from Singapore printing industry  for occupational risk assessment. NanoImpact. 2020 Jul;19. Available from

Johnson AO, Forsyth V, Smith SN, Learman BS, Brauer AL, White AN…Wu W…et al. Transposon Insertion Site Sequencing of Providencia stuartii: Essential Genes,  Fitness Factors for Catheter-Associated Urinary Tract Infection, and the Impact of Polymicrobial Infection on Fitness Requirements. mSphere. 2020 May;5(3):e00412-20.  Available from:

King DM, Hong CKY, Shepherdson JL, Granas DM, Maricque BB, Cohen B. Synthetic and genomic regulatory elements reveal aspects of cis-regulatory grammar in Mouse Embryonic Stem Cells. Elife [Internet]. 2020 Feb 11;9:e41279. Available from:

Menon R, Otto EA, Hoover PJ, Eddy S, Mariani LH, Godfrey B, et al. Single cell transcriptomics identifies focal segmental glomerulosclerosis remission endothelial biomarker. JCI insight [Internet]. 2020 Feb 27;5(6):e133267. Available from:

Rieger MA, King DM, Crosby H, Liu Y, Cohen BA, Dougherty JD. CLIP and Massively Parallel Functional Analysis of CELF6 Reveal a Role in  Destabilizing Synaptic Gene mRNAs through Interaction with 3’ UTR Elements. Cell Rep. 2020 Dec;33(12):108531.  Available from:

Rubenstein JH, Tavakkoli A, Koeppe E, Ulintz P, Inadomi JM, Morgenstern H, et al. Family History of Colorectal or Esophageal Cancer in Barrett’s Esophagus and  Potentially Explanatory Genetic Variants. Clin Transl Gastroenterol. 2020 Apr;11(4):e00151. Available from:

Sas AR, Carbajal KS, Jerome AD, Menon R, Yoon C, Kalinski AL, et al. A new neutrophil subset promotes CNS neuron survival and axon regeneration. Nat Immunol. 2020 Dec;21(12):1496-1505; Available from:

Sorkin M, Huber AK, Hwang C, Carson  4th WF, Menon R, Li J, et al. Regulation of heterotopic ossification by monocytes in a mouse model of aberrant wound healing. Nat Commun [Internet]. 2020 Feb 5;11(1):722. Available from:

Vincenz C, Lovett JL, Wu W, Shedden K, Strassmann BI. Loss of Imprinting in Human Placentas Is Widespread, Coordinated, and Predicts Birth Phenotypes. Mol Biol Evol. 2020 Feb;37(2):429–41. Available from:

Armbruster CE, Forsyth VS, Johnson AO, Smith SN, White AN, Brauer AL…Wu W…et al. Twin arginine translocation, ammonia incorporation, and polyamine biosynthesis are crucial for Proteus mirabilis fitness during bloodstream infection. PLoS Pathog. United States; 2019 Apr;15(4):e1007653.

Brandenburg MD, Martin S. From Presenter to Producer: Librarian as Leader of a Departmental Seminar Series. Sci Technol Libr [Internet]. 2019 Oct 29;1–10. Available from:

Cackowski FC, Wang Y, Decker JT, Sifuentes C, Weindorf S, Jung Y, et al. Detection and isolation of disseminated tumor cells in bone marrow of patients with clinically localized prostate cancer. Prostate. 2019 Oct;79(14):1715–27.

Frydrych LM, Ulintz P, Bankhead A, Sifuentes C, Greenson J, Maguire L, et al. Rectal cancer sub-clones respond differentially to neoadjuvant therapy. Neoplasia. 2019 Sep;21(10):1051–62.

Harder JL, Menon R, Otto EA, Zhou J, Eddy S, Wys NL, et al. Organoid single cell profiling identifies a transcriptional signature of glomerular disease. JCI insight. 2019 Jan;4(1):e122697.

Kim Y, Opron K, Burton ZF. A tRNA- and Anticodon-Centric View of the Evolution of Aminoacyl-tRNA Synthetases, tRNAomes, and the Genetic Code. Life (Basel, Switzerland). Switzerland; 2019 May;9(2).

