PUBLICATIONS

Active Preprints and Upcoming Abstracts/Presentations

Journal Articles

Berginski ME, Jenner MR, Joisa CU, Loeza GH, Golitz BT, Lipner MB, Leary JR, Rashid N, Johnson GL, Yeh JJ, Gomez SM. 2024. Kinome state is predictive of cell viability in pancreatic cancer tumor and cancer-associated fibroblast cell lines. PeerJ 12:e17797.

Chen KA, Gartner V, Darlington KC, Silverstein SR, Kennedy Ng MM, Butler L, Avalos K, Nishiyama NC, Joisa CU, Schaner MR, Lian G, Beasley C, Lau GW, Bauer MJ, Zhu L-C, Kapadia MR, Gomez SM, Furey TS, Sheikh SZ. 2024. Post-operative Crohn’s disease recurrence and infectious complications: A transcriptomic analysis. Digestive diseases and sciences:1–12.

Kirchoff KE, Wellnitz J, Hochuli JE, Maxfield T, Popov KI, Gomez S, Tropsha A. 2024. Utilizing Low-Dimensional Molecular Embeddings for Rapid Chemical Similarity Search. In: Advances in Information Retrieval. Springer Nature Switzerland, 34–49.

Chen KA, Nishiyama NC, Kennedy Ng MM, Shumway A, Joisa CU, Schaner MR, Lian G, Beasley C, Zhu L-C, Bantumilli S, Kapadia MR, Gomez SM, Furey TS, Sheikh SZ. 2024. Linking gene expression to clinical outcomes in pediatric Crohn’s disease using machine learning. Scientific reports 14:1–10.

Gomez SM, Axtman AD, Willson TM, Major MB, Townsend RR, Sorger PK, Johnson GL. 2024. Illuminating function of the understudied druggable kinome. Drug discovery today:103881.

Joisa CU, Chen KA, Berginski M, Beville S, Stuhlmiller T, Okumu D, Golitz BT, Johnson GL, Gomez SM. 2024. Combined kinome inhibition states are predictive of cancer cell line sensitivity to kinase inhibitor combination therapies. Pacific Symposium on Biocomputing. In: Biocomputing 2024. WORLD SCIENTIFIC, 276–290.

Kirchoff KE, Maxfield T, Tropsha A, Gomez SM. 2024. SALSA: Semantically-Aware Latent Space Autoencoder. Proceedings of the AAAI Conference on Artificial Intelligence 38:13211–13219. (also a workshop paper in NeurIPS 2023, New Frontiers of AI for Drug Discovery and Development; arXiv [cs.LG] https://arxiv.org/abs/2310.02744.)

Joisa CU, Chen KA, Berginski ME, Golitz BT, Jenner MR, Herrera Loeza GH, Yeh JJ, Gomez SM. 2023. Integrated Single-Dose Kinome Profiling Data is Predictive of Cancer Cell Line Sensitivity to Kinase Inhibitors. PeerJ 11:e16342 (preprint -bioRxiv:2022.12.06.519165. DOI: 10.1101/2022.12.06.519165)

Chen KA, Kirchoff KE, Butler LR, Holloway AD, Kapadia MR, Kuzmiak CM, Downs-Canner SM, Spanheimer PM, Gallagher KK, Gomez SM. 2023. Analysis of Specimen Mammography with Artificial Intelligence to Predict Margin Status. Annals of surgical oncology. DOI: 10.1245/s10434-023-14083-1.

Chen KA, Goffredo P, Butler LR, Joisa CU, Guillem JG, Gomez SM, Kapadia MR. 2023. Prediction of Pathologic Complete Response for Rectal Cancer Based on Pre-treatment Factors Using Machine Learning. Diseases of the colon and rectum. DOI: 10.1097/DCR.0000000000003038.

Chen KA, Goffredo P, Hu D, Joisa CU, Guillem JG, Gomez SM, Kapadia MR. 2023. Estimating Risk of Locoregional Failure and Overall Survival in Anal Cancer Following Chemoradiation: A Machine Learning Approach. Journal of gastrointestinal surgery: official journal of the Society for Surgery of the Alimentary Tract. DOI: 10.1007/s11605-023-05755-0.

