Publications

  • Functional proteogenomics reveals biomarkers and therapeutic targets in lymphomas. (2017). Rolland DCM, Basrur V, Jeon YK, McNeil-Schwalm C, Fermin D, Conlon KP, Zhou Y, Ng SY, Tsou CC, Brown NA, Thomas DG, Bailey NG, Omenn GS, Nesvizhskii AI, Root DE, Weinstock DM, Faryabi RB, Lim MS, Elenitoba-Johnson KSJ. Proceedings of the National Academy of Sciences of the United States of America, vol 114(25):6581-6586. PMID:28607076

  • SAINTq: Scoring protein-protein interactions in affinity purification - mass spectrometry experiments with fragment or peptide intensity data. (2016). Teo G, Koh H, Fermin D, Lambert JP, Knight JD, Gingras AC, Choi H. Proteomics, vol 16(15-16):2238-45. PMID:27119218

  • QPROT: Statistical method for testing differential expression using protein-level intensity data in label-free quantitative proteomics. (2016). Choi H, Kim S, Fermin D, Tsou CC, Nesvizhskii AI. Journal of proteomics, vol 129():121-126. PMID:26254008

  • Research Resource: Androgen Receptor Activity Is Regulated Through the Mobilization of Cell Surface Receptor Networks. (2016). Hsiao JJ, Ng BH, Smits MM, Martinez HD, Jasavala RJ, Hinkson IV, Fermin D, Eng JK, Nesvizhskii AI, Wright ME. Molecular endocrinology (Baltimore, Md.), vol 29(8):1195-218. PMID:26181434

  • EBprot: Statistical analysis of labeling-based quantitative proteomics data. (2016). Koh HW, Swa HL, Fermin D, Ler SG, Gunaratne J, Choi H. Proteomics, vol 15(15):2580-91. PMID:25913743

  • LuciPHOr2: site localization of generic post-translational modifications from tandem mass spectrometry data. (2015). Fermin D, Avtonomov D, Choi H, Nesvizhskii AI. Bioinformatics (Oxford, England), vol 31(7):1141-3. PMID:25429062

  • Differential proteomic analysis of endemic and sporadic Epstein-Barr virus-positive and negative Burkitt lymphoma. (2015). El-Mallawany NK, Day N, Ayello J, Van de Ven C, Conlon K, Fermin D, Basrur V, Elenitoba-Johnson K, Lim M, Cairo MS. European journal of cancer (Oxford, England : 1990), vol 51(1):92-100. PMID:25466511

  • Global phosphoproteomic profiling reveals distinct signatures in B-cell non-Hodgkin lymphomas. (2014). Rolland D, Basrur V, Conlon K, Wolfe T, Fermin D, Nesvizhskii AI, Lim MS, Elenitoba-Johnson KS. The American journal of pathology, vol 184(5):1331-42. PMID:24667141

  • LuciPHOr: algorithm for phosphorylation site localization with false localization rate estimation using modified target-decoy approach. (2014). Fermin D, Walmsley SJ, Gingras AC, Choi H, Nesvizhskii AI. Molecular & cellular proteomics : MCP, vol 12(11):3409-19. PMID:23918812

  • Integrated phosphoproteomic and metabolomic profiling reveals NPM-ALK-mediated phosphorylation of PKM2 and metabolic reprogramming in anaplastic large cell lymphoma. (2013). McDonnell SR, Hwang SR, Rolland D, Murga-Zamalloa C, Basrur V, Conlon KP, Fermin D, Wolfe T, Raskind A, Ruan C, Jiang JK, Thomas CJ, Hogaboam CM, Burant CF, Elenitoba-Johnson KS, Lim MS. Blood, vol 122(6):958-68. PMID:23814019

  • The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. (2013). Mellacheruvu D, Wright Z, Couzens AL, Lambert JP, St-Denis NA, Li T, Miteva YV, Hauri S, Sardiu ME, Low TY, Halim VA, Bagshaw RD, Hubner NC, Al-Hakim A, Bouchard A, Faubert D, Fermin D, Dunham WH, Goudreault M, Lin ZY, Badillo BG, Pawson T, Durocher D, Coulombe B, Aebersold R, Superti-Furga G, Colinge J, Heck AJ, Choi H, Gstaiger M, Mohammed S, Cristea IM, Bennett KL, Washburn MP, Raught B, Ewing RM, Gingras AC, Nesvizhskii AI. Nature methods, vol 10(8):730-6. PMID:23921808

  • Sparsely correlated hidden Markov models with application to genome-wide location studies. (2013). Choi H, Fermin D, Nesvizhskii AI, Ghosh D, Qin ZS. Bioinformatics (Oxford, England), vol 29(5):533-41. PMID:23325620

  • Reconstructing targetable pathways in lung cancer by integrating diverse omics data. (2014). Balbin OA, Prensner JR, Sahu A, Yocum A, Shankar S, Malik R, Fermin D, Dhanasekaran SM, Chandler B, Thomas D, Beer DG, Cao X, Nesvizhskii AI, Chinnaiyan AM. Nature communications, vol 4():2617. PMID:24135919

  • Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data. (2012). Ning K, Fermin D, Nesvizhskii AI. Journal of proteome research, vol 11(4):2261-71. PMID:22329341

  • Abacus: a computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis. (2011). Fermin D, Basrur V, Yocum AK, Nesvizhskii AI. Proteomics, vol 11(7):1340-5. PMID:21360675

  • Metabolites of purine nucleoside phosphorylase (NP) in serum have the potential to delineate pancreatic adenocarcinoma. (2011). Vareed SK, Bhat VB, Thompson C, Vasu VT, Fermin D, Choi H, Creighton CJ, Gayatri S, Lan L, Putluri N, Thangjam GS, Kaur P, Shabahang M, Giri JG, Nesvizhskii AI, Asea AA, Cashikar AG, Rao A, McLoughlin J, Sreekumar A. PloS one, vol 6(3):e17177. PMID:21448452

  • SAINT: probabilistic scoring of affinity purification-mass spectrometry data. (2011). Choi H, Larsen B, Lin ZY, Breitkreutz A, Mellacheruvu D, Fermin D, Qin ZS, Tyers M, Gingras AC, Nesvizhskii AI. Nature methods, vol 8(1):70-3. PMID:21131968

  • SAW: a method to identify splicing events from RNA-Seq data based on splicing fingerprints. (2010). Ning K, Fermin D. PloS one, vol 5(8):e12047. PMID:20706591

  • Computational analysis of unassigned high-quality MS/MS spectra in proteomic data sets. (2010). Ning K, Fermin D, Nesvizhskii AI. Proteomics, vol 10(14):2712-8. PMID:20455209

  • Quantitative proteomic profiling of prostate cancer reveals a role for miR-128 in prostate cancer. (2010). Khan AP, Poisson LM, Bhat VB, Fermin D, Zhao R, Kalyana-Sundaram S, Michailidis G, Nesvizhskii AI, Omenn GS, Chinnaiyan AM, Sreekumar A. Molecular & cellular proteomics : MCP, vol 9(2):298-312. PMID:19955085