Merrill NM, Lachacz EJ, Vandecan NM, Ulintz PJ, Bao L, Lloyd JP, et al. Molecular determinants of drug response in TNBC cell lines. Breast Cancer Res Treat. 2019 Oct;179(2):337-47.

Nunez FJ, Mendez FM, Kadiyala P, Alghamri MS, Savelieff MG, Garcia-Fabiani MB…Tagett R…et al. IDH1-R132H acts as a tumor suppressor in glioma via epigenetic up-regulation of the DNA damage response. Sci Transl Med. United States; 2019 Feb;11(479).

Perco P, Ju W, Kerschbaum J, Leierer J, Menon R, Zhu C, et al. Identification of dicarbonyl and L-xylulose reductase as a therapeutic target in human chronic kidney disease. JCI insight. 2019 Jun;4(12):e128120.

Salem RM, Todd JN, Sandholm N, Cole JB, Chen W-M, Andrews D…Menon R….et al. Genome-Wide Association Study of Diabetic Kidney Disease Highlights Biology Involved in Glomerular Basement Membrane Collagen. J Am Soc Nephrol. 2019 Oct;30(10):2000–16.

Ulintz PJWu WGates CM. Bioinformatics Analysis of Whole Exome Sequencing Data. Methods Mol Biol. United States; 2019;1881:277–318.

Vincenz C, Lovett JL, Wu W, Shedden K, Strassmann BI. Loss of imprinting in human placentas is widespread, coordinated, and predicts birth phenotypes. Mol Biol Evol. 2019 Oct;37(2):429-41.

Zafar MA, Hammond AJ, Hamaguchi S, Wu W, Kono M, Zhao L, et al. Identification of Pneumococcal Factors Affecting Pneumococcal Shedding Shows that the dlt Locus Promotes Inflammation and Transmission. MBio. 2019 Jun;10(3).

Zieman AG, Poll BG, Ma J, Coulombe PA. Altered keratinocyte differentiation is an early driver of keratin mutation-based palmoplantar keratoderma. Hum Mol Genet. 2019 Jul;28(13):2255–70.

Begley L, Madapoosi S, Opron K, Ndum O, Baptist A, Rysso K, et al. Gut microbiota relationships to lung function and adult asthma phenotype: a pilot study. BMJ open Respir Res. England; 2018;5(1):e000324.

Bohn JA, Van Etten JL, Schagat TL, Bowman BM, McEachin RC, Freddolino PL, et al. Identification of diverse target RNAs that are functionally regulated by human Pumilio proteins. Nucleic Acids Res. England; 2018 Jan; 46(1):362-386.

Brady GF, Kwan R, Ulintz PJ, Nguyen P, Bassirian S, Basrur V, et al. Nuclear lamina genetic variants, including a truncated LAP2, in twins and siblings with nonalcoholic fatty liver disease. Hepatology. United States; 2018 May;67(5):1710-1725. 

Czerniecki SM, Cruz NM, Harder JL, Menon R, Annis J, Otto EA, et al. High-Throughput Screening Enhances Kidney Organoid Differentiation from Human Pluripotent Stem Cells and Enables Automated Multidimensional Phenotyping. Cell Stem Cell. 2018 Jun;22(6):929-940.e4.

Gensterblum-Miller E, Wu W, Sawalha AH. Novel Transcriptional Activity and Extensive Allelic Imbalance in the Human MHC Region. J Immunol. United States; 2018 Feb;200(4):1496-1503.

Gillies CE, Putler R, Menon R, Otto E, Yasutake K, Nair V, et al. An eQTL Landscape of Kidney Tissue in Human Nephrotic Syndrome. Am J Hum Genet. 2018 Aug;103(2):232–44.

Hall H, Ma J, Shekhar S, Leon-Salas WD, Weake VM. Blue light induces a neuroprotective gene expression program in Drosophila photoreceptors. BMC Neurosci. England; 2018 Jul;19(1):43.

