Vishnoi, Monika, et al. "A prognostic matrix gene expression signature defines functional glioblastoma phenotypes and niches." Communications Biology 9.1 (2026): 18.
Martínez-Botía, Patricia, et al. "Toward standardization and a concerted vision for platelet proteomics research: communication from the SSC of the ISTH." Journal of Thrombosis and Haemostasis 23.5 (2025): 1704-1716.
Thapa, Kisan, et al. "Strategies to include prior knowledge in omics analysis with deep neural networks." Patterns 6.3 (2025).
Portier, Irina, et al. "Aging-related alterations in mechanistic target of rapamycin signaling promote platelet hyperreactivity and thrombosis." Journal of Thrombosis and Haemostasis 22.9 (2024): 2576-2588.
Babur, Ozgun, Andrew Emili, and Joseph E. Aslan. "Platelet proteomics emerges from the womb: mass spectrometry insights into neonatal platelet biology." Journal of thrombosis and haemostasis: JTH 22.5 (2024): 1313.
Yashar, William M., et al. "Predicting transcription factor activity using prior biological information." IScience 27.3 (2024).
Onken, Michael D., et al. "Protein kinase signaling networks driven by oncogenic Gq/11 in uveal melanoma identified by phosphoproteomic and bioinformatic analyses." Molecular & Cellular Proteomics 22.11 (2023): 100649.
Somers, Julia, et al. "A framework for considering prior information in network‐based approaches to omics data analysis." Proteomics 23.21-22 (2023): 2200402.
Geffen, Yifat, et al. "Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation." Cell 186.18 (2023): 3945-3967.
Saha, Pritam, et al. "Exploring causal relationships in proteomic profiles in Cytoscape using the CausalPath App." F1000Research 11 (2022): 458.
Yan, Gonghong, et al. "BET inhibition induces vulnerability to MCL1 targeting through upregulation of fatty acid synthesis pathway in breast cancer." Cell reports 40.11 (2022).
Khadka, Prasidda, et al. "PPM1D mutations are oncogenic drivers of de novo diffuse midline glioma formation." Nature communications 13.1 (2022): 604.
Luna, Augustin, et al. "Analyzing causal relationships in proteomic profiles using CausalPath." STAR protocols 2.4 (2021): 100955.
Wong, Jeffrey V., et al. "Science Forum: Author-sourced capture of pathway knowledge in computable form using Biofactoid." Elife 10 (2021): e68292.
Keshishian, Hasmik, et al. "A highly multiplexed quantitative phosphosite assay for biology and preclinical studies." Molecular Systems Biology 17.9 (2021): e10156.
Satpathy, Shankha, et al. "A proteogenomic portrait of lung squamous cell carcinoma." Cell 184.16 (2021): 4348-4371.
Joshi, Sunil K., et al. "The AML microenvironment catalyzes a stepwise evolution to gilteritinib resistance." Cancer cell 39.7 (2021): 999-1014.
Babur, Özgün, et al. "Causal interactions from proteomic profiles: Molecular data meet pathway knowledge." Patterns 2.6 (2021).
Balci, Hasan, et al. "Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps." Bioinformatics 37.10 (2021): 1475-1477.
Babur Ö, Melrose A, Cunliffe J, Klimek J, Pang J, Sepp AL, Zilberman-Rudenko J, Tassi Yunga S, Zheng T, Parra-Izquierdo I, Minnier J. Phosphoproteomic quantitation and causal analysis reveal pathways in GPVI/ITAM-mediated platelet activation programs. Blood. 2020 Jul 8.
Rodchenkov I, Babur O, Luna A, Aksoy BA, Wong JV, Fong D, Franz M, Siper MC, Cheung M, Wrana M, Mistry H. Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. Nucleic acids research. 2020 Jan 8;48(D1):D489-97.
Donehower LA, Soussi T, Korkut A, Liu Y, Schultz A, Cardenas M, Li X, Babur O, Hsu TK, Lichtarge O, Weinstein JN. Integrated analysis of TP53 gene and pathway alterations in the cancer genome atlas. Cell reports. 2019 Jul 30;28(5):1370-84.
Rocheleau AD, Melrose AR, Cunliffe JM, Klimek J, Babur Ö, Tassi Yunga S, Ngo AT, Pang J, David LL, McCarty OJ, Aslan JE. Identification, Quantification, and System Analysis of Protein N‐ε Lysine Methylation in Anucleate Blood Platelets. Proteomics. 2019 Jun;19(11):1900001.
