Panayiotis V. Benos

Publication Activity (10 Years)

Years Active: 2001-2024
Publications (10 Years): 21

Top Topics

Biomedical Data

Causal Discovery

Conditional Independence

Top Venues

J. Am. Medical Informatics Assoc.

Publications

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 Gamsiz Uzun, Casey Overby Taylor, Alper Uzun, Thomas N. Person, Nadav Rappoport, Zhongming Zhao, Marc S. Williams
Enabling the clinical application of artificial intelligence in genomics: a perspective of the AMIA Genomics and Translational Bioinformatics Workgroup. J. Am. Medical Informatics Assoc. 31 (2) (2024)
Ali Tugrul Balci1, Mark Maher Ebeid, Panayiotis V. Benos, Dennis Kostka, Maria Chikina
An intrinsically interpretable neural network architecture for sequence-to-function learning. Bioinform. 39 (Supplement-1) (2023)
Xin Bing, Tyler Lovelace, Florentina Bunea, Marten H. Wegkamp, Sudhir Pai Kasturi, Harinder Singh, Panayiotis V. Benos, Jishnu Das
Essential Regression: A generalizable framework for inferring causal latent factors from multi-omic datasets. Patterns 3 (5) (2022)
Haiyi Mao, Hongfu Liu, Jason Xiaotian Dou, Panayiotis V. Benos
Towards Cross-Modal Causal Structure and Representation Learning. ML4H@NeurIPS (2022)
Haiyi Mao, Minxue Jia, Jason Xiaotian Dou, Haotian Zhang, Panayiotis V. Benos
COEM: Cross-Modal Embedding for MetaCell Identification. CoRR (2022)
Vineet K. Raghu, Xiaoyu Ge, Arun Balajiee, Daniel J. Shirer, Isha Das, Panayiotis V. Benos, Panos K. Chrysanthis
A Pipeline for Integrated Theory and Data-Driven Modeling of Biomedical Data. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (3) (2021)
Haiyi Mao, Matthew J. Broerman, Panayiotis V. Benos
Interpretable Factors in scRNA-seq Data with Disentangled Generative Models. BIBE (2020)
Kristina Buschur, Maria Chikina, Panayiotis V. Benos
Causal network perturbations for instance-specific analysis of single cell and disease samples. Bioinform. 36 (8) (2020)
Vineet K. Raghu, Xiaoyu Ge, Arun Balajee, Daniel J. Shirer, Isha Das, Panayiotis V. Benos, Panos K. Chrysanthis
A Pipeline for Integrated Theory and Data-Driven Modeling of Genomic and Clinical Data. CoRR (2020)
Giorgio Bertolazzi, Panayiotis V. Benos, Michele Tumminello, Claudia Coronnello
An improvement of ComiR algorithm for microRNA target prediction by exploiting coding region sequences of mRNAs. BMC Bioinform. (8) (2020)
Xiaoyu Ge, Vineet K. Raghu, Panos K. Chrysanthis, Panayiotis V. Benos
CausalMGM: an interactive web-based causal discovery tool. Nucleic Acids Res. 48 (Webserver-Issue) (2020)
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
Mixed graphical models for integrative causal analysis with application to chronic lung disease diagnosis and prognosis. Bioinform. 35 (7) (2019)
Vineet K. Raghu, Allen Poon, Panayiotis V. Benos
Evaluation of Causal Structure Learning Methods on Mixed Data Types. CD@KDD (2018)
Dimitris V. Manatakis, Vineet K. Raghu, Panayiotis V. Benos
piMGM: incorporating multi-source priors in mixed graphical models for learning disease networks. Bioinform. 34 (17) (2018)
Artemis G. Hatzigeorgiou, Pantelis G. Bagos, Panayiotis V. Benos, Christoforos Nikolaou, Yves Moreau, Ioannis Kavakiotis
ECCB 2018: The 17th European Conference on Computational Biology. Bioinform. 34 (17) (2018)
Vineet K. Raghu, Joseph D. Ramsey, Alison Morris, Dimitrios V. Manatakis, Peter Spirtes, Panos K. Chrysanthis, Clark Glymour, Panayiotis V. Benos
Comparison of strategies for scalable causal discovery of latent variable models from mixed data. Int. J. Data Sci. Anal. 6 (1) (2018)
Andrew J. Sedgewick, Joseph D. Ramsey, Peter Spirtes, Clark Glymour, Panayiotis V. Benos
