PrePrints (unpublished)

Urbina F, Gomez SM, Gupton SL. Dynamic Spatiotemporal Organization of Exocytosis During Cellular Shape Change. (2017) bioRXiv preprint. https://doi.org/10.1101/185249

Collins KAL, Stuhlmiller T, Zawistowski JS, East MP, Pham T, Hall CR, Goulet DR, Bevill SM, Angus SP, Velarde SH, Sciaky N, Graves LM, Johnson GL, Gomez SM. Proteomic analysis defines kinase taxonomies specific for subtypes of breast cancer. bioRXiv doi: https://doi.org/10.1101/122739

Articles

Perkowski EF, Zulauf KE, Weerakoon D, Hayden JD, Ioerger TR, Oreper D, Gomez SM, Sacchettini JC, Braunstein M. 2017. The EXIT strategy: an approach for identifying bacterial proteins exported during host infection. mBio 8:e00333-17. https://doi.org/10.1128/mBio.00333-17.

Mobley RJ, Raghu D, Duke LD, Abell-Hart K, Zawistowski JS, Lutz K, Gomez SM, Roy S, Homayouni R, Johnson GL, Abell AN. MAP3K4 Kinase Activity Controls Chromatin Remodelers for Transitions Between Epithelial and Mesenchymal Phenotypes in Trophoblast Stem Cells. Cell Reports. 2017 Mar 7;18(10)

Spychala J, Spychala P, Gomez S, Weinreb GE. Visinets: A Web-Based Pathway Modeling and Dynamic Visualization Tool. PloS One. 2015 10 (5): e0123773.

Vitriol EA, McMillen LM, Kapustina M, Gomez SM, Vavylonis D and Zheng JQ. Two functionally distinct sources of actin monomers supply the leading edge of lamellipodia. Cell Reports. 2015. 11

Stuhlmiller TJ, Miller SM, Zawistowski JS, NakamuraK, Beltran A,  Duncan JS, Lutz KA, Granger DA, Reuther RA, Gomez SM, Kuan P-F, Parker JS, Chen X, Sciaky N, Earp HS, Carey LA, Jin J and Johnson GL. Epigenetic inhibition of lapatinib-induced kinome reprogramming in ERBB2-positive breast cancer by targeting BET family bromodomains. Cell Reports 2015. 11

Dickinson AJ, Meyer M, Pawlak EA, Gomez S, Jaspers I, Allbritton NL. Analysis of sphingosine kinase activity in single natural killer cells from peripheral blood. Integr Biol. 2015 Apr 7;7(4):392-401.

Tsai Y, Dominguez D, Gomez S*, and Wang Z*. Transcriptome-wide identification and study of cancer-specific splicing events across multiple tumors. Oncotarget. 2015. Feb 5.

Chan KT, Asokan SB, King SJ, Bo T, Liu W, Berginski ME, Simon JD, Davis IJ, Gomez SM, Sharpless NE and Bear JE. LKB1 loss in melanoma disrupts directional migration toward ECM cues.  J Cell Biol2014, Oct 27;207(2):299-315.

Chu P-H, Tsygankov D, Berginski M, Gomez SM, Elston TC Karginov AV and Hahn KM. Engineered kinase activation reveals unique morphodynamic phenotypes and associated trafficking for Src family isoformsPNAS. 2014, Aug 26;111(34):12420-5.

Berginski ME, Creed SJ, Cochran S, Roadcap DW, Bear JE and Gomez SM. Automated analysis of invadopodia dynamics in live cellsPeerJ. 2014 2 e462. (PrePrint: PeerJ PrePrints 2:e20v1 http://dx.doi.org/10.7287/peerj.preprints.320v1)

Tsai YS, Gomez SM and Wang Z. Prevalent RNA recognition motif duplication in the Human genomeRNA. 2014. May;20(5):702-12.

Karginov AV, Tsygankov D, Berginski M, Chu P-H, Trudeau ED, Yi JJ, Gomez S, Elston TC and Hahn KM. Dissecting motility signaling through activation of specific Src-effector complexes. Nat Chem Biol. 2014, Apr;10(4):286-90.

