Andrea Califano

According to our database, Andrea Califano authored at least 54 papers between 1988 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities.

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

CoRR, 2024

2023

NaRnEA: An Information Theoretic Framework for Gene Set Analysis.

Aaron T. Griffin, Lukas J. Vlahos, Codruta Chiuzan, Andrea Califano

Entropy, March, 2023

2019

SJARACNe: a scalable software tool for gene network reverse engineering from big data.

Alireza Khatamian, Evan O. Paull, Andrea Califano, Jiyang Yu

Bioinform., 2019

2018

ZCCHC17 is a master regulator of synaptic gene expression in Alzheimer's disease.

Zeljko Tomljanovic, Mitesh Patel, William Shin, Andrea Califano, Andrew F. Teich

Bioinform., 2018

iterClust: a statistical framework for iterative clustering analysis.

Hongxu Ding, Wanxin Wang, Andrea Califano

Bioinform., 2018

2017

Systematic, network-based characterization of therapeutic target inhibitors.

Yao Shen, Mariano J. Alvarez, Brygida C. Bisikirska, Alexander Lachmann, Ronald Realubit, Sergey Pampou, Jorida Coku, Charles Karan, Andrea Califano

PLoS Comput. Biol., 2017

Accelerated parallel algorithm for gene network reverse engineering.

Jing He, Zhou Zhou, Michael Reed, Andrea Califano

BMC Syst. Biol., 2017

CTD2 Dashboard: a searchable web interface to connect validated results from the Cancer Target Discovery and Development Network.

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

Database J. Biol. Databases Curation, 2017

2016

ScreenBEAM: a novel meta-analysis algorithm for functional genomics screens via Bayesian hierarchical modeling.

Jiyang Yu, José Silva, Andrea Califano

Bioinform., 2016

ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information.

Alexander Lachmann, Federico M. Giorgi, Gonzalo López, Andrea Califano

Bioinform., 2016

Detection and removal of spatial bias in multiwell assays.

Alexander Lachmann, Federico M. Giorgi, Mariano J. Alvarez, Andrea Califano

Bioinform., 2016

2015

Preface: RECOMB/ISCB Systems Biology, Regulatory Genomics, and DREAM 2014 Special Issue.

Andrea Califano, Manolis Kellis, Gustavo Stolovitzky

J. Comput. Biol., 2015

The Cyni framework for network inference in Cytoscape.

Oriol Guitart-Pla, Manjunath Kustagi, Frank Rügheimer, Andrea Califano, Benno Schwikowski

Bioinform., 2015

DIGGIT: a Bioconductor package to infer genetic variants driving cellular phenotypes.

Mariano J. Alvarez, James C. Chen, Andrea Califano

Bioinform., 2015

2014

A promoter-level mammalian expression atlas.