Kim Y, Kowiatek B, Opron K, Burton ZF. Type-II tRNAs and Evolution of Translation Systems and the Genetic Code. Int J Mol Sci. Switzerland; 2018 Oct;19(10).

Kretzler M, Menon R. Single-Cell Sequencing the Glomerulus, Unraveling the Molecular Programs of Glomerular Filtration, One Cell at a Time. J Am Soc Nephrol. 2018 Aug;29(8):2036–8.

Lundy SK, Nikoopour E, Karoukis AJ, Ohara R, Othman MI, Tagett R, et al. T Helper 1 Cellular Immunity Toward Recoverin Is Enhanced in Patients With Active Autoimmune Retinopathy. Front Med. Switzerland; 2018;5:249.

Martin RM, Cao J, Wu W, Zhao L, Manthei DM, Pirani A, et al. Identification of Pathogenicity-Associated Loci in Klebsiella pneumoniae from Hospitalized Patients. mSystems. United States; 2018;3(3):e00015-18.

Menon R, Otto EA, Kokoruda A, Zhou J, Zhang Z, Yoon E, et al. Single-cell analysis of progenitor cell dynamics and lineage specification in the human fetal kidney. Development. 2018 Aug;145(16):dev164038.

Nedialkov YA, Opron K, Caudill HL, Assaf F, Anderson AJ, Cukier RI, et al. Hinge action versus grip in translocation by RNA polymerase. Transcription. United States; 2018;9(1):1–16.

Opron K, Burton ZF. Ribosome Structure, Function, and Early Evolution. Int J Mol Sci. Switzerland; 2018 Dec;20(1):40.

Park H-R, Harris SM, Boldenow E, McEachin RC, Sartor M, Chames M, et al. Group B Streptococcus Activates Transcriptomic Pathways Related to Premature Birth in Human Extraplacental Membranes In Vitro. Biol Reprod. United States; 2018 Mar;98(3):396-407. 

Stoffel EM, Koeppe E, Everett J, Ulintz P, Kiel M, Osborne J, et al. Germline Genetic Features of Young Individuals With Colorectal Cancer. Gastroenterology. United States; 2018 Mar;154(4):897–905.e1.

Szerlip NJ, Calinescu A, Smith E, Tagett R, Clines KL, Moon HH, et al. Dural Cells Release Factors Which Promote Cancer Cell Malignancy and Induce Immunosuppressive Markers in Bone Marrow Myeloid Cells. Neurosurgery. United States; 2018 Dec;83(6):1306-1316.

Ulintz PJ, Greenson JK, Wu R, Fearon ER, Hardiman KM. Lymph Node Metastases in Colon Cancer are Polyclonal. Clin Cancer Res. United States; 2018 May;24(9):2214-2224.

Warner KA, Oklejas AE, Pearson AT, Zhang Z, Wu W, Divi V, et al. UM-HACC-2A: MYB-NFIB fusion-positive human adenoid cystic carcinoma cell line. Oral Oncol. England; 2018 Dec;87:21–8.

Armbruster CE, Forsyth-DeOrnellas V, Johnson AO, Smith SN, Zhao L, Wu W, et al. Genome-wide transposon mutagenesis of Proteus mirabilis: Essential genes, fitness factors for catheter-associated urinary tract infection, and the impact of polymicrobial infection on fitness requirements. PLoS Pathog. United States; 2017 Jun;13(6):e1006434.

Bender MC, Sifuentes CJ, Denver RJ. Leptin Induces Mitosis and Activates the Canonical Wnt/β-Catenin Signaling Pathway in Neurogenic Regions of Xenopus Tadpole Brain. Front Endocrinol (Lausanne). 2017;8:99.

Brandenburg MD, Garcia-Milian R. Inter-institutional Collaboration for End-user Bioinformatics Training: Cytoscape as a Case. J Med Libr Assoc. 2017 Apr.;105(2):179-84.

Brandenburg MD, Cordell S, Joque J, MacEachern M, Song J. Interdisciplinary Collaboration: Librarian Involvement in Grant Projects. Coll Res Libr. 2017 Mar;78(3):272-82.