Chen KA, Gomez SM, Kapadia MR. 2023. Improving the American College of Surgeons NSQIP Surgical Risk Calculator with Machine Learning. Journal of the American College of Surgeons. DOI: 10.1097/XCS.0000000000000676. (Letter to the Editor)

Butler LR, Chen KA, Hsu J, Kapadia MR, Gomez SM, Farrell TM. 2023. Predicting Readmission after Bariatric Surgery using Machine Learning. Surgery for obesity and related diseases: official journal of the American Society for Bariatric Surgery. DOI: 10.1016/j.soard.2023.05.025.

Hsu JL, Chen KA, Butler LR, Bahraini A, Kapadia MR, Gomez SM, Farrell TM. 2023. Application of machine learning to predict postoperative gastrointestinal bleed in bariatric surgery. Surgical endoscopy. DOI: 10.1007/s00464-023-10156-0.

Chen KA, Joisa CU, Stem JM, Guillem JG, Gomez SM, Kapadia MR. 2023. Prediction of Ureteral Injury During Colorectal Surgery Using Machine Learning. The American surgeon:31348231173981.

Berginski ME, Joisa CU, Golitz BT, Gomez SM. 2023. Kinome Inhibition States and Multiomics Data Enable Prediction of Cell Viability in Diverse Cancer Types. PLoS Computational Biology 19:e1010888. (bioRxiv:2022.04.08.487646. DOI: 10.1101/2022.04.08.487646.)

Chen KA, Joisa CU, Stem J, Guillem JG, Gomez SM, Kapadia MR. Improved prediction of surgical site infection after colorectal surgery using machine learning. 2023. Diseases of the Colon & Rectum. Diseases of the Colon & Rectum DOI: 10.1097/DCR.0000000000002559

Chen KA, Joisa CU, Stitzenberg K, Stem J, Guillem JG, Gomez SM, Kapadia MR. Development and validation of machine learning models to predict readmission after colorectal surgery. 2022. Journal of Gastrointestinal Surgery: official journal of the Society for Surgery of the Alimentary Tract DOI: 10.1007/s11605-022-05443-5

Chen KA, Berginski ME, Desai CS, Guillem JG, Stem J, Gomez SM, Kapadia MR. 2022. Differential Performance of Machine Learning Models in Prediction of Procedure-Specific Outcomes. Journal of gastrointestinal surgery: official journal of the Society for Surgery of the Alimentary Tract. DOI: 10.1007/s11605-022-05332-x.

Jeffries RE, Gomez SM, Macdonald JM, Gamcsik MP. 2022. Direct Detection of Glutathione Biosynthesis, Conjugation, Depletion and Recovery in Intact Hepatoma Cells. International journal of molecular sciences 23:4733.

Kirchoff KE, Gomez SM. EMBER: Multi-label prediction of kinase-substrate phosphorylation events through deep learning. Bioinformatics, 2022;, btac083, (bioRxiv:2020.02.04.934216. DOI: 10.1101/2020.02.04.934216.)

Mestril S, Kim R, Hinman SS, Gomez SM, Allbritton NL. Stem/proliferative and differentiated cells within primary murine colonic epithelium display distinct intracellular free Ca2+ signal codes. 2021. Advanced Healthcare Materials:e210318n

Gulyaeva O, Hu Z, Oprea T, Loyd KCK, Gomez S, Roth BL, McManus MT. Prevalent mouse phenotypes in the unexplored druggable genome. 2021. bioRxiv:2021.11.08.467777. DOI: 10.1101/2021.11.08.467777

Berginski ME, Moret N, Changchang L, Goldfarb D, Sorger PK, Gomez SM. The Dark Kinase Knowledgebase: An Online Compendium of Knowledge and Experimental Results of Understudied Kinases. Nucleic Acid Research. 2020.

Moret N, Liu C, Gyori BM, Bachman JA, Steppi A, Taujale R, Huang L-C, Hug C, Berginski M, Gomez S, Kannan N, Sorger PK. 2020. Exploring the understudied human kinome for research and therapeutic opportunities. bioRxiv:2020.04.02.022277. DOI: 10.1101/2020.04.02.022277.

