Andrea Califano

55 papers A* 9A 2B 2Misc 2Journal 33Unranked 6
YearRankTypeTitle / Venue / Authors
2024 J jnl
How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities.
CoRR
Charlotte Bunne, Yusuf H. Roohani, Yanay Rosen, Ankit Gupta, Xikun Zhang, Marcel Roed, Theo Alexandrov, Mohammed AlQuraishi, Patricia Brennan, Daniel B. Burkhardt, Andrea Califano, Jonah Cool, Abby F. Dernburg, Kirsty Ewing, Emily B. Fox, Matthias Haury, Amy E. Herr, Eric Horvitz, Patrick D. Hsu, Viren Jain, Gregory R. Johnson, Thomas Kalil, David R. Kelley, Shana O. Kelley, Anna Kreshuk, Tim Mitchison, Stephani Otte, Jay Shendure, Nicolas J. Sofroniew, Fabian J. Theis, Christina V. Theodoris, Srigokul Upadhyayula, Marc Valer, Bo Wang, Eric Xing, Serena Yeung-Levy, Marinka Zitnik, Theofanis Karaletsos, Aviv Regev, Emma Lundberg, Jure Leskovec, Stephen R. Quake
2023 J jnl
NaRnEA: An Information Theoretic Framework for Gene Set Analysis.
Entropy
Aaron T. Griffin, Lukas J. Vlahos, Codruta Chiuzan, Andrea Califano
2019 J jnl
SJARACNe: a scalable software tool for gene network reverse engineering from big data.
Bioinform.
Alireza Khatamian, Evan O. Paull, Andrea Califano, Jiyang Yu
2018 J jnl
ZCCHC17 is a master regulator of synaptic gene expression in Alzheimer's disease.
Bioinform.
Zeljko Tomljanovic, Mitesh Patel, William Shin, Andrea Califano, Andrew F. Teich
2018 J jnl
iterClust: a statistical framework for iterative clustering analysis.
Bioinform.
Hongxu Ding, Wanxin Wang, Andrea Califano
2017 J jnl
Accelerated parallel algorithm for gene network reverse engineering.
BMC Syst. Biol.
Jing He, Zhou Zhou, Michael Reed, Andrea Califano
2017 J jnl
CTD2 Dashboard: a searchable web interface to connect validated results from the Cancer Target Discovery and Development Network.
Database J. Biol. Databases Curation
Bülent Arman Aksoy, Vlado Dancík, Kenneth Smith, Jessica N. Mazerik, Zhou Ji, Benjamin E. Gross, Olga Nikolova, Nadia Jaber, Andrea Califano, Stuart L. Schreiber, Daniela S. Gerhard, Leandro Hermida, Subhashini Jagu, Chris Sander, Aris Floratos, Paul A. Clemons
2017 J jnl
Systematic, network-based characterization of therapeutic target inhibitors.
PLoS Comput. Biol.
Yao Shen, Mariano J. Alvarez, Brygida C. Bisikirska, Alexander Lachmann, Ronald Realubit, Sergey Pampou, Jorida Coku, Charles Karan, Andrea Califano
2016 J jnl
ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information.
Bioinform.
Alexander Lachmann, Federico M. Giorgi, Gonzalo López, Andrea Califano
2016 J jnl
Detection and removal of spatial bias in multiwell assays.
Bioinform.
Alexander Lachmann, Federico M. Giorgi, Mariano J. Alvarez, Andrea Califano
2016 J jnl
ScreenBEAM: a novel meta-analysis algorithm for functional genomics screens via Bayesian hierarchical modeling.
Bioinform.
Jiyang Yu, José Silva, Andrea Califano
2015 J jnl
DIGGIT: a Bioconductor package to infer genetic variants driving cellular phenotypes.
Bioinform.
Mariano J. Alvarez, James C. Chen, Andrea Califano
2015 J jnl
Preface: RECOMB/ISCB Systems Biology, Regulatory Genomics, and DREAM 2014 Special Issue.
J. Comput. Biol.
Andrea Califano, Manolis Kellis, Gustavo Stolovitzky
2015 J jnl
The Cyni framework for network inference in Cytoscape.