Koneva LA, Vyas AK, McEachin RC, Puttabyatappa M, Wang H-S, Sartor MA, et al. Developmental programming: Interaction between prenatal BPA and postnatal overfeeding on cardiac tissue gene expression in female sheep. Environ Mol Mutagen. United States; 2017 Jan;58(1):4–18.

Li H, Zhang Y, Guan Y, Menon R, Omenn GS. Annotation of Alternatively Spliced Proteins and Transcripts with Protein-Folding Algorithms and Isoform-Level Functional Networks. Methods Mol Biol. 2017;1558:415–36.

Nguyen T, Tagett R, Diaz D, Draghici S. A novel approach for data integration and disease subtyping. Genome Res. United States; 2017 Dec;27(12):2025–39.

Ramani B, Harris GM, Huang R, Seki T, Murphy GG, Carmo Costa M do…McEachin RC…et al. A knockin mouse model of spinocerebellar ataxia type 3 exhibits prominent aggregate pathology and aberrant splicing of the disease gene transcript. Hum Mol Genet. England; 2017 Jun;26(16):3232-3.

Schlecht SH, Smith LM, Ramcharan MA, Bigelow EM, Nolan BT, Mathis NJ…Menon RMcEachin RC…et al. Canalization Leads to Similar Whole Bone Mechanical Function at Maturity in Two Inbred Strains of Mice. J Bone Miner Res. United States; 2017 May;32(5):1002-13.

Sun Y, Iyer M, McEachin R, Zhao M, Wu Y-M, Cao X, et al. Genome-Wide STAT3 Binding Analysis after Histone Deacetylase Inhibition Reveals Novel Target Genes in Dendritic Cells. J Innate Immun. Switzerland; 2017 Nov;9(2):126-144.

Zhao L, Anderson MT, Wu W, T Mobley HL, Bachman MA. TnseqDiff: identification of conditionally essential genes in transposon sequencing studies. BMC Bioinformatics. England; 2017 Jul;18(1):326.

Zhao L, Wu W, Feng D, Jiang H, Nguyen X. Bayesian Analysis of RNA-Seq Data Using a Family of Negative Binomial Models. Bayesian Anal [Internet]. 2017; Available from:

Armbruster CE, Smith SN, Johnson AO, DeOrnellas V, Eaton KA, Yep A…Wu W…et al. The Pathogenic Potential of Proteus mirabilis is Enhanced by Other Uropathogens During Polymicrobial Urinary Tract Infection. Infect Immun. United States; 2016 Nov;85(2):e00808-16.

Bayliss J, Mukherjee P, Lu C, Jain SU, Chung C, Martinez D…McEachin RC…et al. Lowered H3K27me3 and DNA hypomethylation define poorly prognostic pediatric posterior fossa ependymomas. Sci Transl Med. United States; 2016 Nov;8(366):366ra161.

Bokanizad B, Tagett R, Ansari S, Helmi BH, Draghici S. SPATIAL: A System-level PAThway Impact AnaLysis approach. Nucleic Acids Res. England; 2016 Jun;44(11):5034–44.

Brandenburg MD. Librarian Involvement in tranSMART: a Translational Biomedical Research Platform. In: Conte M, editor. Translating Expertise: Librarian Roles in Translational Research. Lanham, Maryland: Rowan & Littlefield; 2016. p. 27–42.

Brandenburg MD, Joque J. Contextualizing Visualization in Library Services. In: Federer L, editor. The Medical Library Association Guide to Data Management for Librarians. Lanham, Maryland: Rowan & Littlefield; 2016. p. 139–50.

Burton ZF, Opron K, Wei G, Geiger JH. A model for genesis of transcription systems. Transcription. United States; 2016;7(1):1–13.

Georgoff PE, Halaweish I, Nikolian VC, Higgins GA, Bonham T, Tafatia C…Menon R…et al. Alterations in the human proteome following administration of valproic acid. J Trauma Acute Care Surg. United States; 2016 Dec;81(6):1020–7.