Babur Ö, Ngo AT, Rigg RA, Pang J, Rub ZT, Buchanan AE, Mitrugno A, David LL, McCarty OJ, Demir E, Aslan JE. Platelet procoagulant phenotype is modulated by a p38-MK2 axis that regulates RTN4/Nogo proximal to the endoplasmic reticulum: utility of pathway analysis. American Journal of Physiology-Cell Physiology. 2018 May 1;314(5):C603-15.
Valenzuela-Escárcega MA, Babur Ö, Hahn-Powell G, Bell D, Hicks T, Noriega-Atala E, Wang X, Surdeanu M, Demir E, Morrison CT. Large-scale automated machine reading discovers new cancer-driving mechanisms. Database. 2018 Jan 1;2018.
Robertson AG, Shih J, Yau C, Gibb EA, Oba J, Mungall KL, Hess JM, Uzunangelov V, Walter V, Danilova L, Lichtenberg TM. Integrative analysis identifies four molecular and clinical subsets in uveal melanoma. Cancer cell. 2017 Aug 14;32(2):204-20.
Bahceci I, Dogrusoz U, La KC, Babur Ö, Gao J, Schultz N. PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data. Bioinformatics. 2017 Jul 15;33(14):2238-40.
Ngo AT, Thierheimer ML, Babur Ö, Rocheleau AD, Huang T, Pang J, Rigg RA, Mitrugno A, Theodorescu D, Burchard J, Nan X. Assessment of roles for the Rho-specific guanine nucleotide dissociation inhibitor Ly-GDI in platelet function: a spatial systems approach. American Journal of Physiology-Cell Physiology. 2017 Apr 1;312(4):C527-36.
Luna A, Babur Ö, Aksoy BA, Demir E, Sander C. PaxtoolsR: pathway analysis in R using Pathway Commons. Bioinformatics. 2016 Apr 15;32(8):1262-4.
Babur Ö, Gönen M, Aksoy BA, Schultz N, Ciriello G, Sander C, Demir E. Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations. Genome biology. 2015 Dec 1;16(1):45.
Korkut A, Wang W, Demir E, Aksoy BA, Jing X, Molinelli EJ, Babur Ö, Bemis DL, Sumer SO, Solit DB, Pratilas CA. Perturbation biology nominates upstream–downstream drug combinations in RAF inhibitor resistant melanoma cells. Elife. 2015 Aug 18;4:e04640.
Sari M, Bahceci I, Dogrusoz U, Sumer SO, Aksoy BA, Babur Ö, Demir E. SBGNViz: a tool for visualization and complexity management of SBGN process description maps. PloS one. 2015 Jun 1;10(6):e0128985.
Babur Ö, Dogrusoz U, Çakır M, Aksoy BA, Schultz N, Sander C, Demir E. Integrating biological pathways and genomic profiles with ChiBE 2. BMC genomics. 2014 Dec 1;15(1):642.
Aksoy BA, Demir E, Babur Ö, Wang W, Jing X, Schultz N, Sander C. Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles. Bioinformatics. 2014 Jul 15;30(14):2051-9.
Babur Ö, Aksoy BA, Rodchenkov I, Sümer SO, Sander C, Demir E. Pattern search in BioPAX models. Bioinformatics. 2014 Jan 1;30(1):139-40.
Demir E, Babur Ö, Rodchenkov I, Aksoy BA, Fukuda KI, Gross B, Sümer OS, Bader GD, Sander C. Using biological pathway data with paxtools. PLoS Comput Biol. 2013 Sep 19;9(9):e1003194.
Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur Ö, Anwar N, Schultz N, Bader GD, Sander C. Pathway Commons, a web resource for biological pathway data. Nucleic acids research. 2010 Nov 10;39(suppl_1):D685-90.
Babur Ö, Demir E, Gönen M, Sander C, Dogrusoz U. Discovering modulators of gene expression. Nucleic acids research. 2010 Sep 1;38(17):5648-56.
Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'eustachio P, Schaefer C, Luciano J, Schacherer F. The BioPAX community standard for pathway data sharing. Nature biotechnology. 2010 Sep;28(9):935-42.
Babur O, Dogrusoz U, Demir E, Sander C. ChiBE: interactive visualization and manipulation of BioPAX pathway models. Bioinformatics. 2010 Feb 1;26(3):429-31.
Dogrusoz U, Cetintas A, Demir E, Babur O. Algorithms for effective querying of compound graph-based pathway databases. BMC bioinformatics. 2009 Dec 1;10(1):376.