Bioinformatics Publications

Carney SV, Banerjee K, Mujeeb A, Zhu B, Haase S, Varela ML, Kadiyala P, Tronrud CE, Zhu Z, Mukherji D, Gorla P, Sun Y, Tagett R, Núñez FJ, Luo M, Luo W, Ljungman M, Liu Y, Xia Z, Schwendeman A, Qin T, Sartor MA, Costello JF, Cahill DP, Lowenstein PR, Castro MG. Zinc Finger MYND-Type Containing 8 (ZMYND8) is epigenetically regulated in mutant Isocitrate Dehydrogenase 1 (IDH1) glioma to promote radioresistance. Clin Cancer Res. United States; 2023 Jan 24;CCR-22-1896. PMID: 36692427

Kodgule R, Goldman JW, Monovich AC, Saari T, Aguilar AR, Hall CN, Rajesh N, Gupta J, Chu SCA, Ye L, Gurumurthy A, Iyer A, Brown NA, Chiang MY, Cieslik MP, Ryan RJH. ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia. Blood Cancer Discov. United States; 2023 Jan 6;4(1):34–53. PMCID: PMC9820540

Sharma SB, Melvin WJ, Audu CO, Bame M, Rhoads NM, Wu W, Kanthi Y, Knight J, Adili R, Holinstat M, Wakefield TW, Henke P, Moore BB, Gallagher KA, Obi AT. The Histone Methyltransferase MLL1/KMT2A in Monocytes Drives Coronavirus-Associated Coagulopathy and Inflammation. Blood. United States; 2022 Dec 9;blood.2022015917. PMCID: PMC9743412

Brandenburg M, Garcia-Milian R. Librarians and Bioinformatics Communities Working Together to Advance Research and Instruction. In: Piorun M and Raboin R, editors. Cases on Establishing Effective Collaborations in Academic Libraries. Hershey, PA: IGI Global; 2022. p.249-269.

Burton JB, Carruthers NJ, Hou Z, Matherly LH, Stemmer PM. Pattern Analysis of Organellar Maps for Interpretation of Proteomic Data. Proteomes. 2022 May;10(2). Available from

Schmitd LB, Perez-Pacheco C, Bellile EL, Wu W, Casper K, Mierzwa M, et al. Spatial and Transcriptomic Analysis of Perineural Invasion in Oral Cancer. Clin cancer Res. 2022 Aug;28(16):3557-3572. Available from

Sharma SB, Melvin WJ, Audu CO, Bame M, Rhoads NM, Wu W, et al. The Histone Methyltransferase MLL1/KMT2A in Monocytes Drives Coronavirus-Associated Coagulopathy and Inflammation. Blood. 2022 Dec;blood.2022015917. Available from

Zheng Y, Yan RZ, Sun S, Kobayashi M, Xiang L, Yang R…Wu W…et al. Single-cell analysis of embryoids reveals lineage diversification roadmaps of early human development. Cell Stem Cell. 2022 Sep 1;29(9):1402-1419.e8. Available from

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:

Wörmann SM, Zhang A, Thege FI, Cowan RW, Rupani DN, Wang R…Gates C, Wu W…et al. APOBEC3A drives deaminase domain-independent chromosomal instability to promote  pancreatic cancer metastasis. Nat cancer. 2021 Dec;2(12):1338–56. 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;11(8). 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.

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.

Nayak S, Fiaschi M, King D, Tabakin ER, Wood L, Hunt DA. Development of Small Molecular Proteasome Inhibitors Using a Caenorhabditis elegans Screen. Int J Med Chem. United States; 2014;2014:237286.

Nedialkov Y, Assaf F, Opron K, Burton Z. The forward translocation position of Escherichia coli RNA polymerase is stabilized by KCl and Mg2+ and is strongly dependent on a bridge helix N-terminal hinge beta’778-GARKGL-783 (944.2). FASEB J. 2014;28(1 Supplement):944.2.

Omenn GS, Guan Y, Menon R. A new class of protein cancer biomarker candidates: differentially expressed splice variants of ERBB2 (HER2/neu) and ERBB1 (EGFR) in breast cancer cell lines. J Proteomics. Netherlands; 2014 Jul;107:103–12.

Opron K, Xia K, Wei G-W. Fast and anisotropic flexibility-rigidity index for protein flexibility and fluctuation analysis. J Chem Phys. United States; 2014 Jun;140(23):234105.