Berginski ME, Gomez SM. The Focal Adhesion Analysis Server: a web tool for analyzing focal adhesion dynamics. [v1; ref status: indexed] F1000Research. 2013, 2:68 (doi: 10.3410/f1000research.2-68.v1).

Chaki SP, Barhoumi R, Berginksi ME, Sreenivasappa H, Trache A, Gomez SM and Rivera GM. Nck enables directional cell migration through the coordination of polarized membrane protrusion with adhesion dynamicsJ Cell Sci. 2013 Apr 1; 126:1637-1649.

Chen Z, Lessey E, Berginski ME, Cao L, Li J, Trepat X, Itano M, Gomez SM, Kapustina M, Huang C, Burridge K, Truskey G and Jacobson K. Gleevec, an Abl Family Inhibitor, Produces a Profound Change in Cell Shape and MigrationPLoS ONE. 2013 8(1): e52233. doi:10.1371/journal.pone.0052233.

Qi J, Dmochowski j, Banes A, Tsuzaki M, Bynum D, Patterson M, Creighton A, Gomez S, Tech K, Cederlund A and Banes A. Differential Expression and Cellular Localization of Novel Isoforms of the Tendon Biomarker TenomodulinJ Appl Physiol. 2012 Sep;113(6):861-71.

Duncan JS, Whittle MC, Nkamura K, Abell AN, Midland AA, Zawistowksi JS, Johnson NL, Granger DA, Jordan NV, Darr D, Usary J, Major B, He X, Hoadley K, Sharpless NE, Perou CM, Gomez SM, Jin J, Frye SV, Earp HS, Graves LM and Johnson GL. Dynamic reprogramming of the kinome in response to targeted MEK inhibition in triple negative breast cancerCell. 2012 149(2):307-21.

Wu C, Asokan SB, Berginski ME, Sharpless NE, Griffith JD, Gomez SM and Bear JE. Arp2/3 complex is critical for lamellipodia and organization of cell-matrix adhesion but dispensable for fibroblast chemotaxisCell. 2012 Mar 2;148(5):973-87.

Midland AA, Whittle MC, Duncan JS, Abell AN, Nakamura K, Zawistowski JS, Carey LA, Earp HS 3rd, Graves LM, Gomez SM and Johnson GL. Defining the expressed breast cancer kinomeCell Research. 2012 Feb 7. Doi:10.1038/cr.2012.25.

Xu K, Morgan KT, Todd A, Elston TC and Gomez SM. A whole-body model for glycogen regulation reveals a critical role for substrate cycling in maintaining blood glucose homeostasisPLoS Computational Biology. 2011. Dec;7(12):e1002272.

Berginski ME, Vitriol E, Hahn KM and Gomez SM. High-resolution quantification of focal adhesion spatiotemporal dynamics in living cells. PLoS ONE. 2011;6(7):e22025.

Abell AN, Jordan NV, Huang W, Prat A, Midland AA, Johnson NL, Granger DA, Mieczkowski PA, Perou CM, Gomez SM, Li L and Johnson GL. MAP3K4/CBP-Regulated H2B Acetylation Controls Epithelial-Mesenchymal Transition in Trophoblast Stem CellsCell Stem Cell. 2011 May 6;8(5):525-37.

Doolittle JM and Gomez SM. Mapping protein interactions between Dengue virus and its human and insect hosts. PLoS Neglected Tropical Diseases. 2011 Feb 15;5(2):e954.

Doolittle JM and Gomez SM. Structural similarity-based predictions of protein interactions between HIV-1 and Homo sapiens. Virology Journal. 2010 Apr 28;7:82.

Staab J, O’Connell TM, Gomez SM. Enhancing metabolomic data analysis with Progressive Consensus Alignment of NMR Spectra (PCANS)BMC Bioinformatics. 2010, Mar 9;11:123 (“Highly Accessed Article”)

Choi K and Gomez SM. Comparison of phylogenetic trees through alignment of embedded evolutionary distancesBMC Bioinformatics. 2009 Dec 15;10:423.

Johnson GL and Gomez SM. Sequence patches on MAPK surfaces define protein-protein interactionsGenome Biology. 2009;10(6):222.

Yang W, Johnson GL, Gomez SM. Data-driven modeling of cellular stimulation, signaling and output response in RAW 263.7 cellsJ Mol Signal. 2008 May 22;3:11.

