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Bioinformatics Shared Resources

Sanford Burnham Prebys Medical Discovery Institute

publications

SELECTED PUBLICATIONS WE COAUTHORED
  1. Matthias Pauthner, Colin Havenar-Daughton, Devin Sok, ..., Alexey M. Eroshkin, ..., Kai W. Post, ...., Dan H. Barouch, Shane Crotty, Dennis R. Burton. Elicitation of Robust Tier 2 Neutralizing Antibody Responses in Nonhuman Primates by HIV Envelope Trimer Immunization Using Optimized Approaches. Immunity 2017, 46, n6, 1073–108
  2. Gordon BS, Steiner JL, Rossetti ML, Qiao S, Ellisen LW, Govindarajan SS, Eroshkin AM, Williamson DL, Coen PM. REDD1 Induction Regulates the Skeletal Muscle Gene Expression Signature following Acute Aerobic Exercise. Am J Physiol Endocrinol Metab. 2017 Sep 12:ajpendo.00120.2017. doi: 10.1152/ajpendo.00120.2017. [Epub ahead of print] PubMed PMID: 28899858.
  3. Dang J, Tiwari SK, Lichinchi G, Qin Y, Patil VS, Eroshkin AM, Rana TM. Zika Virus Depletes Neural Progenitors in Human Cerebral Organoids through Activation of the Innate Immune Receptor TLR3. Cell Stem Cell. 2016 May 6. pii: S1934-5909(16)30057-1 [Epub ahead of print] PMID: 27162029
  4. Sparks LM, Redman LM, Conley KE, Harper ME, Yi F, Hodges A, Eroshkin A, Costford SR, Gabriel ME, Shook C, Cornnell HH, Ravussin E, Smith SR. Effects of 12 Months of Caloric Restriction on Muscle Mitochondrial Function in Healthy Individls. J Clin Endocrinol Metab. 2017 Jan 1;102(1):111-121. doi: 10.1210/jc.2016-3211.
  5. Sparks LM, Redman LM, Conley KE, Harper ME, Hodges A, Eroshkin A, Costford SR, Gabriel ME, Yi F, Shook C, Cornnell HH, Ravussin E, Smith SR. Differences in Mitochondrial Coupling Reveal a Novel Signature of Mitohormesis in Muscle of Healthy Individuals. J Clin Endocrinol Metab. 2016 Oct 6:jc20162742. PMID: 27710240
  6. Singec I, Crain AM, Hou J, Tobe BT, Talantova M, Winquist AA, Doctor KS, Choy J, Huang X, La Monaca E, Horn DM, Wolf DA, Lipton SA, Gutierrez GJ, Brill LM., Snyder EY. Quantitative Analysis of Human Pluripotency and Neural Specification by In-Depth (Phospho)Proteomic Profiling. Stem Cell Reports. 2016 Sep 13;7(3):527-42. doi: 10.1016/j.stemcr.2016.07.019. Epub 2016 Aug 25.
  7. Komarov AP, Komarova EA, Green K, Novototskaya LR, Baker PS, Eroshkin A, Osterman AL, Chenchick AA, Frangou C, Gudkov AV. Functional genetics-directed identification of novel pharmacological inhibitors of FAS- and TNF-dependent apoptosis that protect mice from acute liver failure. Cell Death Dis. 2016 Mar 17;7:e2145. doi: 10.1038/cddis.2016.45. PMID: 26986512
  8. Landais E, Huang X, Havenar-Daughton C, Murrell B, Price MA, Wickramasinghe L, Ramos A, Bian CB, Simek M, Allen S, Karita E, Kilembe W, Lakhi S, Inambao M, Kamali A, Sanders EJ, Anzala O, Edward V, Bekker LG, Tang J, Gilmour J, Kosakovsky-Pond SL, Phung P, Wrin T, Crotty S, Godzik A, Poignard P. Broadly Neutralizing Antibody Responses in a Large Longitudinal Sub-Saharan HIV Primary Infection Cohort. PLoS Pathog. 2016 Jan 14;12(1), PMID: 26766578
  9. Kim H, Frederick DT, Levesque MP, Cooper ZA, Feng Y, Krepler C, Brill L, Samuels Y, Hayward NK, Perlina A, Piris A, Zhang T, Halaban R, Herlyn MM, Brown KM, Wargo JA, Dummer R, Flaherty KT, Ronai ZA. Downregulation of the Ubiquitin Ligase RNF125 Underlies Resistance of Melanoma Cells to BRAF Inhibitors via JAK1 Deregulation. Cell Rep. 2015 May 28. pii: S2211-1247(15)
  10. Nemzek JA, Hodges AP, He Y. Bayesian network analysis of multi-compartmentalized immune responses in a murine model of sepsis and direct lung injury. BMC Res Notes. 2015;8:516-521.