Perales R, King DM, Aguirre-Chen C, Hammell CM. LIN-42, the Caenorhabditis elegans PERIOD homolog, negatively regulates microRNA  transcription. PLoS Genet. United States; 2014 Jul;10(7):e1004486.

Pimkin M, Kossenkov A V, Mishra T, Morrissey CS, Wu W, Keller CA, et al. Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis. Genome Res. United States; 2014 Dec;24(12):1932–44.

Pope BD, Ryba T, Dileep V, Yue F, Wu W, Denas O, et al. Topologically associating domains are stable units of replication-timing regulation. Nature. England; 2014 Nov;515(7527):402–5.

Roca H, Pande M, Huo JS, Hernandez J, Cavalcoli JD, Pienta KJ, McEachin RC. A bioinformatics approach reveals novel interactions of the OVOL transcription factors in the regulation of epithelial – mesenchymal cell reprogramming and cancer progression. BMC Syst Biol. England; 2014 Mar;8:29.

Smith JE, Brandenburg MD, Conte ML, Song J. Innovative information service development: meeting the information needs of an interdisciplinary, cross-sector research complex. J Med Libr Assoc. United States; 2014 Jan;102(1):8–13.

Wu W, Morrissey CS, Keller CA, Mishra T, Pimkin M, Blobel GA, et al. Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis. Genome Res. United States; 2014 Dec;24(12):1945–62.

Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature. England; 2014 Nov;515(7527):355–64.

Baker BJ, Sheik CS, Taylor CA, Jain S, Bhasi A, Cavalcoli JD, et al. Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling. ISME J. England; 2013 Oct;7(10):1962–73.

Eksi R, Li H-D, Menon R, Wen Y, Omenn GS, Kretzler M, et al. Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data. PLoS Comput Biol. United States; 2013;9(11):e1003314.

Lenkowski JR, Qin Z, Sifuentes CJ, Thummel R, Soto CM, Moens CB, et al. Retinal regeneration in adult zebrafish requires regulation of TGFbeta signaling. Glia. United States; 2013 Oct;61(10):1687–97.

Mitrea C, Taghavi Z, Bokanizad B, Hanoudi S, Tagett R, Donato M, et al. Methods and approaches in the topology-based analysis of biological pathways. Front Physiol. Switzerland; 2013 Oct;4:278.

Nedialkov YA, Opron K, Assaf F, Artsimovitch I, Kireeva ML, Kashlev M, et al. The RNA polymerase bridge helix YFI motif in catalysis, fidelity and translocation. Biochim Biophys Acta. Netherlands; 2013 Feb;1829(2):187–98.

Omenn GS, Menon R, Zhang Y. Innovations in proteomic profiling of cancers: alternative splice variants as a new class of cancer biomarker candidates and bridging of proteomics with structural biology. J Proteomics. Netherlands; 2013 Sep;90:28–37.

Powell C, Grant AR, Cornblath E, Goldman D. Analysis of DNA methylation reveals a partial reprogramming of the Muller glia genome during retina regeneration. Proc Natl Acad Sci U S A. United States; 2013 Dec;110(49):19814–9.

Roca H, Hernandez J, Weidner S, McEachin RC, Fuller D, Sud S, et al. Transcription factors OVOL1 and OVOL2 induce the mesenchymal to epithelial transition in human cancer. PLoS One. United States; 2013;8(10):e76773.

Xia K, Opron K, Wei G-W. Multiscale multiphysics and multidomain models–flexibility and rigidity. J Chem Phys. United States; 2013 Nov;139(19):194109.

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

Krawetz SA, Kruger A, Lalancette C, Tagett R, Anton E, Draghici S, et al. A survey of small RNAs in human sperm. Hum Reprod. England; 2011 Dec;26(12):3401–12.

Ma W, Lager KM, Li X, Janke BH, Mosier DA, Painter LE…Ma J…et al. Pathogenicity of swine influenza viruses possessing an avian or swine-origin PB2  polymerase gene evaluated in mouse and pig models. Virology. United States; 2011 Feb;410(1):1–6.

Mair W, Morantte I, Rodrigues APC, Manning G, Montminy M, Shaw RJ, et al. Lifespan extension induced by AMPK and calcineurin is mediated by CRTC-1 and CREB. Nature. England; 2011 Feb;470(7334):404–8.

McEachin RC. Overlap of genetic influences in phenotypes classically categorized as psychiatric vs medical disorders. World J Med Genet [Internet]. 2011 [cited 2016 Dec 14];1(1):4. Available from:

Menon R, Omenn GS. Identification of alternatively spliced transcripts using a proteomic informatics approach. Methods Mol Biol. United States; 2011;696:319–26.

