Panayiotis V. Benos

45 papers A* 2C 1Misc 4Journal 32Unranked 5

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Addressing Intersectionality, Explainability, and Ethics in AI-Driven Diagnostics: A Rebuttal and Call for Transdiciplinary Action. CoRR Myles Joshua Toledo Tan, Panayiotis V. Benos
2025	J	`jnl`	Engineering Spatial and Molecular Features from Cellular Niches to Inform Predictions of Inflammatory Bowel Disease. CoRR Myles Joshua Toledo Tan, Maria Kapetanaki, Panayiotis V. Benos
2025	—	`conf`	Predicting Pneumococcal Meningitis from Demographics and Early AMR Signals. BCB Michael Aaron G. Sy, Garrett Ellward, Daniel M. Czyz, Vidhu Kariyawasam, Panayiotis V. Benos, Simone Marini
2024	J	`jnl`	A hybrid constrained continuous optimization approach for optimal causal discovery from biological data. Bioinform. Yuehua Zhu, Panayiotis V. Benos, Maria Chikina
2024	J	`jnl`	CellularPotts.jl: simulating multiscale cellular models in Julia. Bioinform. Robert W. Gregg, Panayiotis V. Benos
2024	J	`jnl`	Enabling the clinical application of artificial intelligence in genomics: a perspective of the AMIA Genomics and Translational Bioinformatics Workgroup. J. Am. Medical Informatics Assoc. Nephi A. Walton, Radhakrishnan Nagarajan, Chen Wang, Murat Sincan, Robert R. Freimuth, David B. Everman, Derek C. Walton, Scott P. McGrath, Dominick J. Lemas, Panayiotis V. Benos, Alexander V. Alekseyenko, Qianqian Song, Ece D. Gamsiz Uzun, Casey Overby Taylor, Alper Uzun, Thomas N. Person, Nadav Rappoport, Zhongming Zhao, Marc S. Williams
2024	A*	`conf`	Learning Identifiable Factorized Causal Representations of Cellular Responses. NeurIPS Haiyi Mao, Romain Lopez, Kai Liu, Jan-Christian Huetter, David Richmond, Panayiotis V. Benos, Lin Qiu
2024	J	`jnl`	Learning Identifiable Factorized Causal Representations of Cellular Responses. CoRR Haiyi Mao, Romain Lopez, Kai Liu, Jan-Christian Hütter, David Richmond, Panayiotis V. Benos, Lin Qiu
2023	J	`jnl`	An intrinsically interpretable neural network architecture for sequence-to-function learning. Bioinform. Ali Tugrul Balci, Mark Maher Ebeid, Panayiotis V. Benos, Dennis Kostka, Maria Chikina
2022	J	`jnl`	COEM: Cross-Modal Embedding for MetaCell Identification. CoRR Haiyi Mao, Minxue Jia, Jason Xiaotian Dou, Haotian Zhang, Panayiotis V. Benos
2022	J	`jnl`	Essential Regression: A generalizable framework for inferring causal latent factors from multi-omic datasets. Patterns Xin Bing, Tyler Lovelace, Florentina Bunea, Marten H. Wegkamp, Sudhir Pai Kasturi, Harinder Singh, Panayiotis V. Benos, Jishnu Das
2022	—	`conf`	Towards Cross-Modal Causal Structure and Representation Learning. ML4H@NeurIPS Haiyi Mao, Hongfu Liu, Jason Xiaotian Dou, Panayiotis V. Benos
2021	J	`jnl`	A Pipeline for Integrated Theory and Data-Driven Modeling of Biomedical Data. IEEE ACM Trans. Comput. Biol. Bioinform. Vineet K. Raghu, Xiaoyu Ge, Arun Balajiee, Daniel J. Shirer, Isha Das, Panayiotis V. Benos, Panos K. Chrysanthis
2020	J	`jnl`	A Pipeline for Integrated Theory and Data-Driven Modeling of Genomic and Clinical Data. CoRR Vineet K. Raghu, Xiaoyu Ge, Arun Balajee, Daniel J. Shirer, Isha Das, Panayiotis V. Benos, Panos K. Chrysanthis
2020	J	`jnl`	An improvement of ComiR algorithm for microRNA target prediction by exploiting coding region sequences of mRNAs. BMC Bioinform. Giorgio Bertolazzi, Panayiotis V. Benos, Michele Tumminello, Claudia Coronnello
2020	J	`jnl`	Causal network perturbations for instance-specific analysis of single cell and disease samples. Bioinform. Kristina Buschur, Maria Chikina, Panayiotis V. Benos
2020	J	`jnl`	CausalMGM: an interactive web-based causal discovery tool. Nucleic Acids Res. Xiaoyu Ge, Vineet K. Raghu, Panos K. Chrysanthis, Panayiotis V. Benos
2020	C	`conf`	Interpretable Factors in scRNA-seq Data with Disentangled Generative Models. BIBE Haiyi Mao, Matthew J. Broerman, Panayiotis V. Benos
2019	J	`jnl`	Mixed graphical models for integrative causal analysis with application to chronic lung disease diagnosis and prognosis. Bioinform. Andrew J. Sedgewick, Kristina Buschur, Ivy Shi, Joseph D. Ramsey, Vineet K. Raghu, Dimitris V. Manatakis, Yingze Zhang, Jessica Bon, Divay Chandra, Chad Karoleski, Frank C. Sciurba, Peter Spirtes, Clark Glymour, Panayiotis V. Benos
2018	J	`jnl`	Comparison of strategies for scalable causal discovery of latent variable models from mixed data. Int. J. Data Sci. Anal. Vineet K. Raghu, Joseph D. Ramsey, Alison Morris, Dimitrios V. Manatakis, Peter Spirtes, Panos K. Chrysanthis, Clark Glymour, Panayiotis V. Benos