Gomez SM, Choi K, Wu Y. Prediction of protein-protein interaction networksCurr Protoco Bioinformatics. 2008 Jun;Chapter 8:Unit 8.2.

Rosinski-Chupin I, Briolay J, Brouilly P, Perrot S, Gomez SM, Chertemps T, Roth CW, Keime C, Gandrillon O, Couble P, Brey PT. SAGE analysis of mosquito salivary gland transcriptomes during plasmodium invasionCell Microbiol. 2007 Mar;9(3):708-724.

Li J, Riehle MM, Zhang Y, Xu J, Odul F, Gomez SM, Eiglmeier K, Ueberheide BM, Shabanowitz J, Hunt DF, Ribeiro JMC, Vernick KD. Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithmsGenome Biol. 2006;7(3):R24.

Gomez S.M.*, Eiglmeier K*, Segurens B, Dehoux P, Couloux A, Scarpelli C, Wincker P, Weissenbach J, Brey PT, Roth CW.   Pilot Anopheles gambiae full – length cDNA study: Sequencing and initial characterization of 35,575 clonesGenome Biol. 2005;6(4):R39. (* – contributed equally to this work)

Chien M, Morozova I, Shi S, Sheng H, Chen J, Gomez SM, Asamani G, Hill K, Nuara J, Feder M, Rineer J, Greenberg JJ, Steshenko V, Park SH, Zhao B, Teplitskaya E, Edwards JR, Pampou S, Georghiou A, Chou IC, Iannuccilli W, Ulz ME, Kim DH, Geringer-Sameth A, Goldsberry C, Morozov P, Fischer SG, Segal G, Qu X, Rzhetsky A, Zhang P, Cayanis E, De Jong PJ, Ju J, Kalachikov S, Shuman HA, Russo JJ. The genomic sequence of the accidental pathogen Legionella pneumophila. Science. 2004 Sep 24;305(5692):1966-8.

Gomez SM, Noble WS, Rzhetsky A.  Learning to predict protein-protein interactions from protein sequencesBioinformatics. 2003 Oct 12;19(15):1875-81.

Gomez SM.  Network approaches to genome annotation and the challenge of Anopheles gambiaeMol Cells. 2003 Apr 30;15(2): 159-63.

Gomez SM. Prediction of protein-protein interaction networks. Curr Protoco Bioinformatics. 2003 May;Chapter8:Unit 8.2.

Krauthammer M, Kra P, Iossifov I, Gomez SM, Hripcsak G, Hatzivassiloglou V, Friedman C, Rzhetsky A.  Of truth and pathways: chasing bits of information through myriads of articlesBioinformatics. 2002;18 Suppl 1:S249-S257. (ISMB paper)

Gomez SM, Rzhetsky A. Towards the prediction of complete protein-protein interaction networksPac Symp Biocomput. 2002:413-24.

Gomez SM, Lo SH, Rzhetsky A. Probabilistic prediction of unknown metabolic and signal-transduction networks. Genetics. 2001 Nov;159(3): 1291-8.

Rzhetsky A, Gomez SM.  Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genomeBioinformatics. 2001 Oct;17(10):988-96.

Rzhetsky A, Koike T, Kalachikov S, Gomez SM, Krauthammer M, Kaplan SH, Kra P, Russo JJ, Friedman CA.  A Knowledge model for analysis and simulation of regulatory networksBioinformatics. 2000 Dec;16(12):1120-8.

Gomez SM, Choy G, Kabir N, Leonard EF. Capture of rare cells in suspension with antibody-coated polystyrene beadsBiotechnol Prog. 1999 Mar-Apr;15(2):238-44.

Omurtag AC, Stickel VG Jr, Gomez SM, Leonard EF, Chevray R. Transport and separation of particles by chaotic advectionProceedings Theme A, 27th Congress of the Int’l Assoc. for Hydraulic Research, Water Resources Engineering Division/ASCE. 1997:40-45.

Abstracts

Demby K, Gomez SM, Peden D. Engineering Solutions to Health Problems: A Workshop to Develop and Sustain Clinician-Engineer Collaborations. SciTS, June 2-5, Bethesda MD, 2015.