Hardiman KM, Ulintz PJ, Kuick RD, Hovelson DH, Gates CMBhasi AGrant AR, et al. Intra-tumor genetic heterogeneity in rectal cancer. Lab Invest. United States; 2016 Jan;96(1):4–15.

Kim H-E, Grant AR, Simic MS, Kohnz RA, Nomura DK, Durieux J, et al. Lipid Biosynthesis Coordinates a Mitochondrial-to-Cytosolic Stress Response. Cell. United States; 2016 Sep;166(6):1539–1552.e16.

Li H-D, Menon R, Eksi R, Guerler A, Zhang Y, Omenn GS, et al. A Network of Splice Isoforms for the Mouse. Sci Rep. England; 2016 Apr;6:24507.

Ma J, Brennan KJ, D’Aloia MR, Pascuzzi PE, Weake VM. Transcriptome Profiling Identifies Multiplexin as a Target of SAGA Deubiquitinase Activity in Glia Required for Precise Axon Guidance During Drosophila Visual Development. G3 (Bethesda). United States; 2016 Aug;6(8):2435–45.

Martin RM, Cao J, Brisse S, Passet V, Wu W, Zhao L, et al. Molecular Epidemiology of Colonizing and Infecting Isolates of Klebsiella pneumoniae. mSphere. United States; 2016;1(5):e00261-16.

Menon S, Lu C, Menon R, Schwartz J, Guan Y. Effects of Antioxidants in Human Cancers: Differential Effects on Non-Coding Intronic RNA Expression. Antioxidants (Basel, Switzerland). Switzerland; 2016 Jan;5(1).

Nguyen T, Diaz D, Tagett R, Draghici S. Overcoming the matched-sample bottleneck: an orthogonal approach to integrate omic data. Sci Rep. England; 2016 Jul;6:29251.

Nguyen T, Tagett R, Donato M, Mitrea C, Draghici S. A novel bi-level meta-analysis approach: applied to biological pathway analysis. Bioinformatics. England; 2016 Feb;32(3):409–16.

Opron K, Xia K, Burton Z, Wei G-W. Flexibility-rigidity index for protein-nucleic acid flexibility and fluctuation analysis. J Comput Chem. United States; 2016 May;37(14):1283–95.

Panwar B, Menon R, Eksi R, Li H-D, Omenn GS, Guan Y. Genome-Wide Functional Annotation of Human Protein-Coding Splice Variants Using Multiple Instance Learning. J Proteome Res. United States; 2016 Jun;15(6):1747–53.

Pedersen EA, Menon R, Bailey KM, Thomas DG, Van Noord RA, Tran J, et al. Activation of Wnt/beta-Catenin in Ewing Sarcoma Cells Antagonizes EWS/ETS Function and Promotes Phenotypic Transition to More Metastatic Cell States. Cancer Res. United States; 2016 Sep;76(17):5040–53.

Sifuentes CJ, Kim J-W, Swaroop A, Raymond PA. Rapid, Dynamic Activation of Muller Glial Stem Cell Responses in Zebrafish. Invest Ophthalmol Vis Sci. United States; 2016 Oct;57(13):5148–60.

Wettlaufer SH, Scott JP, McEachin RC, Peters-Golden M, Huang SK. Reversal of the Transcriptome by Prostaglandin E2 during Myofibroblast Dedifferentiation. Am J Respir Cell Mol Biol. United States; 2016 Jan;54(1):114–27.

Zhang X, Damacharla D, Ma D, Qi Y, Tagett R, Draghici S, et al. Quantitative proteomics reveals novel protein interaction partners of PP2A catalytic subunit in pancreatic beta-cells. Mol Cell Endocrinol. Ireland; 2016 Mar;424:1–11.

Bachman MA, Breen P, Deornellas V, Mu Q, Zhao L, Wu W, Cavalcoli JD, et al. Genome-Wide Identification of Klebsiella pneumoniae Fitness Genes during Lung Infection. MBio. United States; 2015 Jun;6(3):e00775.