  11. Yuki R, Aoyama K, Kubota S, Yamaguchi N, Kubota S, Hasegawa H, Morii M, Huang X, Liu K, Williams R, Fukuda MN, Yamaguchi N. Overexpression of zinc-finger protein 777 (ZNF777) inhibits proliferation at low cell density through down-regulation of FAM129A. J Cell Biochem. 2015;116(6):954-68.
  12. Blouw B, Patel M, Iizuka S, Abdullah C, You WK, Huang X, Li JL, Diaz B, Stallcup WB, Courtneidge SA. The invadopodia scaffold protein Tks5 is required for the growth of human breast cancer cells in vitro and in vivo. PLoS One. 2015 Mar 31;10(3)
  13. Ratnikov BI, Cieplak P, Gramatikoff K, Pierce J, Eroshkin A, Igarashi Y, Kazanov M, Sun Q, Godzik A, Osterman A, Stec B, Strongin A, Smith JW. Basis for substrate recognition and distinction by matrix metalloproteinases. Proc Natl Acad Sci U S A. 2014 Sep 22. pii: 201406134. [Epub ahead of print]
  14. Chan SF, Huang X, McKercher SR, Zaidi R, Okamoto SI, Nakanishi N, Lipton SA. Transcriptional profiling of MEF2-regulated genes in human neural progenitor cells derived from embryonic stem cells. Genom Data. 2015 Mar 1;3:24-27.
  15. Okamoto S, Nakamura T, Cieplak P, Chan SF, Kalashnikova E, Liao L, Saleem S, Han X, Clemente A, Nutter A, Sances S, Brechtel C, Haus D, Haun F, Sanz-Blasco S, Huang X, Li H, Zaremba JD, Cui J, Gu Z, Nikzad R, Harrop A, McKercher SR, Godzik A, Yates JR 3rd, Lipton SA. S-nitrosylation-mediated redox transcriptional switch modulates neurogenesis and neuronal cell death. Cell Rep. 2014 Jul 10;8(1):217-28. doi: 10.1016/j.celrep.2014.06.005. Epub 2014 Jul 4.
  16. Eroshkin AM, Leblanc A, Weekes D, Post K, Li Z, Rajput A, Butera ST, Burton DR, Godzik A. bNAber: database of broadly neutralizing HIV antibodies. Nucleic Acids Res. 2014 Jan 1;42(1):D1133-9.
  17. Yang CC, Chung A, Ku CY, Brill LM, Williams R, Wolf DA. Systems analysis of the prostate tumor suppressor NKX3.1 supports roles in DNA repair and luminal cell differentiation [v1; ref status: indexed, http://f1000r.es/35m] F1000Research 2014, 3:115
  18. Maung R, Hoefer MM, Sanchez AB, Sejbuk NE, Medders KE, Desai MK, Catalan IC, Dowling CC, de Rozieres CM, Garden GA, Russo R, Roberts AJ, Williams R, Kaul M. CCR5 Knockout Prevents Neuronal Injury and Behavioral Impairment Induced in a Transgenic Mouse Model by a CXCR4-Using HIV-1 Glycoprotein 120. J Immunol. 2014 Aug 15;193(4):1895-910.
  19. Losfeld ME, Ng BG, Kircher M, Buckingham KJ, Turner EH, Eroshkin A, Smith JD, Shendure J, Nickerson DA, Bamshad MJ; University of Washington Center for Mendelian Genomics, Freeze HH. A new congenital disorder of glycosylation caused by a mutation in SSR4, the signal sequence receptor 4 protein of the TRAP complex. Hum Mol Genet. 2014, 23 (6): 1602-1605.
  20. Sugihara K, Shibata TK, Takata K, Kimura T, Kanayama N, Williams R, Hatakeyama S, Akama TO, Kuo CW, Khoo KH, Fukuda MN. Attenuation of fibroblast growth factor signaling by poly-N-acetyllactosamine type glycans. FEBS Lett. 2013 Oct 1;587(19):3195-201. 
  21. Rico-Bautista E, Zhu W, Kitada S, Ganapathy S, Lau E, Krajewski S, Ramirez J, Bush JA, Yuan Z, Wolf DA. Small molecule-induced mitochondrial disruption directs prostate cancer inhibition via UPR signaling. Oncotarget. 2013 Aug;4(8):1212-29.