Bioinform.
Oriol Guitart-Pla, Manjunath Kustagi, Frank Rügheimer, Andrea Califano, Benno Schwikowski
2014 J jnl
RECOMB/ISCB Systems Biology, Regulatory Genomics, and DREAM 2013 Special Issue.
J. Comput. Biol.
Andrea Califano, Manolis Kellis, Gustavo Stolovitzky
2013 J jnl
Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling.
PLoS Comput. Biol.
Erhan Bilal, Janusz Dutkowski, Justin Guinney, In Sock Jang, Benjamin A. Logsdon, Gaurav Pandey, Benjamin A. Sauerwine, Yishai Shimoni, Hans Kristian Moen Vollan, Brigham H. Mecham, Oscar M. Rueda, Jorg Tost, Christina Curtis, Mariano J. Alvarez, Vessela N. Kristensen, Samuel Aparicio, Anne-Lise Børresen-Dale, Carlos Caldas, Andrea Califano, Stephen H. Friend, Trey Ideker, Eric E. Schadt, Gustavo A. Stolovitzky, Adam A. Margolin
2013 J jnl
Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2012 Special Issue.
J. Comput. Biol.
Andrea Califano, Manolis Kellis, Gustavo Stolovitzky
2012 J jnl
Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2011 Special Issue.
J. Comput. Biol.
Andrea Califano, Manolis Kellis, Gustavo Stolovitzky
2012 J jnl
Using systems and structure biology tools to dissect cellular phenotypes.
J. Am. Medical Informatics Assoc.
Aris Floratos, Barry Honig, Dana Pe'er, Andrea Califano
2011 — conf
Keynote: A systems biology approach to integrative cancer genomics.
ICCABS
Andrea Califano
2011 J jnl
Preface.
J. Comput. Biol.
Manolis Kellis, Andrea Califano, Ziv Bar-Joseph
2010 J jnl
geWorkbench: an open source platform for integrative genomics.
Bioinform.
Aris Floratos, Kenneth Smith, Zhou Ji, John Watkinson, Andrea Califano
2009 Misc conf
Dissecting the Interface Between Signaling and Transcriptional Regulation in Human B Cells.
Pacific Symposium on Biocomputing
Kai Wang, Mariano J. Alvarez, Brygida C. Bisikirska, Rune Linding, Katia Basso, Riccardo Dalla Favera, Andrea Califano
2009 Misc conf
Master Regulators Used As Breast Cancer Metastasis Classifier.
Pacific Symposium on Biocomputing
Wei Keat Lim, Eugenia Lyashenko, Andrea Califano
2009 J jnl
New JBI emphasis on translational bioinformatics.
J. Biomed. Informatics
Edward H. Shortliffe, Andrea Califano, Lawrence Hunter
2007 J jnl
ChIP-on-chip significance analysis reveals ubiquitous transcription factor binding.
BMC Bioinform.
Adam A. Margolin, Teresa Palomero, Adolfo A. Ferrando, Andrea Califano, Gustavo Stolovitzky
2007 — conf
Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks.
ISMB/ECCB (Supplement of Bioinformatics)
Wei Keat Lim, Kai Wang, Céline Lefebvre, Andrea Califano
2007 J jnl
Hui-Huang Hsu, Advanced Data Mining Technologies in Bioinformatics, Editors: Idea Group Publishing, pp 239.
J. Biomed. Informatics
Andrea Califano
2006 — conf
A Context-Specific Network of Protein-DNA and Protein-Protein Interactions Reveals New Regulatory Motifs in Human B Cells.
Systems Biology and Computational Proteomics
Céline Lefebvre, Wei Keat Lim, Katia Basso, Riccardo Dalla Favera, Andrea Califano
2006 J jnl
ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context.
BMC Bioinform.
Adam A. Margolin, Ilya Nemenman, Katia Basso, Chris Wiggins, Gustavo Stolovitzky, Riccardo Dalla Favera, Andrea Califano
2006 B conf
Genome-Wide Discovery of Modulators of Transcriptional Interactions in Human B Lymphocytes.