Burkewitz K, Morantte I, Weir HJM, Yeo R, Zhang Y, Huynh FK…Grant AR…et al. Neuronal CRTC-1 governs systemic mitochondrial metabolism and lifespan via a catecholamine signal. Cell. United States; 2015 Feb;160(5):842–55.

Cang Z, Mu L, Wu K, Opron K, Xia K, Wei G-W. A topological approach for protein classification. Mol Based Math Biol. 2015;3(1):140–62.

Chen AT-Y, Guo C, Itani OA, Budaitis BG, Williams TW, Hopkins CE, McEachin RCPande MGrant AR…et al. Longevity Genes Revealed by Integrative Analysis of Isoform-Specific daf-16/FoxO  Mutants of Caenorhabditis elegans. Genetics. United States; 2015 Oct;201(2):613–29.

Chua JP, Reddy SL, Yu Z, Giorgetti E, Montie HL, Mukherjee S…McEachin RC…et al. Disrupting SUMOylation enhances transcriptional function and ameliorates polyglutamine androgen receptor-mediated disease. J Clin Invest. United States; 2015 Feb;125(2):831–45.

Dogan N, Wu W, Morrissey CS, Chen K-B, Stonestrom A, Long M, et al. Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility. Epigenetics Chromatin. England; 2015;8:16.

Faulk C, Kim JH, Jones TR, McEachin RC, Nahar MS, Dolinoy DC, et al. Bisphenol A-associated alterations in genome-wide DNA methylation and gene expression patterns reveal sequence-dependent and non-monotonic effects in human fetal liver. Environ epigenetics. England; 2015 Dec;1(1):dvv006.

Feig M, Wang B, Sharma M, Burton Z, Opron K, Cukier R, et al. 10 How is fidelity maintained in nucleic acids? Two tales in DNA repair and DNA transcription from computer simulations. J Biomol Struct Dyn. England; 2015;33 Suppl 1:6–7.

Grigoroiu M, Tagett R, Draghici S, Dima S, Nastase A, Florea R, et al. Gene-expression Profiling in Non-small Cell Lung Cancer with Invasion of Mediastinal Lymph Nodes for Prognosis Evaluation. Cancer Genomics Proteomics. Greece; 2015;12(5):231–42.

Horvatovich P, Lundberg EK, Chen Y-J, Sung T-Y, He F, Nice EC…Menon R…et al. Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project. J Proteome Res. United States; 2015 Sep;14(9):3415–31.

Li H-D, Menon R, Govindarajoo B, Panwar B, Zhang Y, Omenn GS, et al. Functional Networks of Highest-Connected Splice Isoforms: From The Chromosome 17  Human Proteome Project. J Proteome Res. United States; 2015 Sep;14(9):3484–91.

Ma J, Lang Y, Strayer D, Richt J, Ma W. Leukocyte Interferon-α-n3 Inhibits Influenza A Viral Replication in Human Alveolar Epithelial A549 Cells. J Antivir Antiretrovir. 2015;7(4):104–7.

Menon R, Panwar B, Eksi R, Kleer C, Guan Y, Omenn GS. Computational Inferences of the Functions of Alternative/Noncanonical Splice Isoforms Specific to HER2+/ER-/PR- Breast Cancers, a Chromosome 17 C-HPP Study. J Proteome Res. United States; 2015 Sep;14(9):3519–29.

Opron K, Xia K, Wei G-W. Communication: Capturing protein multiscale thermal fluctuations. J Chem Phys. United States; 2015 Jun;142(21):211101.

Panwar B, Menon R, Eksi R, Omenn GS, Guan Y. MI-PVT: A Tool for Visualizing the Chromosome-Centric Human Proteome. J Proteome Res. United States; 2015 Sep;14(9):3762–7.

Ramani B, Harris GM, Huang R, Seki T, Murphy GG, Costa M do C…McEachin RC…et al. A knockin mouse model of spinocerebellar ataxia type 3 exhibits prominent aggregate pathology and aberrant splicing of the disease gene transcript. Hum Mol Genet. England; 2015 Mar;24(5):1211–24.