Doolittle-Hall JM, Rothwell R, Morris TL, Grange D, Arnold RR, Santor RB, Thomas DL, Dominick L, Shanle EK, Baines AT, Gomez SM, Strahl BD and Webster-Cyriaque J. Kaposi’s Sarcoma-associated Herpesvirus Reactivation by Bacteria involves the Hypoxia Response and Epigenetic Regulation. Dental Research Day, UNC-Chapel Hill, Feb. 25, 2015.

Collins KAL, Stuhlmiller TJ, Pham TT, Angus S, Duncan JS, Whittle MC, Graves LM, Johnson GL and Gomez SM. The Activation State of the Breast Cancer Kinome: Characterization of Subtypes and Identification of Key Regulatory Kinases. BMES Annual Meeting, San Antonio, TX, Oct. 22-25, 2014. (Nominated as a top presentation in the Bioinformatics, Computational and Systems Biology Track)

Chu P-H, Karginov AV, Tsygankov DM, Berginski ME, Gomez SM, Elston TC and Hahn KM. RapR analogs of Src, Fyn, Yes and Lyn: new tools for activation of specific kinase isoforms in vivo demonstrate specific roles for isoforms in cell motility. ASCB 2012 Annual Conference, San Francisco, CA, Dec. 15-19, 2012.

Karginov AV, Tsygankov DM, Berginski ME, Trudeau ED, Chu P-H, Yi JJ, Gomez SM, Elston TC and Hahn KM. Engineered manipulation of signaling networks: Novel control of kinase activation and interactions dissects parallel Src pathways. ASCB 2012 Annual Conference, San Francisco, CA, Dec. 15-19, 2012.

Jeffries RE, Xu K, Gomez S, Macdonald J and Gamcsik M. Modeling and experimental correlation of the glutathione metabolic network. BMES Annual Conference, Atlanta, GA, Oct.24-27, 2012.

Tsai Y, Gomez S and Wang Z. Identification of prevelant RNA recognition motif duplication suggests cooperative binding of RNA targets.  ISMB AS-SIG, Long Beach, CA, July 15-17, 2012.

Banes AJ, Qi J, Dmochowski JM, Tsuzaki M, Banes AN, Byunum D, Gomez S and Wall ME. Tenocytes, phenotypes, biomarkers and functions: Roles in bioartificial tendons. Proceedings of the ASME 2011 Summer Bioengineering Conference SBC2011, Farmington, PA. June 22-25, 2011.

Zhu H, Liying Z, Staab J, Sedykh A, Tang H, Gomez S, Rusyn I and Tropsha A. Incorporation of ToxCast in vitro assay data and relevant toxicity pathway information improves the external prediction accuracy of Quantitative Structure-Activity Relationship (QSAR) Models of Chemical Hepatotoxicity. Society of Toxicology Annual Meeting, Washington DC, March 6-10, 2011.

Xu K, Kirchberg C, Gomez SM and Morgan K. Development of a transcript profile for fasting as a confounding variable in toxicogenomic studies. Society of Toxicology Annual Meeting, Washington DC, March 6-10, 2011.

Berginski ME, Vitriol E, Hahn KM and Gomez SM. Quantifying Focal Adhesion Spatiotemporal Dynamics Through Computational Image Analysis. 8th Annual Rocky Mountain Bioinformatics Conference, Snowmass, CO. December 9-11, 2010.

Creed SJ, Berginski M, Chan KT, Higgins C, Aloor HL, Roadcap D, Gomez SM, Bear JE, “Coronin 2A and Focal Adhesion Kinase in Cellular Migration and Invasion”, ASCB Annual Meeting, Philadelphia PA, December 11-15, 2010.

Duncan J, Whittle M, Abell A, Midland A, Gomez SM, Frye S, Jin J, Graves LM and Johnson, GL. Monitoring kinome behavior of breast cancer cells in response to lapatinib using proteo-genomics. Gordon Research Conference: Phosphorylation & G-Protein Mediated Signaling Networks. University of New England, Biddeford, ME. June 6-11, 2010.

