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Systems Biology
Phospho-proteomics, Cellular Signaling, Network Biology of Complex Diseases

Network Science
Graph Algorithms, Graph Machine Learning, Efficient Algorithms for Big Networks

Computational Genomics
Sequencing, Genome-Wide Association Studies, Epistasis, Metagenomics

Women's Health
Pre-term Birth, Intimate Partner Violence, Electronic Health Records, Social Networks

Clean Energy
Photovoltaic Systems, Forecasting, Degradation Science

High Performance Computing and Distributed Systems

Survey/Review/Opinion Papers

Systems Biology

• Prediction of kinase-substrate associations using the functional landscape of kinases and phosphorylation sites (with M. Ayati, S. Yılmaz, et al.), PSB, 2023. pdf | software
• Functional characterization of co-phosphorylation networks, (with M. Ayati, S. Yilmaz et al.), Bioinformatics, 2022. pdf
• Protein biomarkers in monocytes and CD4+ lymphocytes for predicting lithium treatment response of bipolar disorder: A feasibility study with tyramine-based signal-amplified flow cytometry (with K. Gao, D. Kaplan, et al.), Psychopharmacology Bulletin, 2022.
• Robust inference of kinase activity using functional networks (with S. Yılmaz, M. Ayati, et al.), Nature Communications, 2021. pdf | tool | code | website
  • Conference Version: RECOMB'2021 (Best Paper Award)
• Co-phosphorylation networks reveal subtype-specific signaling modules in breast cancer (with M. Ayati and M. R. Chance), Bioinformatics, 2020. pdf
• DeepKinZero: zero-shot learning for predicting kinase-phosphosite associations involving under-studied kinases (with I. Deznabi, Ö. Taştan et al.), Bioinformatics, 2020. pdf | code
• CoPhosK: A Method for comprehensive kinase-substrate annotation using co-phosphorylation analysis (with M. Ayati, M. R. Chance et al.), PLoS Computational Biology, 2019. pdf | tool
  • Presented at the Highlights Track of ACM-BCB'2019
• Interplay of transcriptional signaling by progesterone, cyclic AMP, and inflammation in myometrial cells: implications for the control of human parturition (with Z. Stanfield, S. Mesiano et al.), Molecular Human Reproduction, 2019. pdf
  
• Myometrial transcriptional signatures of human parturition (with Z. Stanfield, S. Mesiano et al.), Frontiers in Genetics - Systems Biology, 2019. pdf
  