  22. Feng Y, Lau E, Scortegagna M, Ruller C, De SK, Barile E, Krajewski S, Aza-Blanc P, Williams R, Pinkerton AB, Jackson M, Chin L, Pellecchia M, Bosenberg M, Ronai ZA.  Inhibition of melanoma development in the Nras((Q61K)) ::Ink4a(-/-) mouse model by the small molecule BI-69A11. Pigment Cell Melanoma Res. 2013 Jan;26(1):136-42
  23. Nakanishi N, Ryan SD, Zhang X, Khan A, Holland T, Cho EG, Huang X, Liao FF, Xu H, Lipton SA, Tu S. Synaptic Protein α1-Takusan Mitigates Amyloid-β-Induced Synaptic Loss via Interaction with Tau and Postsynaptic Density-95 at Postsynaptic Sites. J Neurosci. 2013 Aug 28;33(35):14170-83
  24. Ng BG, Buckingham KJ, Raymond K, Kircher M, Turner EH, He M, Smith JD, Eroshkin A, Szybowska M, Losfeld ME, Chong JX, Kozenko M, Li C, Patterson MC, Gilbert RD, Nickerson DA, Shendure J, Bamshad MJ, Freeze HH. Mosaicism of the UDP-galactose transporter SLC35A2 causes a congenital disorder of glycosylation. Am J Hum Genet. 2013 Apr 4;92(4):632-6
  25. Rothman A, Davidson S, Wiencek RG, Evans WN, Restrepo H, Sarukhanov V, Ruoslahti E, Williams R, Mann D. Vascular histomolecular analysis by sequential endoarterial biopsy in a shunt model of pulmonary hypertension. Pulm Circ. 2013 Jan;3(1):50-7.
  26. Kim JY, Valencia T, Abu-Baker S, Linares J, Lee SJ, Yajima T, Chen J, Eroshkin A, Castilla EA, Brill LM, Medvedovic M, Leies M, Moscat J, Diaz-Meco MT.c-Myc phosphorylation by PKCζ represses prostate tumorigenesis. Proc Natl Acad Sci U S A. 2013 Apr 16;110(16):6418-23.
  27. Ng BG, Hackmann K, Jones MA, Eroshkin AM, He P, Wiliams R, Bhide S, Cantagrel V, Gleeson JG, Paller AS, Schnur RE, Tinschert S, Zunich J, Hegde MR, Freeze HH. .Mutations in the Glycosylphosphatidylinositol Gene PIGL Cause CHIME Syndrome.Am J Hum Genet. 2012, 90(4):685-8.
  28. Banerjee S, Liao L, Russo R, Nakamura T, McKercher SR, Okamoto S, Haun F, Nikzad R, Zaidi R, Holland E, Eroshkin A, Yates JR 3rd, Lipton SA. Isobaric tagging-based quantification by mass spectrometry of differentially regulated proteins in synaptosomes of HIV/gp120 transgenic mice: Implications for HIV-associated neurodegeneration. Experimental Neurology, 236: 298-306, 2012. PMCID: PMC3392539
  29. Pei Y, Moore CE, Wang J, Tewari AK, Eroshkin A, Cho YJ, Witt H, Korshunov A, Read TA, Sun JL, Schmitt EM, Miller CR, Buckley AF, McLendon RE, Westbrook TF, Northcott PA, Taylor MD, Pfister SM, Febbo PG, Wechsler-Reya RJ. An Animal Model of MYC-Driven Medulloblastoma. Cancer Cell. 2012, 21(2):155-67.
  30. Kazanov MD, Igarashi Y, Eroshkin AM, Cieplak P, Ratnikov B, Zhang Y, Li Z, Godzik A, Osterman AL, Smith JW. Structural determinants of limited proteolysis. J Proteome Res. 2011 Aug 5;10(8):3642-51. Epub 2011 Jul 8.