O’Connell TM, Staab J and Gomez SM. Enhancing metabolomic data analysis with Progressive Consensus Alignment of NMR Spectra (PCANS). 5th International Conference of the Metabolomics Society, Aug 30th – Sep 2nd, 2009, Edmonton, Canada

Berginski ME, Vitriol E, Hahn KM and Gomez SM. Comprehensive Spatiotemporal Analysis of Focal Adhesion Dynamics in Living Cells. Biomedical Engineering Society Annual Meeting, Pittsburgh, PA. October  7-10, 2009.

Choi K, Staab J, Elston TC and Gomez SM. Dimension reduction and functional relevance in ToxCast chemical toxicity data. EPA ToxCast Data Analysis Summit, Durham, NC. May 14-15, 2009

Staab J, Choi K, Elston TC and Gomez SM. Establishing a biological context for ToxCast chemical toxicity data. EPA ToxCast Data Analysis Summit, Durham, NC. May 14-15, 2009.

Berginski M, Vitriol E, Hahn K, Gomez SM. Focal adhesion dynamics analysis through quantitative image processing. Joint RECOMB Satellite Conference on Regulatory Genomics – Systems Biology – DREAM3, MIT/Broad Institute/CSAIL, Cambridge MA, Oct. 29 – Nov. 2, 2008.

Wu Y, Gomez SM. Predicting protein-protein interactions via Bayesian data weighting and integration. Institute of Biological Engineering Annual Conference, Chapel Hill, NC. March 7-10, 2008.

Berginski M., Gomez SM. Automatic Characterization of Focal Adhesions in TIRF Microscopy Images. Institute of Biological Engineering Annual Conference, Chapel Hill, NC. March 7-10, 2008. *Poster received 3rd place in graduate student poster competition.

Choi K, Gomez SM. Comparison of phylogenetic trees via evolutionary space alignment: Application to the detection of protein coevolution. Institute of Biological Engineering Annual Conference, Chapel Hill, NC. March 7-10, 2008.

Peters S, Walker G, Gomez SM. Microfluidic Device for Controlled Reagent Delivery to Cell Culture. Institute of Biological Engineering Annual Conference, Chapel Hill, NC. March 7-10, 2008.

Staab J, O’Connell T, Gomez SM. Peak Alignment of NMR Spectroscopy Data to Enhance Metabolomic Analysis. Institute of Biological Engineering Annual Conference, Chapel Hill, NC. March 7-10, 2008.

Roth C, Eiglmeier K, Gomez SM, Holm I, Dehoux P, Brey P, Rzhetsky A, Segurnes B, Jaillon O, Winker P, Weissenbach J. Improving the annotation quality of the Anopheles gambiae genome. EMBO meeting. Kolymbari, Crete. August 13-19, 2003.

Gomez SM. Prediction of protein interaction networks and application to Anopheles gambiae. EMBO meeting. Kolymbari, Crete. August 13-19, 2003.

Rzhetsky A, Krauthammer M, Koike T, Kra P, Gomez SM, Yu H, Duboue P, Weng W, Johnson SB, Hatzivassiloglou V,  Friedman C. Geneways: A system for mining text and for integrating data on molecular pathways. German Conference on Bioinformatics. 2001

Gomez SM, Kim S, Stickel V, Chevray R, Leonard EF. Affinity Separation of nucleated erythrocytes from maternal blood via chaotic advection. AIChE Annual Meeting. 1997

Choy G, Kim S, Gomez SM, Kabir N, Hodgson P, Maddiwar P, Leonard EF. Cell capture on antibody-coated polystyrene beads. Artificial Organs. 1997;21(6).

Gomez SM, Hodgson J, Kabir N, Maddiwar P, Goldbard S, Leonard EF. Collecting cells on spheres: How shear affects adhesion. AIChE Annual Meeting. 1996.

Gomez SM, Luttges MW. Characterization of a particle bound auxin binding site from clover callus grown under different gravitational environments. ASGSB Bulletin. 1993;7(1):40.

Gomez, SM and Luttges, M.W. Methodology development for the design of controlled ecological life support systems. NASA Graduate Student Researchers Program Annual Symposium, Washington D.C. 1992.

Hoehn, A. Abrahamson, K.S., Gomez, S.M., Voorhees, M. and Luttges, M.W. (1992) Seed germination and early plant development onboard STS-50/USML-1. ASGSB Bulletin (6)1:38.