Mixed Graphical Models for Causal Analysis of Multi-modal Variables. CoRR (2017)
Vineet K. Raghu, Xiaoyu Ge, Panos K. Chrysanthis, Panayiotis V. Benos
Integrated Theory-and Data-Driven Feature Selection in Gene Expression Data Analysis. ICDE (2017)
Andrew J. Sedgewick, Ivy Shi, Rory M. Donovan, Panayiotis V. Benos
Learning mixed graphical models with separate sparsity parameters and stability-based model selection. BMC Bioinform. 17 (S-5) (2016)
Grace T. Huang, Ioannis Tsamardinos, Vineet K. Raghu, Naftali Kaminski, Panayiotis V. Benos
T-ReCS: Stable Selection of Dynamically Formed Groups of Features with Application to Prediction of Clinical Outcomes. Pacific Symposium on Biocomputing (2015)
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
The center for causal discovery of biomedical knowledge from big data. J. Am. Medical Informatics Assoc. 22 (6) (2015)
Grace T. Huang, Kathryn I. Cunningham, Panayiotis V. Benos, Chakra Chennubhotla
Spectral Clustering Strategies for Heterogeneous Disease Data. Pacific Symposium on Biocomputing (2013)
Claudia Coronnello, Panayiotis V. Benos
ComiR: combinatorial microRNA target prediction tool. Nucleic Acids Res. 41 (Webserver-Issue) (2013)
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
Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density. PLoS Comput. Biol. 8 (12) (2012)
Grace T. Huang, Charalambos Athanassiou, Panayiotis V. Benos
mirConnX: condition-specific mRNA-microRNA network integrator. Nucleic Acids Res. 39 (Web-Server-Issue) (2011)
Sabah Kadri, Veronica F. Hinman, Panayiotis V. Benos
prediction of microRNAs using hierarchical hidden Markov models. BMC Bioinform. 10 (S-1) (2009)
Alain B. Tchagang, Kevin V. Bui, Thomas McGinnis, Panayiotis V. Benos
Extracting biologically significant patterns from short time series gene expression data. BMC Bioinform. 10 (2009)
Alain B. Tchagang, Ahmed H. Tewfik, Panayiotis V. Benos
Biological evaluation of biclustering algorithms using Gene Ontology and chIP-chip data. ICASSP (2008)
Shaun Mahony, Philip E. Auron, Panayiotis V. Benos
Inferring protein-DNA dependencies using motif alignments and mutual information. ISMB/ECCB (Supplement of Bioinformatics) (2007)
Shaun Mahony, Panayiotis V. Benos
STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res. 35 (Web-Server-Issue) (2007)
Shaun Mahony, Philip E. Auron, Panayiotis V. Benos
DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies. PLoS Comput. Biol. 3 (3) (2007)
Shaun Mahony, Panayiotis V. Benos, Terry J. Smith, Aaron Golden
Self-organizing neural networks to support the discovery of DNA-binding motifs. Neural Networks 19 (6-7) (2006)
Shaun Mahony, Aaron Golden, Terry J. Smith, Panayiotis V. Benos
Improved detection of DNA motifs using a self-organized clustering of familial binding profiles. ISMB (Supplement of Bioinformatics) (2005)
Steven Ringquist, Christopher Pecoraro, Crystal M. S. Gilchrist, Alexis Styche, William A. Rudert, Panayiotis V. Benos, Massimo Trucco
v2: web-based selection of oligonucleotide primer trios for genotyping of human and mouse polymorphisms. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)
Christopher T. Workman, Yutong Yin, David L. Corcoran, Trey Ideker, Gary D. Stormo, Panayiotis V. Benos
enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)
David L. Corcoran, Eleanor Feingold, Panayiotis V. Benos
FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)
Panayiotis V. Benos, Alan S. Lapedes, D. S. Fields, Gary D. Stormo
SAMIE: Statistical Algorithm for Modeling Interaction Energies. Pacific Symposium on Biocomputing (2001)