Menon R, Roy A, Mukherjee S, Belkin S, Zhang Y, Omenn GS. Functional implications of structural predictions for alternative splice proteins expressed in Her2/neu-induced breast cancers. J Proteome Res. United States; 2011 Dec;10(12):5503–11.

Rowley MJ, Avrutsky MI, Sifuentes CJ, Pereira L, Wierzbicki AT. Independent chromatin binding of ARGONAUTE4 and SPT5L/KTF1 mediates transcriptional gene silencing. PLoS Genet. United States; 2011 Jun;7(6):e1002120.

Wu W, Cheng Y, Keller CA, Ernst J, Kumar SA, Mishra T, et al. Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. Genome Res. United States; 2011 Oct;21(10):1659–71.

Bhasi A, Senalik D, Simon PW, Kumar B, Manikandan V, Philip P, et al. RoBuST: an integrated genomics resource for the root and bulb crop families Apiaceae and Alliaceae. BMC Plant Biol. England; 2010 Aug;10:161.

Brandenburg MD, Doss A, Frederick TE. Evaluation of a library outreach program to research labs. Med Ref Serv Q [Internet]. 2010 Jul [cited 2014 Dec 12];29(3):249–59. Available from:

Gao J, Tarcea VG, Karnovsky A, Mirel BR, Weymouth TE, Beecher CW, Cavalcoli JD, et al. Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks. Bioinformatics. England; 2010 Apr;26(7):971–3.

Hutt DM, Herman D, Rodrigues APC, Noel S, Pilewski JM, Matteson J, et al. Reduced histone deacetylase 7 activity restores function to misfolded CFTR in cystic fibrosis. Nat Chem Biol. United States; 2010 Jan;6(1):25–33.

McEachin RC, Chen H, Sartor MA, Saccone SF, Keller BJ, Prossin AR, Cavalcoli JD, et al. A genetic network model of cellular responses to lithium treatment and cocaine abuse in bipolar disorder. BMC Syst Biol. England; 2010 Nov;4:158.

McEachin RC, Saccone NL, Saccone SF, Kleyman-Smith YD, Kar T, Kare RK…Cavalcoli JD…et al. Modeling complex genetic and environmental influences on comorbid bipolar disorder with tobacco use disorder. BMC Med Genet. England; 2010 Jan;11:14.

Menon R, Omenn GS. Proteomic characterization of novel alternative splice variant proteins in human  epidermal growth factor receptor 2/neu-induced breast cancers. Cancer Res. United States; 2010 May;70(9):3440–9.

Omenn GS, Yocum AK, Menon R. Alternative splice variants, a new class of protein cancer biomarker candidates:  findings in pancreatic cancer and breast cancer with systems biology implications. Dis Markers. United States; 2010;28(4):241–51.

Otto EA, Hurd TW, Airik R, Chaki M, Zhou W, Stoetzel C…Cavalcoli JD…et al. Candidate exome capture identifies mutation of SDCCAG8 as the cause of a retinal-renal ciliopathy. Nat Genet. United States; 2010 Oct;42(10):840–50.

Senapathy P, Bhasi A, Mattox J, Dhandapany PS, Sadayappan S. Targeted genome-wide enrichment of functional regions. PLoS One. United States; 2010 Jun;5(6):e11138.

Bai Y, Sartor M, Cavalcoli J. Current status and future perspectives for sequencing livestock genomes. J Anim Sci Biotechnol. England; 2012 Mar;3(1):8.

Bedoyan JK, Schaibley VM, Peng W, Bai Y, Mondal K, Shetty AC, et al. Disruption of RAB40AL function leads to Martin–Probst syndrome, a rare X-linked  multisystem neurodevelopmental human disorder. J Med Genet. England; 2012 May;49(5):332–40.

Brandenburg MD, Song J. Broadening instructional scope with network visualization. J Med Libr Assoc. United States; 2012 Oct;100(4):313–6.

Huang SK, Scruggs AM, Donaghy J, McEachin RC, Fisher AS, Richardson BC, et al. Prostaglandin E(2) increases fibroblast gene-specific and global DNA methylation  via increased DNA methyltransferase expression. FASEB J  Off Publ Fed Am Soc  Exp Biol. United States; 2012 Sep;26(9):3703–14.

Kireeva ML, Opron K, Seibold SA, Domecq C, Cukier RI, Coulombe B, et al. Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase. BMC Biophys. England; 2012 Jun;5:11.