• ELF3 is an antagonist of oncogenic-signalling-induced expression of EMT-TF ZEB1 (with D. Liu, R. M. Ewing et al.), Cancer Biology and Therapy, 2018. pdf
• Phospho-proteomics profiling of non-small cell lung cancer cells treated with a novel phosphatase activator (with D. D. Wiredja, M. R. Chance, et al.), Proteomics, 2017. pdf
• Drug response prediction as a link prediction problem (with Z. Stanfield and M. Coşkun), Scientific Reports, 2017. pdf
  • Presented at the Highlights Track of ACM-BCB'2017 and the Networks Track of ISMB'2017
• The KSEA-App: A tool for kinase activity inference from quantitative phospho-proteomics (with D. D. Wiredja and M. R. Chance), Bioinformatics, 2017. pdf
• Visually meaningful histopathological features for automatic grading of prostate cancer (with M. K. Niazi, M. N Gurcan et al.), IEEE JBHI, 2017. pdf
• PoCos: Population covering locus sets for risk assessment in complex diseases (with M. Ayati), PLoS Computational Biology, 2016. pdf
  •Conference version: ACM-BCB'2015
• MOBAS: Identification of disease-associated protein subnetworks using modularity-based scoring (with M. Ayati, S. Erten, and M. R. Chance). EURASIP J. Bioinformatics and Systems Biology, 2015. pdf
  •Conference version: EvoBio'2014
• Network-based integration of disparate omics data to identify “silent players” in cancer (with M. Ruffalo and R. Sharan), PLoS Computational Biology, 2015. pdf
• Whole-exome sequencing enhances prognostic classification of myeloid malignancies (with M. Ruffalo, T. LaFramboise et al.), Journal of Biomedical Informatics, 2015. pdf
• Comprehensive evaluation of the performance of composite gene features in predicting cancer outcome (with D. Hou), Cancer Informatics, 2015. pdf
• Network signatures of survival in glioblastoma multiforme (with V. Patel, M. R. Chance et al.) PLoS Computational Biology, 2013. pdf
• Gene interaction enrichment and network analysis to identify dysregulated pathways in cancer, (with Y. Liu, J. Barnholtz-Sloan, andM. R. Chance), BMC Systems Biology, 2012. pdf
• Identifying stage-specific protein subnetworks for colorectal cancer (with S. Erten, S. A. Chowdhury et al.), BMC Proceedings, 2012. pdf
  • Special Issue of GLBIO'2012
• Network-based approaches for extending the Wnt signaling pathway and identifying context-specific subnetworks (with S. Saha, R. Ewing et al.), Int'l J. Computational Biology and Drug Design, 2012. pdf
• Gene, pathway and network frameworks to identify epistatic interactions of single nucleotide polymorphisms derived from GWAS data (with Y. Liu, M. R. Chance et al.), BMC Systems Biology, 2012. pdf
• VAVIEN: An algorithm for prioritizing candidate disease genes based on topological similarity in protein interaction networks (with S. Erten and G. Bebek), Journal of Computational Biology, 2011. pdf
  • Conference version: RECOMB'2011
• DADA: Degree-aware algorithms for network-based disease gene prioritization (with S. Erten, G. Bebek, and R. Ewing), BMC BioData Mining, 2011. Software   pdf
  • Conference version: EvoBio'2010 ( Best Paper Award)
• Systems biology analysis of gene expression and genome-wide association study data in obstructive sleep apnea (with Y. Liu, M. R. Chance et al.), PSB, 2011. pdf
• Subnetwork state functions define dysregulated subnetworks in cancer (with S. A. Chowdhury, R. K. Nibbe, and M. R. Chance), Journal of Computational Biology, 2011. pdf
  • Conference version: RECOMB'2010
• An integrative -omics approach to identify functional subnetworks in human colorectal cancer (with R. K. Nibbe and M. R. Chance), PLoS Computational Biology, 2010. pdf
• Identification of coordinately dysregulated subnetworks in complex phenotypes (with S. A. Chowdhury), PSB, 2010. pdf
• Functional characterization and topological modularity of molecular interaction networks (with J. Pandey and A. Grama), BMC Bioinformatics, 2010. pdf
  • Special Issue of APBC'2010
• Phylogenetic analysis of modularity in protein interaction networks (with S. Erten, X. Li, et al.), BMC Bioinformatics, 2009. pdf
  • Conference version: OCCBIO'2009
• Functional coherence in domain interaction networks (with J. Pandey, A. Grama, et al.), Bioinformatics, 2008. pdf
  • Special Issue of ECCB'2008
• Annotating pathways in interaction networks (with J. Pandey, W. Szpankowski, and A. Grama), PSB, 2008. pdf
• Assessing significance of connectivity and conservation in protein interaction networks (with W. Szpankowski and A. Grama), Journal of Computational Biology, 2007. pdf
  • Conference version: RECOMB'2006
• Functional annotation of regulatory pathways (with J. Pandey, A. Grama, et al.), Bioinformatics, 2007. pdf
  • Special Issue of ISMB/ECCB'2007
  
• Detecting conserved interaction patterns in biological networks (with Y. Kim, A. Grama, et al.), Journal of Computational Biology, 2006. pdf
• Pairwise alignment of protein interaction networks (with Y. Kim, A. Grama, et al.), Journal of Computational Biology, 2006. pdf
  • Conference version: RECOMB'2005
• Inferring functional information from domain co-evolution (with Y. Kim, S. Subramaniam, et al.), Bioinformatics, 2006. pdf
• An efficient algorithm for detecting frequent subgraphs in biological networks (with A. Grama and W. Szpankowski), BioInformatics, 2004. pdf
  • Special Issue of ISMB/ECCB'2004