Singhal S, Gomez SM, Burch CL. Recombination drives the evolution of mutational robustness. Current Opinion in Systems Biology. 2019. 13:142-149.

Metz KS, Deoudes EM, Berginski ME, Jimenez-Ruiz I, Aksoy BA, Hammerbacher J, Gomez SM, Phanstiel, DH. Coral: Clear and Customizable Visualization of Human Kinome Data. Cell Syst. 2018;7: 347–350.e1.

Oprea TI, Bologa CG, Brunak S, Campbell A, Gan G, Gaulton A, Gomez SM, Guha R, Hersey A, Holmes J, Jadhav A, Jensen LJ, Johnson GL, Karlson A, Leach AR, Ma’ayan A, Malovannaya A, Mani S, Mathias SL, McManus M, Meehan T, von Mering C, Muthas D, Nguyen DC, Overington JP, Papadatos G, Qin J, Reich C, Roth BL, Schürer SC, Simeonov A, Sklar LA, Simeonov A, Southall N, Tomita S, Tudose I, Ursu O, Vidović D, Waller A, Westergaard S, Yang JJ, Zahoranszky-Kohalmi G. Unexplored Therapeutic Opportunities in the Human Genome. Nat. Rev. Drug Discov. 2018. Feb 23.

Collins KAL, Stuhlmiller T, Zawistowski JS, East MP, Pham T, Hall CR, Goulet DR, Bevill SM, Angus SP, Velarde SH, Sciaky N, Oprea TI, Graves LM, Johnson GL, Gomez SM. Proteomic analysis of the breast cancer kinome integrates understudied kinases into functional networks. Oncotarget. 2018.

Urbina FL, Gomez SM, Gupton SL. Spatiotemporal organization of exocytosis emerges during neuronal shape change. J Cell Biol. 2018.

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. 

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 Biol. 2014, 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 isoforms. PNAS. 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 cells. PeerJ. 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 genome. RNA. 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. 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 dynamics. J 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 Migration. PLoS 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 Tenomodulin. J 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 cancer. Cell. 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 chemotaxis. Cell. 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 kinome. Cell 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 homeostasis. PLoS 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 Cells. Cell 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 distances. BMC Bioinformatics. 2009 Dec 15;10:423.

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

Yang W, Johnson GL, Gomez SM. Data-driven modeling of cellular stimulation, signaling and output response in RAW 264.7 cells.  J Mol Signal. 2008 May 22;3:11.

Gomez SM, Choi K, Wu Y. Prediction of protein-protein interaction networks. Curr 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 invasion. Cell 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 algorithms. Genome 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 clones. Genome 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 sequences. Bioinformatics. 2003 Oct 12;19(15):1875-81.

Gomez SM.  Network approaches to genome annotation and the challenge of Anopheles gambiae. Mol 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 articles. Bioinformatics. 2002;18 Suppl 1:S249-S257. (ISMB paper)

Gomez SM, Rzhetsky A. Towards the prediction of complete protein-protein interaction networks. Pac 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 genome. Bioinformatics. 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 networks. Bioinformatics. 2000 Dec;16(12):1120-8.

Gomez SM, Choy G, Kabir N, Leonard EF. Capture of rare cells in suspension with antibody-coated polystyrene beads. Biotechnol 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 advection. Proceedings Theme A, 27th Congress of the Int’l Assoc. for Hydraulic Research, Water Resources Engineering Division/ASCE. 1997:40-45.

Abstracts

Chen KA, Bhamidipati D, Tabet J, Joisa CU, Stem JM, Guillem JG, Gomez SM, Kapadia MR, Predicting Response to Chemotherapy in Colorectal Cancer Using a Clinical-Genomic Machine Learning Model. ASCRS Annual Scientific Meeting, June 2, 2024, Baltimore, Maryland (selected for presentation)

Chen KA, Goffrendo P, Butler LR, Joisa CU, Stem JM, Guillem JG, Gomez SM, Kapadia MR. 2023. Genomic and transcriptomic predictors of pathologic complete response for rectal cancer: A machine learning approach.  Journal of the American College of Surgeons 237(5):p S70-S109, November 2023.

Chen K, Stem J, Guillem JG, Gomez SM, Kapadia MR. 2023. Predicting Ileus after Colorectal Surgery Using Machine Learning. Journal of the American College of Surgeons 236:S22.