Liu Q, Qiao C, Marjuki H, Bawa B, Ma J, Guillossou S, et al. Combination of PB2 271A and SR polymorphism at positions 590/591 is critical for  viral replication and virulence of swine influenza virus in cultured cells and in vivo. J Virol. United States; 2012 Jan;86(2):1233–7.

Ma W, Liu Q, Bawa B, Qiao C, Qi W, Shen H…Ma J…et al. The neuraminidase and matrix genes of the 2009 pandemic influenza H1N1 virus cooperate functionally to facilitate efficient replication and transmissibility in pigs. J Gen Virol. England; 2012 Jun;93(Pt 6):1261–8.

McEachin RC, Sannareddy KS, Cavalcoli JD, Karnovsky A, Vink JM, Sartor MA. Convergence of genetic influences in comorbidity. BMC Bioinformatics. England; 2012 Mar;13 Suppl 2:S8.

Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM…Wu W…et al. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol. England; 2012 Aug;13(8):418.

The ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature [Internet]. 2012;489:57–74. Available from:

Vilchez D, Morantte I, Liu Z, Douglas PM, Merkwirth C, Rodrigues APC, et al. RPN-6 determines C. elegans longevity under proteotoxic stress conditions. Nature. England; 2012 Sep;489(7415):263–8.

Zhao J, Schloss PD, Kalikin LM, Carmody LA, Foster BK, Petrosino JF, Cavalcoli JD, et al. Decade-long bacterial community dynamics in cystic fibrosis airways. Proc Natl Acad Sci U S A. United States; 2012 Apr;109(15):5809–14.

Black MH, Fingerlin TE, Allayee H, Zhang W, Xiang AH, Trigo E…McEachin RC…et al. Evidence of interaction between PPARG2 and HNF4A contributing to variation in insulin sensitivity in Mexican Americans. Diabetes. United States; 2008 Apr;57(4):1048–56.

Chen X, Ulintz PJ, Simon ES, Williams JA, Andrews PC. Global topology analysis of pancreatic zymogen granule membrane proteins. Mol Cell Proteomics. United States; 2008 Dec;7(12):2323–36.

Dore LC, Amigo JD, Dos Santos CO, Zhang Z, Gai X, Tobias JW…Wu W…et al. A GATA-1-regulated microRNA locus essential for erythropoiesis. Proc Natl Acad Sci U S A. United States; 2008 Mar;105(9):3333–8.

McEachin RC, Keller BJ, Saunders EFH, McInnis MG. Modeling gene-by-environment interaction in comorbid depression with alcohol use  disorders via an integrated bioinformatics approach. BioData Min. England; 2008 Jul;1(1):2.

Regulapati R, Bhasi A, Singh CK, Senapathy P. Origination of the split structure of spliceosomal genes from random genetic sequences. PLoS One. United States; 2008;3(10):e3456.

Ulintz PJ, Bodenmiller B, Andrews PC, Aebersold R, Nesvizhskii AI. Investigating MS2/MS3 matching statistics: a model for coupling consecutive stage mass spectrometry data for increased peptide identification confidence. Mol Cell Proteomics. United States; 2008 Jan;7(1):71–87.

Zandi PP, Zollner S, Avramopoulos D, Willour VL, Chen Y, Qin ZS…McEachin R…et al. Family-based SNP association study on 8q24 in bipolar disorder. Am J Med Genet B Neuropsychiatr Genet. United States; 2008 Jul;147B(5):612–8.

Bhasi A, Philip P, Manikandan V, Senapathy P. ExDom: an integrated database for comparative analysis of the exon-intron structures of protein domains in eukaryotes. Nucleic Acids Res. England; 2009 Jan;37(Database issue):D703-11.

Bhasi A, Philip P, Sreedharan VT, Senapathy P. AspAlt: A tool for inter-database, inter-genomic and user-specific comparative analysis of alternative transcription and alternative splicing in 46 eukaryotes. Genomics. United States; 2009 Jul;94(1):48–54.

Bertucci F, Le Doussal JM, Birnbaum D, Tagett R, Martinec A, Hermitte F, et al. Prognostic value of the genomic grade index (GGi) as compared to centrally measured Ki-67 IHC and mitotic index in early breast cancer patients. J Clin Oncol. United States; 2009 May;27(15_suppl):11094.

Carpentier S, Bertucci F, Tagett R, Finetti P, Jacquemier J, Le Doussal JM, et al. A single genomic HER2 assay for the protein expression and the DNA amplification  status. J Clin Oncol. United States; 2009 May;27(15_suppl):e22082.