RECOMB
Kai Wang, Ilya Nemenman, Nilanjana Banerjee, Adam A. Margolin, Andrea Califano
2006 — conf
Transcription Factor Centric Discovery of Regulatory Elements in Mammalian Genomes Using Alignment-Independent Conservation Maps.
Comparative Genomics
Nilanjana Banerjee, Andrea Califano
2003 J jnl
CASTOR: Clustering Algorithm for Sequence Taxonomical Organization and Relationships.
J. Comput. Biol.
Agatha H. Liu, Andrea Califano
2001 J jnl
Functional classification of proteins by pattern discovery and top-down clustering of primary sequences.
IBM Syst. J.
Agatha H. Liu, Andrea Califano
2000 A conf
Analysis of Gene Expression Microarrays for Phenotype Classification.
ISMB
Andrea Califano, Gustavo Stolovitzky, Yuhai Tu
2000 J jnl
SPLASH: structural pattern localization analysis by sequential histograms.
Bioinform.
Andrea Califano
2000 J jnl
Systematic and Fully Automated Identification of Protein Sequence Patterns.
J. Comput. Biol.
Reece Hart, Ajay K. Royyuru, Gustavo Stolovitzky, Andrea Califano
2000 B conf
Systematic and automated discovery of patterns in PROSITE families.
RECOMB
Reece Hart, Ajay K. Royyuru, Gustavo Stolovitzky, Andrea Califano
1999 — ch.
Representation and Matching of Small Flexible Molecules in Large Databases of 3D Molecular Information.
Pattern Discovery in Biomolecular Data
Isidore Rigoutsos, Daniel E. Platt, Andrea Califano, B. David Silverman
1998 — conf
A High-Dimensional Indexing Scheme for Scalable Fingerprint-Based Identification.
ACCV (1)
Andrea Califano, Bob Germain, Scott Colville
1996 J jnl
Data- and Model-Driven Multiresolution Processing.
Comput. Vis. Image Underst.
Andrea Califano, Rick Kjeldsen, Ruud M. Bolle
1994 J jnl
Multidimensional Indexing for Recognizing Visual Shapes.
IEEE Trans. Pattern Anal. Mach. Intell.
Andrea Califano, Rakesh Mohan
1993 A conf
FLASH: A Fast Look-Up Algorithm for String Homology.
ISMB
Andrea Califano, Isidore Rigoutsos
1993 A* conf
FLASH: a fast look-up algorithm for string homology.
CVPR
Andrea Califano, Isidore Rigoutsos
1993 A* conf
Systematic design of indexing strategies for object recognition.
CVPR
Andrea Califano, Rakesh Mohan
1992 J jnl
A Complete and Extendable Approach to Visual Recognition.
IEEE Trans. Pattern Anal. Mach. Intell.
Ruud M. Bolle, Andrea Califano, Rick Kjeldsen
1992 J jnl
The Multiple Window Parameter Transform.
IEEE Trans. Pattern Anal. Mach. Intell.
Andrea Califano, Ruud M. Bolle
1991 A* conf
Multidimensional indexing for recognizing visual shapes.
CVPR
Andrea Califano, Rakesh Mohan
1990 A* conf
Active 3D object models.
ICCV
Ruud M. Bolle, Andrea Califano, Rick Kjeldsen, Rakesh Mohan
1990 — conf
Data and model driven foveation.
ICPR (1)
Andrea Califano, Rick Kjeldsen, Ruud M. Bolle
1990 A* conf
Generalized Shape Autocorrelation.
AAAI
Andrea Califano, Rakesh Mohan
1989 A* conf
A Homogeneous Framework for Visual Recognition.
IJCAI
Rick Kjeldsen, Ruud M. Bolle, Andrea Califano, Russell W. Taylor
1989 A* conf
Generalized neighborhoods: a new approach to complex parameter feature extraction.
CVPR
Andrea Califano, Ruud M. Bolle, Russell W. Taylor
1989 A* conf
Visual recognition using concurrent and layered parameter networks.
CVPR
Ruud M. Bolle, Andrea Califano, Rick Kjeldsen, Russell W. Taylor
1988 A* conf
Feature Recognition Using Correlated Information Contained in Multiple Neighborboods.
AAAI
Andrea Califano