Chen K, Stem J, Guillem JG, Gomez SM, Kapadia MR. 2023. Development and Validation of Machine Learning Models to Predict Ureteral Injury during Colorectal Surgery. Journal of the American College of Surgeons 236:S20.

Chen KA, Goffredo P, Butler LR, Stem J, Guillem JG, Gomez SM, Kapadia MR. Prediction of Pathologic Complete Response for Rectal Cancer Based on Pre-treatment Factors Using Machine Learning. American Society of Colon and Rectal Surgeons (ASCRS) 2023 Annual Scientific Meeting, June 4, 2023, Seattle, Washington (poster)

Chen KA, Goffredo P, Stem J, Guillem JG, Gomez SM, Kapadia MR. Estimating Risk of Locoregional Failure in Anal Cancer Following Chemoradiation: A Machine Learning Approach. American Society of Colon and Rectal Surgeons (ASCRS), Annual Scientific Meeting, June 4, 2023, Seattle, Washington (poster)

Butler LR, Chen KA, Hsu J, Gomez SM, Kapadia MR, Farrell TM. Predicting Readmission after Bariatric Surgery Using Machine Learning. Academic Surgical Congress, February 7, 2023 (presentation)

Hsu J, Chen KA, Butler LR, Bahraini A, Gomez SM, Kapadia MR, Farrell TM. Application of Machine Learning to Predict Postoperative Gastrointestinal Bleed in Bariatric Surgery. 2023 Society of American Gastroenterological and Endoscopic Surgeons (SAGES) Annual Meeting, April 1, 2023

Chen KA, Stem J, Guillem J, Gomez S, Kapadia M. Predicting surgical site infection after colorectal surgery using machine learning. American Society of Colon and Rectal Surgeons (ASCRS) 2022 Annual Scientific Meeting

Chen KA, Berginsk M, Guillem J, Gomez S, Kapadia M. Prediction of Anastomotic Leak after Colectomy Using Machine Learning. American College of Surgeons (ACS) 2022 Annual Academic Clinical Congress

Chen KA, Stem J, Guillem,Gomez S, Kapadia M. Development of Machine Learning Models to Predict Readmission after Colorectal Surgery. Society of American Gastrointestinal and Endoscopic Surgeons (SAGES) 2022 Annual Meeting (podium presentation)

Chen KA, Feinberg A, Gomez S, Gallagher K. Computer Vision Analysis of Specimen Mammography. American College of Surgeons Clinical Congress. October 2021. Virtual.

Robson IS, Berginski ME, Gomez SM. Kinotype to phenotype: Perturbed phosphoproteomic state predicts cancer cell growth rates in vitro. AACR Virtual Special Conference on Artificial Intelligence, Diagnosis, and Imaging, January 13-14, 2021

Chen KA, Robson I, Gomez S and Fichera A. Computer Vision Analysis of Total Mesorectal Excision Specimens. 15th Annual Academic Surgical Congress, Lake Buena Vista, FL; February 4-6, 2020.

Gomez S. FastTraCS – A novel continuous improvement engine for translational medicine. Arlington, VA, Sept. 26-27, 2019. (https://clic-ctsa.org/publications/fasttracs-novel-continuous-improvement-engine-translational-medicine)

Collins KAL, Stuhlmiller TJ, Zawistowski JS, East MP, Pham TT, Hall CR, Goulet DR, Bevill SM, Angus SP, Velarde SH, Sciaky N, Graves LM, Johnson GL and Gomez SM. Defining subtype taxonomies and functional architectures of the breast cancer kinome. International Conference on Systems Biology, Blacksburg, VA; August 6-12, 2017

Stuhlmiller TJ, Samantha MM, Zawistowski JS, Duncan JS, Angus SP, Granger DA, Reuther RA, Collins KA, Gomez SM, Kuan PF, Chen X, Sciaky N, Johnson GL. BET Bromodomain Inhibition Targets Adaptive Responses to Lapatinib in HER2-Positive Breast Cancer. Molecular Cancer Research: MCR 14 (2 Supplement). American Association for Cancer Research: B25–B25, 2016.

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.