Cheng Y, Wu W, Kumar SA, Yu D, Deng W, Tripic T, et al. Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression. Genome Res. United States; 2009 Dec;19(12):2172–84.

Keller BJ, McEachin RC. Identifying hypothetical genetic influences on complex disease phenotypes. BMC Bioinformatics. England; 2009 Feb;10 Suppl 2:S13.

Menon R, Zhang Q, Zhang Y, Fermin D, Bardeesy N, DePinho RA, et al. Identification of novel alternative splice isoforms of circulating proteins in a  mouse model of human pancreatic cancer. Cancer Res. United States; 2009 Jan;69(1):300–9.

Ulintz PJ, Yocum AK, Bodenmiller B, Aebersold R, Andrews PC, Nesvizhskii AI. Comparison of MS(2)-only, MSA, and MS(2)/MS(3) methodologies for phosphopeptide identification. J Proteome Res. United States; 2009 Feb;8(2):887–99.

Zhang Y, Wu W, Cheng Y, King DC, Harris RS, Taylor J, et al. Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA  by GATA1. Nucleic Acids Res. England; 2009 Nov;37(21):7024–38.

Bhasi A, Pandey RV, Utharasamy SP, Senapathy P. EuSplice: a unified resource for the analysis of splice signals and alternative splicing in eukaryotic genes. Bioinformatics. England; 2007 Jul;23(14):1815–23.

Chen J, Blackwell TW, Fermin D, Menon R, Chen Y, Gao J, et al. Evolutionary-conserved gene expression response profiles across mammalian tissues. OMICS. United States; 2007;11(1):96–115.

Rodrigues APC, Grant BJ, Godzik A, Friedberg I. The 2006 automated function prediction meeting. BMC bioinformatics. England; 2007. p. S1-4.

Slabinski L, Jaroszewski L, Rodrigues APC, Rychlewski L, Wilson IA, Lesley SA, et al. The challenge of protein structure determination–lessons from structural genomics. Protein Sci. United States; 2007 Nov;16(11):2472–82.

Tian Y, McEachin RC, Santos C, States DJ, Patel JM. SAGA: a subgraph matching tool for biological graphs. Bioinformatics. England; 2007 Jan;23(2):232–9.

Fermin D, Allen BB, Blackwell TW, Menon R, Adamski M, Xu Y, Ulintz P, et al. Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics. Genome Biol. England; 2006;7(4):R35.

Grant BJ, Rodrigues APC, ElSawy KM, McCammon JA, Caves LSD. Bio3d: an R package for the comparative analysis of protein structures. Bioinformatics. England; 2006 Nov;22(21):2695–6.

Honore P, Granjeaud S, Tagett R, Deraco S, Beaudoing E, Rougemont J, et al. MicroArray Facility: a laboratory information management system with extended support for Nylon based technologies. BMC Genomics. England; 2006 Sep;7:240.

Huo JS, McEachin RC, Cui TX, Duggal NK, Hai T, States DJ, et al. Profiles of growth hormone (GH)-regulated genes reveal time-dependent responses and identify a mechanism for regulation of activating transcription factor 3 by GH. J Biol Chem. United States; 2006 Feb;281(7):4132–41.

Rodrigues APC, Grant BJ, Hubbard RE. sgTarget: a target selection resource for structural genomics. Nucleic Acids Res. England; 2006 Jul;34(Web Server issue):W225-30.

Ulintz PJ, Zhu J, Qin ZS, Andrews PC. Improved classification of mass spectrometry database search results using newer  machine learning approaches. Mol Cell Proteomics. United States; 2006 Mar;5(3):497–509.

Wang P, Dai M, Xuan W, McEachin RC, Jackson AU, Scott LJ, et al. SNP Function Portal: a web database for exploring the function implication of SNP alleles. Bioinformatics. England; 2006 Jul;22(14):e523-9.

Adamski M, Blackwell T, Menon R, Martens L, Hermjakob H, Taylor C, et al. Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project. Proteomics. Germany; 2005 Aug;5(13):3246–61.

Omenn GS, States DJ, Adamski M, Blackwell TW, Menon R, Hermjakob H, et al. Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics. Germany; 2005 Aug;5(13):3226–45.

Bertucci F, Finetti P, Rougemont J, Charafe-Jauffret E, Nasser V, Loriod B…Tagett R…et al. Gene expression profiling for molecular characterization of inflammatory breast cancer and prediction of response to chemotherapy. Cancer Res. United States; 2004 Dec;64(23):8558–65.