The Fantom Consortium, RIKEN PMII, RIKEN CLST (DGT), Alistair R. R. Forrest, Hideya Kawaji, Michael Rehli, J. Kenneth Baillie, Michiel J. L. de Hoon, Vanja Haberle, Timo Lassmann, Ivan V. Kulakovskiy, Marina Lizio, Masayoshi Itoh, Robin Andersson, Christopher J. Mungall, Terrence F. Meehan, Sebastian Schmeier, Nicolas Bertin, Mette Jørgensen, Emmanuel Dimont, Erik Arner, Christian Schmidl, Ulf Schaefer, Yulia A. Medvedeva, Charles Plessy, Morana Vitezic, Jessica Severin, Colin A. M. Semple, Yuri Ishizu, Robert S. Young, Margherita Francescatto, Intikhab Alam, Davide Albanese, Gabriel M. Altschuler, Takahiro Arakawa, John A. C. Archer, Peter Arner, Magda Babina, Sarah Rennie, Piotr J. Balwierz, Anthony G. Beckhouse, Swati Pradhan-Bhatt, Judith A. Blake, Antje Blumenthal, Beatrice Bodega, Alessandro Bonetti, James Briggs, Frank Brombacher, A. Maxwell Burroughs, Andrea Califano, Carlo V. Cannistraci, Daniel Carbajo, Yun Chen, Marco Chierici, Yari Ciani, Hans Clevers, Emiliano Dalla, Carrie A. Davis, Michael Detmar, Alexander D. Diehl, Taeko Dohi, Finn Drabløs, Albert S. B. Edge, Matthias Edinger, Karl Ekwall, Mitsuhiro Endoh, Hideki Enomoto, Michela Fagiolini, Lynsey Fairbairn, Hai Fang, Mary C. Farach-Carson, Geoffrey J. Faulkner, Alexander V. Favorov, Malcolm E. Fisher, Martin C. Frith, Rie Fujita, Shiro Fukuda, Cesare Furlanello, Masaaki Furuno, Jun-ichi Furusawa, Teunis B. Geijtenbeek, Andrew P. Gibson, Thomas R. Gingeras, Daniel Goldowitz, Julian Gough, Sven Guhl, Reto Guler, Stefano Gustincich, Thomas J. Ha, Masahide Hamaguchi, Mitsuko Hara, Matthias Harbers, Jayson Harshbarger, Akira Hasegawa, Yuki Hasegawa, Takehiro Hashimoto, Meenhard Herlyn, Kelly J. Hitchens, Shannan J. Ho Sui, Oliver M. Hofmann, Ilka Hoof, Fumi Hori, Lukasz Huminiecki, Kei Iida, Tomokatsu Ikawa, Boris R. Jankovic, Hui Jia, Anagha Joshi, Giuseppe Jurman, Bogumil Kaczkowski, Chieko Kai, Kaoru Kaida, Ai Kaiho, Kazuhiro Kajiyama, Mutsumi Kanamori-Katayama, Artem S. Kasianov, Takeya Kasukawa, Shintaro Katayama, Sachi Kato, Shuji Kawaguchi, Hiroshi Kawamoto, Yuki I. Kawamura, Tsugumi Kawashima, Judith S. Kempfle, Tony J. Kenna, Juha Kere, Levon M. Khachigian, Toshio Kitamura, S. Peter Klinken, Alan J. Knox, Miki Kojima, Soichi Kojima, Naoto Kondo, Haruhiko Koseki, Shigeo Koyasu, Sarah Krampitz, Atsutaka Kubosaki, Andrew T. Kwon, Jeroen F. J. Laros, Weonju Lee, Andreas Lennartsson, Kang Li, Berit Lilje, Leonard Lipovich, Alan Mackay-Sim, Ri-ichiroh Manabe, Jessica Cara Mar, Benoit Marchand, Anthony Mathelier, Niklas Mejhert, Alison M. Meynert, Yosuke Mizuno, David A. de Lima Morais, Hiromasa Morikawa, Mitsuru Morimoto, Kazuyo Moro, Efthymios Motakis, Hozumi Motohashi, Christine Mummery, Mitsuyoshi Murata, Sayaka Nagao-Sato, Yutaka Nakachi, Fumio Nakahara, Toshiyuki Nakamura, Yukio Nakamura, Kenichi Nakazato, Erik van Nimwegen, Noriko Ninomiya, Hiromi Nishiyori, Shohei Noma, Tadasuke Nozaki, Soichi Ogishima, Naganari Ohkura, Hiroko Ohmiya, Hiroshi Ohno, Mitsuhiro Ohshima, Mariko Okada-Hatakeyama, Yasushi Okazaki, Valerio Orlando, Dmitry A. Ovchinnikov, Arnab Pain, Robert Passier, Margaret Patrikakis, Helena Persson, Silvano Piazza, James G. D. Prendergast, Owen J. L. Rackham, Jordan A. Ramilowski, Mamoon Rashid, Timothy Ravasi, Patrizia Rizzu, Marco Roncador, Sugata Roy, Morten B. Rye, Eri Saijyo, Antti Sajantila, Akiko Saka, Shimon Sakaguchi, Mizuho Sakai, Hiroki Sato, Hironori Sato, Suzana Savvi, Alka Saxena, Claudio Schneider, Erik A. Schultes, Gundula G. Schulze-Tanzil, Anita Schwegmann, Thierry Sengstag, Guojun Sheng, Hisashi Shimoji, Yishai Shimoni, Jay W. Shin, Christophe Simon, Daisuke Sugiyama, Takaaki Sugiyama, Masanori Suzuki, Naoko Suzuki, Rolf K. Swoboda, Peter A. C. 't Hoen, Michihira Tagami, Naoko Takahashi, Jun Takai, Hiroshi Tanaka, Hideki Tatsukawa, Zuotian Tatum, Mark Thompson, Hiroo Toyoda, Tetsuro Toyoda, Eivind Valen, Marc van de Wetering, Linda M. van den Berg, Roberto Verardo, Dipti Vijayan, Ilya E. Vorontsov, Wyeth W. Wasserman, Shoko Watanabe, Christine A. Wells, Louise N. Winteringham, Ernst Wolvetang, Emily J. Wood, Yoko Yamaguchi, Masayuki Yamamoto, Misako Yoneda, Yohei Yonekura, Shigehiro Yoshida, Susan E. Zabierowski, Peter G. Zhang, Xiaobei Zhao, Silvia Zucchelli, Kim M. Summers, Harukazu Suzuki, Carsten O. Daub, Jun Kawai, Peter Heutink, Winston Hide, Tom C. Freeman, Boris Lenhard, Vladimir B. Bajic, Martin S. Taylor, Vsevolod J. Makeev, Albin Sandelin, David A. Hume, Piero Carninci, Yoshihide Hayashizaki