Sun Y, Oravecz-Wilson K, Mathewson N, Wang Y, McEachin R, Liu C, et al. Mature T cell responses are controlled by microRNA-142. J Clin Invest. United States; 2015 Jul;125(7):2825–40.

Wang B, Opron K, Burton ZF, Cukier RI, Feig M. Five checkpoints maintaining the fidelity of transcription by RNA polymerases in  structural and energetic details. Nucleic Acids Res. England; 2015 Jan;43(2):1133–46.

Wisloff U, Bye A, Stolen T, Kemi OJ, Pollott GE, Pande MMcEachin RC, et al. Blunted cardiomyocyte remodeling response in exercise-resistant rats. Journal of the American College of Cardiology. United States; 2015. p. 1378–80.

Xia K, Opron K, Wei G-W. Multiscale Gaussian network model (mGNM) and multiscale anisotropic network model (mANM). J Chem Phys. United States; 2015 Nov;143(20):204106.

Xia K, Opron K, Wei G-W. Correlation function based Gaussian network models. arXiv. 2015;arXiv:1503.05927

Bai Y, Hassler J, Ziyar A, Li P, Wright Z, Menon R…Cavalcoli JD…et al. Novel bioinformatics method for identification of genome-wide non-canonical spliced regions using RNA-Seq data. PLoS One. United States; 2014;9(7):e100864.

Baird NA, Douglas PM, Simic MS, Grant AR, Moresco JJ, Wolff SC, et al. HSF-1-mediated cytoskeletal integrity determines thermotolerance and life span. Science. United States; 2014 Oct;346(6207):360–3.

Broberg CA, Wu W, Cavalcoli JD, Miller VL, Bachman MA. Complete Genome Sequence of Klebsiella pneumoniae Strain ATCC 43816 KPPR1, a Rifampin-Resistant Mutant Commonly Used in Animal, Genetic, and Molecular Biology Studies. Genome Announc. United States; 2014 Sep;2(5).

Caruso M, Ma D, Msallaty Z, Lewis M, Seyoum B, Al-janabi W…Tagett R…et al. Increased interaction with insulin receptor substrate 1, a novel abnormality in insulin resistance and type 2 diabetes. Diabetes. United States; 2014 Jun;63(6):1933–47.

Chen Y, Chen Q, McEachin RC, Cavalcoli JD, Yu X. H2A.B facilitates transcription elongation at methylated CpG loci. Genome Res. United States; 2014 Apr;24(4):570–9.

Cheng Y, Ma Z, Kim B-H, Wu W, Cayting P, Boyle AP, et al. Principles of regulatory information conservation between mouse and human. Nature. England; 2014 Nov;515(7527):371–5.

Farr AR, Wu W, Choi B, Cavalcoli JD, Laouar Y. CD1d-unrestricted NKT cells are endowed with a hybrid function far superior than  that of iNKT cells. Proc Natl Acad Sci U S A. United States; 2014 Sep;111(35):12841–6.

Huang SK, Scruggs AM, McEachin RC, White ES, Peters-Golden M. Lung fibroblasts from patients with idiopathic pulmonary fibrosis exhibit genome-wide differences in DNA methylation compared to fibroblasts from nonfibrotic lung. PLoS One. United States; 2014;9(9):e107055.

Li H-D, Menon R, Omenn GS, Guan Y. The emerging era of genomic data integration for analyzing splice isoform function. Trends Genet. England; 2014 Aug;30(8):340–7.

Li H-D, Menon R, Omenn GS, Guan Y. Revisiting the identification of canonical splice isoforms through integration of functional genomics and proteomics evidence. Proteomics. Germany; 2014 Dec;14(23–24):2709–18.

Ma J, Weake VM. Affinity-based isolation of tagged nuclei from Drosophila tissues for gene expression analysis. J Vis Exp. United States; 2014 Mar;(85).

Menon R, Im H, Zhang EY, Wu S-L, Chen R, Snyder M, et al. Distinct splice variants and pathway enrichment in the cell-line models of aggressive human breast cancer subtypes. J Proteome Res. United States; 2014 Jan;13(1):212–27.

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