Network Science

• Canonical representation of biological networks using graph convolution (With M. Li and M. Coşkun), ACM-BCB, 2023. pdf
• Generalized Gromov Wasserstein distance for seed-informed network alignment (with M.Li), Complex Networks, 2023. pdf
• Consensus embedding for multiple networks: Computation and applications (with M. Li and M. Coşkun), Network Science, 2022. pdf
  • Conference version: Complex Networks, 2020. pdf
• Random walks with variable restarts for negative-example-informed label propagation" (with S. Maxwell), preprint, 2021. pdf
• Node similarity based graph convolution for link prediction in biological networks (with M.Coşkun), Bioinformatics, 2021. pdf | code
• Fast computation of Katz index for efficient processing of link prediction queries (with M. Coşkun and A. Baggag), Data Mining and Knowledge Discovery, 2021. pdf
• Integrated querying and version control of context-specific biological networks (with T. Cowman, M. Coşkun, et al.), Database, 2020. pdf | code
• Indexed fast network proximity querying (with M. Coşkun and A. Grama), PVLDB, 2018. pdf
• Querying of disparate association and interaction data in biomedical applications (with S. Qiao and M. Özsoyoğlu), IEEE/ACM TCBB, 2018. pdf
  • Conference version: ACM-BCB'2015 (Best Student Paper Award)
• Drug response prediction as a link prediction problem (with Z. Stanfield and M. Coşkun), Scientific Reports, 2017. pdf
  • Presented at the Highlights Track of ACM-BCB'2017 and the Networks Track of ISMB'2017
• Linearity of network proximity measures: implications for set-based queries and significance testing (with S. Maxwell and M. R. Chance), Bioinformatics, 2017. pdf
• Effects of emotion and topic area on topic shifts in social media discussions (with K. Topal and T. Özsoyoğlu), Social Network Analysis and Mining, 2017. pdf
  • Conference version: ASONAM'2016
• Efficient processing of network proximity queries via Chebyshev acceleration (with M. Coşkun and A. Grama), ACM-KDD, 2016. pdf
• Link prediction in large networks by comparing the global view of nodes in the network (with M. Coşkun), ICDM Workshop on Data Mining in Networks, 2015. pdf
• Efficiently enumerating all connected induced subgraphs of a large molecular network (with S. Maxwell and M. R. Chance), AlCoB, 2014. pdf
• VAVIEN: An algorithm for prioritizing candidate disease genes based on topological similarity in protein interaction networks (with S. Erten and G. Bebek), Journal of Computational Biology, 2011. pdf
  • Conference version: RECOMB'2011

Women's Health

• Comprehensive analysis of electronic health records to characterize the association between intimate partner violence and mental health (with G. Karakurt, S. Yilmaz, et al.), AMIA Informatics Summit, 2023. pdf | citation | bibtex
• Characterizing disparities in the treatment of intimate partner violence (with C. Oguztuzun and G. Karakurt), AMIA Informatics Summit, 2023. pdf | citation | bibtex
• Identification of intimate partner violence from free text descriptions in social media (with P. T. Ha, G. Karakurt, et al.), Journal of Computational Social Science, 2022. pdf | tool
• Adverse health correlates of intimate partner violence against older women: Mining electronic health records (with S. Yılmaz, G. Karakurt, et al.), preprint, 2022. pdf
• Data-driven identification of subtypes of intimate partner violence (with A. Hacıaliefendioğlu, G. Karakurt et al.), Scientific Reports, 2021. pdf
• Co-occurrence patterns of intimate partner violence (with A. Hacıefendioğlu, G. Karakurt, et al.), Pacific Symposium on Biocomputing (PSB), 2021. pdf
• Identifying health correlates of intimate partner violence against pregnant women (with S. Yılmaz, G. Karakurt, et al.), Health Information Science and Systems, 2020. pdf
• Interplay between traumatic brain injury and intimate partner violence: data driven analysis utilizing electronic health records (with L. Liu, G. Karakurt et al.), BMC Women's Health, 2020. pdf
• Interplay of transcriptional signaling by progesterone, cyclic AMP, and inflammation in myometrial cells: implications for the control of human parturition (with Z. Stanfield, S. Mesiano et al.), Molecular Human Reproduction, 2019. pdf
  
• Myometrial transcriptional signatures of human parturition (with Z. Stanfield, S. Mesiano et al.), Frontiers in Genetics - Systems Biology, 2019. pdf
  
• Network map of adverse health effects among victims of intimate partner violence (with K. Whiting, L. Liu, and G. Karakurt), PSB, 2017. pdf
• Mining Electronic Health Records Data: Domestic Violence and Adverse Health Effects (with G. Karakurt, V. Patel, and K. Whiting), J. Family Violence, 2017. pdf

