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Andrea Califano

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affiliation: Columbia University, New York City, USA

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2020 – today

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2024
[i1]
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  - journals/corr/abs-2409-11654
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Charlotte Bunne, Yusuf 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:
How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities. CoRR abs/2409.11654 (2024)
2023
[j33]
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  - journals/entropy/GriffinVCC23
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Aaron T. Griffin, Lukas J. Vlahos, Codruta Chiuzan, Andrea Califano:
NaRnEA: An Information Theoretic Framework for Gene Set Analysis. Entropy 25(3): 542 (2023)

2010 – 2019

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2019
[j32]
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  - journals/bioinformatics/KhatamianPCY19
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Alireza Khatamian, Evan O. Paull, Andrea Califano, Jiyang Yu:
SJARACNe: a scalable software tool for gene network reverse engineering from big data. Bioinform. 35(12): 2165-2166 (2019)
2018
[j31]
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Zeljko Tomljanovic, Mitesh Patel, William Shin, Andrea Califano, Andrew F. Teich:
ZCCHC17 is a master regulator of synaptic gene expression in Alzheimer's disease. Bioinform. 34(3): 367-371 (2018)
[j30]
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Hongxu Ding, Wanxin Wang, Andrea Califano:
iterClust: a statistical framework for iterative clustering analysis. Bioinform. 34(16): 2865-2866 (2018)
2017
[j29]
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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:
CTD2 Dashboard: a searchable web interface to connect validated results from the Cancer Target Discovery and Development Network. Database J. Biol. Databases Curation 2017: bax054 (2017)
[j28]
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Jing He, Zhou Zhou, Michael Reed, Andrea Califano:
Accelerated parallel algorithm for gene network reverse engineering. BMC Syst. Biol. 11(S-4): 85-97 (2017)
[j27]
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Yao Shen, Mariano J. Alvarez, Brygida C. Bisikirska, Alexander Lachmann, Ronald Realubit, Sergey Pampou, Jorida Coku, Charles Karan, Andrea Califano:
Systematic, network-based characterization of therapeutic target inhibitors. PLoS Comput. Biol. 13(10) (2017)
2016
[j26]
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Jiyang Yu, José Silva, Andrea Califano:
ScreenBEAM: a novel meta-analysis algorithm for functional genomics screens via Bayesian hierarchical modeling. Bioinform. 32(2): 260-267 (2016)
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Alexander Lachmann, Federico M. Giorgi, Mariano J. Alvarez, Andrea Califano:
Detection and removal of spatial bias in multiwell assays. Bioinform. 32(13): 1959-1965 (2016)
[j24]
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Alexander Lachmann, Federico M. Giorgi, Gonzalo López, Andrea Califano:
ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information. Bioinform. 32(14): 2233-2235 (2016)
2015
[j23]
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Oriol Guitart-Pla, Manjunath Kustagi, Frank Rügheimer, Andrea Califano, Benno Schwikowski:
The Cyni framework for network inference in Cytoscape. Bioinform. 31(9): 1499-1501 (2015)
[j22]
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Mariano J. Alvarez, James C. Chen, Andrea Califano:
DIGGIT: a Bioconductor package to infer genetic variants driving cellular phenotypes. Bioinform. 31(24): 4032-4034 (2015)
[j21]
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Andrea Califano, Manolis Kellis, Gustavo Stolovitzky:
Preface: RECOMB/ISCB Systems Biology, Regulatory Genomics, and DREAM 2014 Special Issue. J. Comput. Biol. 22(4): 251-252 (2015)
2014
[j20]
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Andrea Califano, Manolis Kellis, Gustavo Stolovitzky:
RECOMB/ISCB Systems Biology, Regulatory Genomics, and DREAM 2013 Special Issue. J. Comput. Biol. 21(5): 371-372 (2014)
[j19]
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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:
A promoter-level mammalian expression atlas. Nat. 507(7493): 462-470 (2014)
2013
[j18]
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Andrea Califano, Manolis Kellis, Gustavo Stolovitzky:
Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2012 Special Issue. J. Comput. Biol. 20(5): 373-374 (2013)
[j17]
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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:
Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling. PLoS Comput. Biol. 9(5) (2013)
2012
[j16]
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Aris Floratos, Barry Honig, Dana Pe'er, Andrea Califano:
Using systems and structure biology tools to dissect cellular phenotypes. J. Am. Medical Informatics Assoc. 19(2): 171-175 (2012)
[j15]
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Andrea Califano, Manolis Kellis, Gustavo Stolovitzky:
Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2011 Special Issue. J. Comput. Biol. 19(2): 101 (2012)
2011
[j14]
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Manolis Kellis, Andrea Califano, Ziv Bar-Joseph:
Preface. J. Comput. Biol. 18(2): 131 (2011)
[c21]
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Andrea Califano:
Keynote: A systems biology approach to integrative cancer genomics. ICCABS 2011: 1
2010
[j13]
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Aris Floratos, Kenneth Smith, Zhou Ji, John Watkinson, Andrea Califano:
geWorkbench: an open source platform for integrative genomics. Bioinform. 26(14): 1779-1780 (2010)