Birnbaum D, Bertucci F, Ginestier C, Tagett R, Jacquemier J, Charafe-Jauffret E. Basal and luminal breast cancers: basic or luminous? (review). Int J Oncol. Greece; 2004 Aug;25(2):249–58.

Bertucci F, Loriod B, Nasser V, Granjeaud S, Tagett R, Braud A-C, et al. Gene expression profiling of breast carcinomas using nylon DNA arrays. C R Biol. France; 2003;326(10–11):1031–9.

Bertucci F, Viens P, Tagett R, Nguyen C, Houlgatte R, Birnbaum D. DNA arrays in clinical oncology: promises and challenges. Lab Invest. United States; 2003 Mar;83(3):305–16.

Liu R, McEachin RC, States DJ. Computationally identifying novel NF-kappa B-regulated immune genes in the human genome. Genome Res. United States; 2003 Apr;13(4):654–61.

Rodrigues A, Hubbard RE. Making decisions for structural genomics. Brief Bioinform. England; 2003 Jun;4(2):150–67.

Bertucci F, Eisinger F, Tagett R, Sobol H, Birnbaum D. Re: Gene expression profiles of BRCA1-linked, BRCA2-linked, and sporadic ovarian cancers. Journal of the National Cancer Institute. United States; 2002. p. 1506–7.

Bertucci F, Nasser V, Granjeaud S, Eisinger F, Adelaide J, Tagett R, et al. Gene expression profiles of poor-prognosis primary breast cancer correlate with survival. Hum Mol Genet. England; 2002 Apr;11(8):863–72.

Nal B, Mohr E, Silva M-I Da, Tagett R, Navarro C, Carroll P, et al. Wdr12, a mouse gene encoding a novel WD-Repeat Protein with a notchless-like amino-terminal domain. Genomics. United States; 2002 Jan;79(1):77–86.

Ramialison M, Mohr E, Nal B, Saboul T, Carrier A, Tagett R, et al. Expression profiling in mouse fetal thymus reveals clusters of coordinately expressed genes that mark individual stages of T-cell ontogeny. Immunogenetics. United States; 2002 Oct;54(7):469–78.

Bertucci F, Houlgatte R, Benziane A, Granjeaud S, Adelaide J, Tagett R, et al. Gene expression profiling of primary breast carcinomas using arrays of candidate genes. Hum Mol Genet. England; 2000 Dec;9(20):2981–91.

Ghosh S, Watanabe RM, Valle TT, Hauser ER, Magnuson VL, Langefeld CD…McEachin RC…et al. The Finland-United States investigation of non-insulin-dependent diabetes mellitus genetics (FUSION) study. I. An autosomal genome scan for genes that predispose to type 2 diabetes. Am J Hum Genet. United States; 2000 Nov;67(5):1174–85.

Watanabe RM, Ghosh S, Langefeld CD, Valle TT, Hauser ER, Magnuson VL…McEachin RC…et al. The Finland-United States investigation of non-insulin-dependent diabetes mellitus genetics (FUSION) study. II. An autosomal genome scan for diabetes-related quantitative-trait loci. Am J Hum Genet. United States; 2000 Nov;67(5):1186–200.

Bertucci F, Houlgatte R, Nguyen C, Benziane A, Nasser V, Granjeaud S, Tagett B, et al. [Molecular typing of breast cancer: transcriptomics and DNA microarrays]. Bull Cancer. France; 2001 Mar;88(3):277–86.

Bertucci F, Loriod B, Tagett R, Granjeaud S, Birnbaum D, Nguyen C, et al. [DNA arrays: technological aspects and applications]. Bull Cancer. France; 2001 Mar;88(3):243–52.

Phadke ND, Molloy MP, Steinhoff SA, Ulintz PJ, Andrews PC, Maddock JR. Analysis of the outer membrane proteome of Caulobacter crescentus by two-dimensional electrophoresis and mass spectrometry. Proteomics. Germany; 2001 May;1(5):705–20.

Bernard K, Cambiaggi A, Guia S, Bertucci F, Granjeaud S, Tagett R, et al. Engagement of natural cytotoxicity programs regulates AP-1 expression in the NKL  human NK cell line. J Immunol. United States; 1999 Apr;162(7):4062–8.

Bertucci F, Van Hulst S, Bernard K, Loriod B, Granjeaud S, Tagett R, et al. Expression scanning of an array of growth control genes in human tumor cell lines. Oncogene. England; 1999 Jul;18(26):3905–12.

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