  31. Forcales SV, Albini S, Giordani L, Malecova B, Cignolo L, Chernov A, Coutinho P, Saccone V, Consalvi S, Williams R, Wang K, Wu Z, Baranovskaya S, Miller A, Dilworth FJ, Puri PL. Signal-dependent incorporation of MyoD-BAF60c into Brg1-based SWI/SNF chromatin-remodelling complex. EMBO J. 2011 Nov 8;31(2):301-16
  32. Hebbard L, Cecena G, Golas J, Sawada J, Ellies LG, Charbono A, Williams R, Jimenez RE, Wankell M, Arndt KT, Dejoy SQ, Rollins RA, Diesl V, Follettie M, Chen L, Rosfjord E, Komatsu M, Boschelli F, Oshima RG. Control of mammary tumor differentiation by SKI-606 (bosutinib). Oncogene, 30: 301-312, 2011
  33. Müller FJ, Schuldt BM, Williams R, Mason D, Altun G, Papapetrou EP, Danner S, Goldmann JE, Herbst A, Schmidt NO, Aldenhoff JB, Laurent LC, Loring JF. A bioinformatic assay for pluripotency in human cells. Natute Methods. 2011 Apr;8(4):315-7. Epub 2011 Mar 6
  34. Krajewska M, You Z, Rong J, Kress C, Huang X, Yang J, Kyoda T, Leyva R, Banares S, Hu Y, Sze CH, Whalen MJ, Salmena L, Hakem R, Head BP, Reed JC, Krajewski S. Neuronal deletion of caspase 8 protects against brain injury in mouse models of controlled cortical impact and kainic acid-induced excitotoxicity. PLoS One. 2011;6(9):e24341.
  35. Williams, R.,  Schuldt B.,  Mueller, F. A guide to stem cell identification: Progress and challenges in system-wide predictive testing with complex biomarkers.  Bioessays, 2011 Nov;33(11):880-90
  36. Ichikawa M, Williams R, Wang L, Vogl T, Srikrishna G. S100A8/A9 activate key genes and pathways in colon tumor progression.  Mol Cancer Res. 2011 Feb;9(2):133-48. Epub 2011 Jan 12.
  37. Shah M, Bhoumik A, Goel V, Dewing A, Breitwieser W, Kluger H, Krajewski S, Krajewska M, Dehart J, Lau E, Kallenberg DM, Jeong H, Eroshkin A, Bennett DC, Chin L, Bosenberg M, Jones N, Ronai ZA. A Role for ATF2 in Regulating MITF and Melanoma Development. PLoS Genet. 2010 Dec 23;6(12)
  38. Radiation Sensitivity and Tumor Susceptibility in ATM Phospho-Mutant ATF2 Mice. Li S, Ezhevsky S, Dewing A, Cato MH, Scortegagna M, Bhoumik A, Breitwieser W, Braddock D, Eroshkin A, Qi J, Chen M, Kim JY, Jones S, Jones N, Rickert R, Ronai ZA. Genes Cancer. 2010 Apr 1;1(4):316-330.
  39. Microarray-based transcriptional and epigenetic profiling of matrix metalloproteinases, collagens, and related genes in cancer.  Chernov AV, Baranovskaya S, Golubkov VS, Wakeman DR, Snyder EY, Williams R, Strongin AY.J Biol Chem. 2010 Jun 18;285(25):19647-59. Epub 2010 Apr 19
  40. Chen Q, Williams R, Healy CL, Wright CD, Wu SC, O'Connell TD. An association between gene expression and better survival in female mice following myocardial infarction.  J Mol Cell Cardiol. 2010 Nov;49(5):801-11. Epub 2010 Aug 6
  41. Qi J, Nakayama K, Cardiff RD, Borowsky AD, Kaul K, Williams R, Krajewski S, Mercola D, Carpenter PM, Bowtell D, Ronai ZA. Siah2-dependent concerted activity of HIF and FoxA2 regulates formation of neuroendocrine phenotype and neuroendocrine prostate tumors.Cancer Cell. 2010 Jul 13;18(1):23-38
  42. Hebbard L, Cecena G, Golas J, Sawada J, Ellies LG, Charbono A, Williams R, Jimenez RE, Wankell M, Arndt KT, Dejoy SQ, Rollins RA, Diesl V, Follettie M, Chen L, Rosfjord E, Cardiff RD, Komatsu M, Boschelli F, Oshima RG. Control of mammary tumor differentiation by SKI-606 (bosutinib).  Oncogene. 2010 Sep 6. [Epub ahead of print]
  43. Timmer JC, Zhu W, Pop C, Regan T, Snipas SJ, Eroshkin AM, Riedl SJ, Salvesen GS. Structural and kinetic determinants of protease substrates. Nat Struct Mol Biol. 2009 Oct;16(10):1101-8. Epub 2009 Sep 20.