2000 – 2009

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2009
[j12]
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Edward H. Shortliffe, Andrea Califano, Lawrence Hunter:
New JBI emphasis on translational bioinformatics. J. Biomed. Informatics 42(2): 199-200 (2009)
[c20]
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Kai Wang, Mariano J. Alvarez, Brygida C. Bisikirska, Rune Linding, Katia Basso, Riccardo Dalla Favera, Andrea Califano:
Dissecting the Interface Between Signaling and Transcriptional Regulation in Human B Cells. Pacific Symposium on Biocomputing 2009: 264-275
[c19]
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Wei Keat Lim, Eugenia Lyashenko, Andrea Califano:
Master Regulators Used As Breast Cancer Metastasis Classifier. Pacific Symposium on Biocomputing 2009: 504-515
2007
[j11]
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Adam A. Margolin, Teresa Palomero, Adolfo A. Ferrando, Andrea Califano, Gustavo Stolovitzky:
ChIP-on-chip significance analysis reveals ubiquitous transcription factor binding. BMC Bioinform. 8(S-8) (2007)
[j10]
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Andrea Califano:
Hui-Huang Hsu, Advanced Data Mining Technologies in Bioinformatics, Editors: Idea Group Publishing, pp 239. J. Biomed. Informatics 40(5): 603-604 (2007)
[c18]
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Wei Keat Lim, Kai Wang, Céline Lefebvre, Andrea Califano:
Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks. ISMB/ECCB (Supplement of Bioinformatics) 2007: 282-288
2006
[j9]
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Adam A. Margolin, Ilya Nemenman, Katia Basso, Chris Wiggins, Gustavo Stolovitzky, Riccardo Dalla Favera, Andrea Califano:
ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context. BMC Bioinform. 7(S-1) (2006)
[c17]
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Céline Lefebvre, Wei Keat Lim, Katia Basso, Riccardo Dalla Favera, Andrea Califano:
A Context-Specific Network of Protein-DNA and Protein-Protein Interactions Reveals New Regulatory Motifs in Human B Cells. Systems Biology and Computational Proteomics 2006: 42-56
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Nilanjana Banerjee, Andrea Califano:
Transcription Factor Centric Discovery of Regulatory Elements in Mammalian Genomes Using Alignment-Independent Conservation Maps. Comparative Genomics 2006: 200-214
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Kai Wang, Ilya Nemenman, Nilanjana Banerjee, Adam A. Margolin, Andrea Califano:
Genome-Wide Discovery of Modulators of Transcriptional Interactions in Human B Lymphocytes. RECOMB 2006: 348-362
2003
[j8]
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Agatha H. Liu, Andrea Califano:
CASTOR: Clustering Algorithm for Sequence Taxonomical Organization and Relationships. J. Comput. Biol. 10(1): 21-45 (2003)
2001
[j7]
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Agatha H. Liu, Andrea Califano:
Functional classification of proteins by pattern discovery and top-down clustering of primary sequences. IBM Syst. J. 40(2): 379-393 (2001)
2000
[j6]
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Andrea Califano:
SPLASH: structural pattern localization analysis by sequential histograms. Bioinform. 16(4): 341-357 (2000)
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Reece Hart, Ajay K. Royyuru, Gustavo Stolovitzky, Andrea Califano:
Systematic and Fully Automated Identification of Protein Sequence Patterns. J. Comput. Biol. 7(3-4): 585-600 (2000)
[c14]
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Andrea Califano, Gustavo Stolovitzky, Yuhai Tu:
Analysis of Gene Expression Microarrays for Phenotype Classification. ISMB 2000: 75-85
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Reece Hart, Ajay K. Royyuru, Gustavo Stolovitzky, Andrea Califano:
Systematic and automated discovery of patterns in PROSITE families. RECOMB 2000: 147-154