Nat., 2014

RECOMB/ISCB Systems Biology, Regulatory Genomics, and DREAM 2013 Special Issue.

Andrea Califano, Manolis Kellis, Gustavo Stolovitzky

J. Comput. Biol., 2014

2013

Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling.

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

PLoS Comput. Biol., 2013

Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2012 Special Issue.

Andrea Califano, Manolis Kellis, Gustavo Stolovitzky

J. Comput. Biol., 2013

2012

Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2011 Special Issue.

Andrea Califano, Manolis Kellis, Gustavo Stolovitzky

J. Comput. Biol., 2012

Using systems and structure biology tools to dissect cellular phenotypes.

Aris Floratos, Barry Honig, Dana Pe'er, Andrea Califano

J. Am. Medical Informatics Assoc., 2012

2011

Preface.

Manolis Kellis, Andrea Califano, Ziv Bar-Joseph

J. Comput. Biol., 2011

Keynote: A systems biology approach to integrative cancer genomics.

Andrea Califano

Proceedings of the IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, 2011

2010

geWorkbench: an open source platform for integrative genomics.

Aris Floratos, Kenneth Smith, Zhou Ji, John Watkinson, Andrea Califano

Bioinform., 2010

2009

New JBI emphasis on translational bioinformatics.

Edward H. Shortliffe, Andrea Califano, Lawrence Hunter

J. Biomed. Informatics, 2009

Dissecting the Interface Between Signaling and Transcriptional Regulation in Human B Cells.

Kai Wang, Mariano J. Alvarez, Brygida C. Bisikirska, Rune Linding, Katia Basso, Riccardo Dalla Favera, Andrea Califano

Proceedings of the Biocomputing 2009: Proceedings of the Pacific Symposium, 2009

Master Regulators Used As Breast Cancer Metastasis Classifier.

Wei Keat Lim, Eugenia Lyashenko, Andrea Califano

Proceedings of the Biocomputing 2009: Proceedings of the Pacific Symposium, 2009

2007

Hui-Huang Hsu, Advanced Data Mining Technologies in Bioinformatics, Editors: Idea Group Publishing, pp 239.

Andrea Califano

J. Biomed. Informatics, 2007

ChIP-on-chip significance analysis reveals ubiquitous transcription factor binding.

Adam A. Margolin, Teresa Palomero, Adolfo A. Ferrando, Andrea Califano, Gustavo Stolovitzky

BMC Bioinform., 2007

Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks.

Wei Keat Lim, Kai Wang, Céline Lefebvre, Andrea Califano

Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007

2006

ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context.

Adam A. Margolin, Ilya Nemenman, Katia Basso, Chris Wiggins, Gustavo Stolovitzky, Riccardo Dalla Favera, Andrea Califano

BMC Bioinform., 2006

Genome-Wide Discovery of Modulators of Transcriptional Interactions in Human B Lymphocytes.

Kai Wang, Ilya Nemenman, Nilanjana Banerjee, Adam A. Margolin, Andrea Califano

Proceedings of the Research in Computational Molecular Biology, 2006

A Context-Specific Network of Protein-DNA and Protein-Protein Interactions Reveals New Regulatory Motifs in Human B Cells.