Genomics and Sequencing

• Uncovering complementary sets of variants for predicting quantitative phenotypes (with S. Yılmaz, Ö. Taştan et al.), Bioinformatics, 2022. pdf | code
• Circulating microbial content in myeloid malignancy patients is associated with disease subtypes and patient outcomes (with J. Woerner, T. LaFramboise, et al.), Nature Communications, 2022. pdf
• Characterizing human genomic co-evolution in locus-gene regulatory interactions (with D. Savel), BioData Mining, 2019. pdf
• Cross-population analysis for functional characterization of type II diabetes variants (with D. Elmansy), BMC Bioinformatics, 2019. pdf
  • Conference Version: CNB-MAC'2018
• Prioritizing tests of epistasis through hierarchical representation of genomic redundancies (with T. Cowman), Nucleic Acids Research, 2017. pdf
  • Presented at the Highlights Track of RECOMB'2018
• Pluribus - Exploring the limits of error correction using a suffix tree (with D. Savel, T. LaFramboise, and A. Grama), IEEE/ACM TCBB, 2017. pdf
  • Conference version: ACM-BCB'2013
• DB2: a probabilistic approach for accurate detection of tandem duplication breakpoints using paired-end reads (with G. Yavaş, T. LaFramboise et al.), BMC Genomics, 2014. pdf
• Discovery of common sequences absent in the human reference genome using pooled samples from next generation sequencing (with Y. Liu, M. R. Chance, et al.), BMC Genomics, 2014. pdf
• Accurate estimation of short read mapping quality for next generation genome sequencing (with M. Ruffalo, T. LaFramboise et al.), Bioinformatics, 2012. pdf
  • Special Issue of ECCB'2012
• Comparative analysis of algorithms for next generation sequencing read alignment (with M. Ruffalo and T. LaFramboise), Bioinformatics, 2011. pdf
• Optimization algorithms for identification and genotyping of copy number polymorphisms in human populations (with G. Yavaş and T. LaFramboise), PRIB, 2010. pdf
• An optimization framework for unsupervised identification of rare copy number variation from SNP array data (with G. Yavaş, T. LaFramboise, et al.), Genome Biology, 2009. pdf

Clean Energy

• Spatio-temporal graph neural network for performance prediction of photovoltaic power systems (with A. M. Karimi, R. H. French, et al.), IAAI, 2021. pdf
• Toward findable, accessible, interoperable and reusable (FAIR) photovoltaic system time series data" (with A. Nihar, R. French, et al.), IEEE PVSC, 2021. pdf
• Generalized and Mechanistic PV Module Performance Prediction from Computer Vision and Machine Learning on Electroluminescence Images (with A. M. Karimi, R.H. French et al.), IEEE Journal of Photovoltaics, 2020. pdf
  • Conference version: WCPEC'2018

High-Performance Computing and Distributed Systems

• Weighted matrix ordering and parallel banded preconditioners for iterative linear system solvers (with M. Manguoglu, A. Grama, and A. H. Sameh), SIAM Journal on Scientific Computing, 2010. pdf
• Efficient tag detection in RFID systems (with B. Carbunar, A. Grama, et al.), Journal of Parallel & Distributed Computing, 2009. pdf
  • Conference version: SECON'2005
• Semantic indexing in structured peer-to-peer networks (with R. A. Ferreira, S. Jagannathan, and A. Grama), Journal of Parallel and Distributed Computing, 2008. pdf
• PHALANX: A graph theoretic framework for test case prioritization (with M. K. Ramanathan, A. Grama, and S. Jagannathan), SAC, 2008. pdf
• Non-orthogonal decomposition of binary matrices for bounded-error data compression and analysis (with A. Grama and N. Ramakrishnan), ACM Trans. Mathematical Software, 32(1), 2006. pdf
  • Conference version: PKDD'2002
• Conquest: A coarse-grained algorithm for constructing summaries of distributed discrete datasets (with J. Chi and A. Grama), Algorithmica, 2006. pdf
  • Conference version: SIAM Data Mining'2004
• Compression, clustering and pattern discovery in very high dimensional discrete-attribute datasets (with A. Grama and N. Ramakrishnan), IEEE Trans. Knowledge and Data Engineering, 2005. pdf
  • Conference version: ACM-KDD'2003
• Iterative-improvement-based declustering heuristics for multi-disk databases (with C. Aykanat), Information Systems, 2005. pdf

Survey/Review/Opinion Papers

• Using protein interaction networks to understand complex diseases, IEEE Computer, 2012. pdf
• Network biology methods integrating biological data for translational science (with G. Bebek, N. D. Price, and M. R. Chance), Briefings in Bioinformatics, 2012. pdf
• Protein-protein interaction networks and subnetworks in the biology of disease (with R. K. Nibbe, M. R. Chance, et al.), WIREs Systems Biology and Medicine, 2011. pdf
• Algorithmic and analytical methods in network biology, WIREs Systems Biology & Medicine, 2010. pdf