2018	J	`jnl`	ECCB 2018: The 17th European Conference on Computational Biology. Bioinform. Artemis G. Hatzigeorgiou, Pantelis G. Bagos, Panayiotis V. Benos, Christoforos Nikolaou, Yves Moreau, Ioannis Kavakiotis
2018	—	`conf`	Evaluation of Causal Structure Learning Methods on Mixed Data Types. CD@KDD Vineet K. Raghu, Allen Poon, Panayiotis V. Benos
2018	J	`jnl`	piMGM: incorporating multi-source priors in mixed graphical models for learning disease networks. Bioinform. Dimitris V. Manatakis, Vineet K. Raghu, Panayiotis V. Benos
2017	A*	`conf`	Integrated Theory-and Data-Driven Feature Selection in Gene Expression Data Analysis. ICDE Vineet K. Raghu, Xiaoyu Ge, Panos K. Chrysanthis, Panayiotis V. Benos
2017	J	`jnl`	Mixed Graphical Models for Causal Analysis of Multi-modal Variables. CoRR Andrew J. Sedgewick, Joseph D. Ramsey, Peter Spirtes, Clark Glymour, Panayiotis V. Benos
2016	J	`jnl`	Learning mixed graphical models with separate sparsity parameters and stability-based model selection. BMC Bioinform. Andrew J. Sedgewick, Ivy Shi, Rory M. Donovan, Panayiotis V. Benos
2015	Misc	`conf`	T-ReCS: Stable Selection of Dynamically Formed Groups of Features with Application to Prediction of Clinical Outcomes. Pacific Symposium on Biocomputing Grace T. Huang, Ioannis Tsamardinos, Vineet K. Raghu, Naftali Kaminski, Panayiotis V. Benos
2015	J	`jnl`	The center for causal discovery of biomedical knowledge from big data. J. Am. Medical Informatics Assoc. Gregory F. Cooper, Ivet Bahar, Michael J. Becich, Panayiotis V. Benos, Jeremy M. Berg, Jeremy U. Espino, Clark Glymour, Rebecca Crowley Jacobson, Michelle Kienholz, Adrian V. Lee, Xinghua Lu, Richard Scheines
2013	J	`jnl`	ComiR: combinatorial microRNA target prediction tool. Nucleic Acids Res. Claudia Coronnello, Panayiotis V. Benos
2013	Misc	`conf`	Spectral Clustering Strategies for Heterogeneous Disease Data. Pacific Symposium on Biocomputing Grace T. Huang, Kathryn I. Cunningham, Panayiotis V. Benos, Chakra S. Chennubhotla
2012	J	`jnl`	Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density. PLoS Comput. Biol. Claudia Coronnello, Ryan J. Hartmaier, Arshi Arora, Luai Huleihel, Kusum V. Pandit, Abha S. Bais, Michael Butterworth, Naftali Kaminski, Gary D. Stormo, Steffi Oesterreich, Panayiotis V. Benos
2011	—	`ch.`	Biclustering of DNA Microarray Data: Theory, Evaluation, and Applications. Handbook of Research on Computational and Systems Biology Alain B. Tchagang, Youlian Pan, Fazel Famili, Ahmed H. Tewfik, Panayiotis V. Benos
2011	J	`jnl`	mirConnX: condition-specific mRNA-microRNA network integrator. Nucleic Acids Res. Grace T. Huang, Charalambos Athanassiou, Panayiotis V. Benos
2009	J	`jnl`	Extracting biologically significant patterns from short time series gene expression data. BMC Bioinform. Alain B. Tchagang, Kevin V. Bui, Thomas McGinnis, Panayiotis V. Benos
2009	J	`jnl`	HHMMiR: efficient BMC Bioinform. Sabah Kadri, Veronica F. Hinman, Panayiotis V. Benos
2008	Misc	`conf`	Biological evaluation of biclustering algorithms using Gene Ontology and chIP-chip data. ICASSP Alain B. Tchagang, Ahmed H. Tewfik, Panayiotis V. Benos
2007	J	`jnl`	DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies. PLoS Comput. Biol. Shaun Mahony, Philip E. Auron, Panayiotis V. Benos
2007	—	`conf`	Inferring protein-DNA dependencies using motif alignments and mutual information. ISMB/ECCB (Supplement of Bioinformatics) Shaun Mahony, Philip E. Auron, Panayiotis V. Benos
2007	J	`jnl`	STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res. Shaun Mahony, Panayiotis V. Benos
2006	J	`jnl`	Self-organizing neural networks to support the discovery of DNA-binding motifs. Neural Networks Shaun Mahony, Panayiotis V. Benos, Terry J. Smith, Aaron Golden
2005	J	`jnl`	FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting. Nucleic Acids Res. David L. Corcoran, Eleanor Feingold, Panayiotis V. Benos
2005	—	`conf`	Improved detection of DNA motifs using a self-organized clustering of familial binding profiles. ISMB (Supplement of Bioinformatics) Shaun Mahony, Aaron Golden, Terry J. Smith, Panayiotis V. Benos
2005	J	`jnl`	SOP Nucleic Acids Res. Steven Ringquist, Christopher Pecoraro, Crystal M. S. Gilchrist, Alexis Styche, William A. Rudert, Panayiotis V. Benos, Massimo Trucco
2005	J	`jnl`	enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res. Christopher T. Workman, Yutong Yin, David L. Corcoran, Trey Ideker, Gary D. Stormo, Panayiotis V. Benos
2001	Misc	`conf`	SAMIE: Statistical Algorithm for Modeling Interaction Energies. Pacific Symposium on Biocomputing Panayiotis V. Benos, Alan S. Lapedes, D. S. Fields, Gary D. Stormo