Céline Lefebvre, Wei Keat Lim, Katia Basso, Riccardo Dalla Favera, Andrea Califano

Proceedings of the Systems Biology and Computational Proteomics, 2006

Transcription Factor Centric Discovery of Regulatory Elements in Mammalian Genomes Using Alignment-Independent Conservation Maps.

Nilanjana Banerjee, Andrea Califano

Proceedings of the Comparative Genomics, 2006

2003

CASTOR: Clustering Algorithm for Sequence Taxonomical Organization and Relationships.

Agatha H. Liu, Andrea Califano

J. Comput. Biol., 2003

2001

Functional classification of proteins by pattern discovery and top-down clustering of primary sequences.

Agatha H. Liu, Andrea Califano

IBM Syst. J., 2001

2000

Systematic and Fully Automated Identification of Protein Sequence Patterns.

Reece Hart, Ajay K. Royyuru, Gustavo Stolovitzky, Andrea Califano

J. Comput. Biol., 2000

SPLASH: structural pattern localization analysis by sequential histograms.

Andrea Califano

Bioinform., 2000

Systematic and automated discovery of patterns in PROSITE families.

Reece Hart, Ajay K. Royyuru, Gustavo Stolovitzky, Andrea Califano

Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, 2000

Analysis of Gene Expression Microarrays for Phenotype Classification.

Andrea Califano, Gustavo Stolovitzky, Yuhai Tu

Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, 2000

1999

Representation and Matching of Small Flexible Molecules in Large Databases of 3D Molecular Information.

Isidore Rigoutsos, Daniel E. Platt, Andrea Califano, B. David Silverman

Proceedings of the Pattern Discovery in Biomolecular Data: Tools, 1999

1998

A High-Dimensional Indexing Scheme for Scalable Fingerprint-Based Identification.

Andrea Califano, Bob Germain, Scott Colville

Proceedings of the Computer Vision, 1998

1996

Data- and Model-Driven Multiresolution Processing.

Andrea Califano, Rick Kjeldsen, Ruud M. Bolle

Comput. Vis. Image Underst., 1996

1994

Multidimensional Indexing for Recognizing Visual Shapes.

Andrea Califano, Rakesh Mohan

IEEE Trans. Pattern Anal. Mach. Intell., 1994

1993

FLASH: a fast look-up algorithm for string homology.

Andrea Califano, Isidore Rigoutsos

Proceedings of the Conference on Computer Vision and Pattern Recognition, 1993

Systematic design of indexing strategies for object recognition.

Andrea Califano, Rakesh Mohan

Proceedings of the Conference on Computer Vision and Pattern Recognition, 1993

1992

The Multiple Window Parameter Transform.

Andrea Califano, Ruud M. Bolle

IEEE Trans. Pattern Anal. Mach. Intell., 1992

A Complete and Extendable Approach to Visual Recognition.

Ruud M. Bolle, Andrea Califano, Rick Kjeldsen

IEEE Trans. Pattern Anal. Mach. Intell., 1992

1990

Data and model driven foveation.

Andrea Califano, Rick Kjeldsen, Ruud M. Bolle

Proceedings of the 10th IAPR International Conference on Pattern Recognition, 1990

Active 3D object models.

Ruud M. Bolle, Andrea Califano, Rick Kjeldsen, Rakesh Mohan

Proceedings of the Third International Conference on Computer Vision, 1990

Generalized Shape Autocorrelation.

Andrea Califano, Rakesh Mohan

Proceedings of the 8th National Conference on Artificial Intelligence. Boston, Massachusetts, USA, July 29, 1990

1989

A Homogeneous Framework for Visual Recognition.

Rick Kjeldsen, Ruud M. Bolle, Andrea Califano, Russell W. Taylor

Proceedings of the 11th International Joint Conference on Artificial Intelligence. Detroit, 1989

Generalized neighborhoods: a new approach to complex parameter feature extraction.

Andrea Califano, Ruud M. Bolle, Russell W. Taylor

Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 1989

Visual recognition using concurrent and layered parameter networks.

Ruud M. Bolle, Andrea Califano, Rick Kjeldsen, Russell W. Taylor

Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 1989

1988

Feature Recognition Using Correlated Information Contained in Multiple Neighborboods.

Andrea Califano

Proceedings of the 7th National Conference on Artificial Intelligence, 1988