1990 – 1999

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1999
[p1]
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Isidore Rigoutsos, Daniel E. Platt, Andrea Califano, B. David Silverman:
Representation and Matching of Small Flexible Molecules in Large Databases of 3D Molecular Information. Pattern Discovery in Biomolecular Data 1999: 111-129
1998
[c12]
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Andrea Califano, Bob Germain, Scott Colville:
A High-Dimensional Indexing Scheme for Scalable Fingerprint-Based Identification. ACCV (1) 1998: 32-39
1996
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Andrea Califano, Rick Kjeldsen, Ruud M. Bolle:
Data- and Model-Driven Multiresolution Processing. Comput. Vis. Image Underst. 63(1): 27-49 (1996)
1994
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Andrea Califano, Rakesh Mohan:
Multidimensional Indexing for Recognizing Visual Shapes. IEEE Trans. Pattern Anal. Mach. Intell. 16(4): 373-392 (1994)
1993
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Andrea Califano, Isidore Rigoutsos:
FLASH: a fast look-up algorithm for string homology. CVPR 1993: 353-359
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Andrea Califano, Rakesh Mohan:
Systematic design of indexing strategies for object recognition. CVPR 1993: 709-710
[c9]
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Andrea Califano, Isidore Rigoutsos:
FLASH: A Fast Look-Up Algorithm for String Homology. ISMB 1993: 56-64
1992
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Ruud M. Bolle, Andrea Califano, Rick Kjeldsen:
A Complete and Extendable Approach to Visual Recognition. IEEE Trans. Pattern Anal. Mach. Intell. 14(5): 534-548 (1992)
[j1]
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Andrea Califano, Ruud M. Bolle:
The Multiple Window Parameter Transform. IEEE Trans. Pattern Anal. Mach. Intell. 14(12): 1157-1170 (1992)
1991
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Andrea Califano, Rakesh Mohan:
Multidimensional indexing for recognizing visual shapes. CVPR 1991: 28-34
1990
[c7]
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Andrea Califano, Rakesh Mohan:
Generalized Shape Autocorrelation. AAAI 1990: 1067-1073
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Ruud M. Bolle, Andrea Califano, Rick Kjeldsen, Rakesh Mohan:
Active 3D object models. ICCV 1990: 329-333
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Andrea Califano, Rick Kjeldsen, Ruud M. Bolle:
Data and model driven foveation. ICPR (1) 1990: 1-7

1980 – 1989

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1989
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Andrea Califano, Ruud M. Bolle, Russell W. Taylor:
Generalized neighborhoods: a new approach to complex parameter feature extraction. CVPR 1989: 192-199
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Ruud M. Bolle, Andrea Califano, Rick Kjeldsen, Russell W. Taylor:
Visual recognition using concurrent and layered parameter networks. CVPR 1989: 625-631
[c2]
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Rick Kjeldsen, Ruud M. Bolle, Andrea Califano, Russell W. Taylor:
A Homogeneous Framework for Visual Recognition. IJCAI 1989: 1578-1584
1988
[c1]
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Andrea Califano:
Feature Recognition Using Correlated Information Contained in Multiple Neighborboods. AAAI 1988: 831-836

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