  44. Shiryaev SA, Remacle AG, Savinov AY, Chernov AV, Cieplak P, Radichev IA, Williams R, Shiryaeva TN, Gawlik K, Postnova TI, Ratnikov BI, Eroshkin AM, Motamedchaboki K, Smith JW, Strongin AY. Inflammatory proprotein convertase-matrix metalloproteinase proteolytic pathway in antigen-presenting cells as a step to autoimmune multiple sclerosis. J Biol Chem. 2009 Sep 2. [Epub ahead of print]
  45. Müller FJ, Laurent LC, Kostka D, Ulitsky I, Williams R, Lu C, Park IH, Rao MS, Shamir R, Schwartz PH, Schmidt NO, Loring JF.Regulatory networks define phenotypic classes of human stem cell lines.  Nature. 2008 Sep 18;455(7211):401-5.
  46. Qi J, Nakayama K, Gaitonde S, Goydos JS, Krajewski S, Eroshkin A, Bar-Sagi D, Bowtell D, Ronai Z. The ubiquitin ligase Siah2 regulates tumorigenesis and metastasis by HIF-dependent and -independent pathways. Proc Natl Acad Sci U S A. 2008 Oct 28;105(43):16713-8. 2008;
  47. Igarashi Y., Heureux E., Doctor KS., Talwar P., Gramatikova S., Gramatikoff K., Zhang Y., Blinov M., Ibragimova SS., Boyd S., Ratnikov B., Cieplak P., Godzik A., Smith JW., Osterman AL., and Eroshkin AM. PMAP: databases for analyzing proteolytic events and pathways Nucl. Acids Res. 2009 37: D611-D618
  48. Knowles L., Yang C., Osterman A., Smith J. Inhibition of Fatty-acid Synthase Induces Caspase-8-mediated Tumor Cell Apoptosis by Up-regulating DDT4 J. Biol. Chem., Vol. 283, 46, 31378-31384, November 14, 2008.
  49. Lopez-Bergami P, Huang C, Goydos JS, Yip D, Bar-Eli M, Herlyn M, Smalley KS, Mahale A, Eroshkin A, Aaronson S, Ronai Z. Rewired ERK-JNK signaling pathways in melanoma. Cancer Cell. 2007 May;11(5):447-60.
  50. Rozanov DV, Savinov AY, Williams R, Liu K, Golubkov VS, Krajewski S, Strongin AY. Molecular signature of MT1-MMP: transactivation of the downstream universal gene network in cancer. Cancer Res. 2008 Jun 1;68(11):4086-96.
  51. Wen F, Tynan JA, Cecena G, Williams R, Múnera J, Mavrothalassitis G, Oshima RG. Ets2 is required for trophoblast stem cell self-renewal. Dev Biol. 2007 Dec 1;312(1):284-99.
  52. Noberini, R., Koolpe, M., Peddibhotla, S., Dahl, R., Su, Y., Cosford, N. D. P., Roth, G. P., Pasquale, E. B. Small molecules can selectively inhibit ephrin binding to the EphA4 and EphA2 receptors. J. Biol. Chem. (2008) 283, 29461-72.
  53. Narisawa S, Hoylaerts MF, Doctor KS, Fukuda MN, Alpers DH, Millán JL. A novel phosphatase upregulated in Akp3 knockout mice. Am J Physiol Gastrointest Liver Physiol. 2007 Nov;293(5):G1068-77.
  54. Timmer J.C., Enoksson M., Wildfang E., Zhu W., Igarashi Y., Denault J.B., Ma Y., Dummitt B., Chang Y.H., Mast A.E., Eroshkin A., Smith J.W., Tao W.A., Salvesen G.S.. Profiling constitutive proteolytic events in vivo. Biochem J. 2007, 407(1):41
  55. Tu S., Shin Y., Zago W.M., States B.A., Eroshkin A., Lipton S.A., Tong G.G., Nakanishi N. Takusan: a large gene family that regulates synaptic activity. Neuron. 2007, 55(1):69-85.
  56. Enoksson M., Li J., Ivancic M.M., Timmer J.C., Wildfang E., Eroshkin A., Salvesen G.S., Tao W.A. Identification of proteolytic cleavage sites by quantitative proteomics. J Proteome Res. 2007, 6(7):2850-8.
  57. Igarashi Y, Eroshkin A, Gramatikova S, Gramatikoff K, Zhang Y, Smith JW, Osterman AL, Godzik A. CutDB: a proteolytic event database. Nucleic Acids Res. 2007 Jan;35(Database issue):D546-9. Epub 2006. 
  58. Doctor KS, Reed JC, Godzik A, Bourne PE. The apoptosis database. Cell Death Differ. 2003 Jun;10(6):621-33. Review.
  59. Reed JC, Doctor KS, Godzik A. The domains of apoptosis: a genomics perspective. Sci STKE. 2004 Jun 22;2004(239):re9. Review.​