Feature Recognition Using Correlated Information Contained in Multiple Neighborboods. - Andrea Califano (AAAI, 1988)

Visual recognition using concurrent and layered parameter networks. - Ruud M. Bolle; Andrea Califano; Rick Kjeldsen; Russell W. Taylor (CVPR, 1989)

Generalized neighborhoods: a new approach to complex parameter feature extraction. - Andrea Califano; Ruud M. Bolle; Russell W. Taylor (CVPR, 1989)

A Homogeneous Framework for Visual Recognition. - Rick Kjeldsen; Ruud M. Bolle; Andrea Califano; Russell W. Taylor (IJCAI, 1989)

Generalized Shape Autocorrelation. - Andrea Califano; Rakesh Mohan (AAAI, 1990)

Active 3D object models. - Ruud M. Bolle; Andrea Califano; Rick Kjeldsen; Rakesh Mohan (ICCV, 1990)

Data and model driven foveation. - Andrea Califano; Rick Kjeldsen; Ruud M. Bolle (ICPR (1), 1990)

Multidimensional indexing for recognizing visual shapes. - Andrea Califano; Rakesh Mohan (CVPR, 1991)

A Complete and Extendable Approach to Visual Recognition. - Ruud M. Bolle; Andrea Califano; Rick Kjeldsen (IEEE Trans. Pattern Anal. Mach. Intell., 1992)

The Multiple Window Parameter Transform. - Andrea Califano; Ruud M. Bolle (IEEE Trans. Pattern Anal. Mach. Intell., 1992)

Systematic design of indexing strategies for object recognition. - Andrea Califano; Rakesh Mohan (CVPR, 1993)

FLASH: A Fast Look-Up Algorithm for String Homology. - Andrea Califano; Isidore Rigoutsos (ISMB, 1993)

Data- and Model-Driven Multiresolution Processing. - Andrea Califano; Rick Kjeldsen; Ruud M. Bolle (Comput. Vis. Image Underst., 1996)

A High-Dimensional Indexing Scheme for Scalable Fingerprint-Based Identification. - Andrea Califano; Bob Germain; Scott Colville (ACCV (1), 1998)

Representation and Matching of Small Flexible Molecules in Large Databases of 3D Molecular Information. - Isidore Rigoutsos; Daniel E. Platt; Andrea Califano; B. David Silverman (Pattern Discovery in Biomolecular Data, 1999)

Analysis of Gene Expression Microarrays for Phenotype Classification. - Andrea Califano; Gustavo Stolovitzky; Yuhai Tu (ISMB, 2000)

Systematic and automated discovery of patterns in PROSITE families. - Reece Hart; Ajay K. Royyuru; Gustavo Stolovitzky; Andrea Califano (RECOMB, 2000)

SPLASH: structural pattern localization analysis by sequential histograms. - Andrea Califano (Bioinform., 2000)

Systematic and Fully Automated Identification of Protein Sequence Patterns. - Reece Hart; Ajay K. Royyuru; Gustavo Stolovitzky; Andrea Califano (J. Comput. Biol., 2000)

Functional classification of proteins by pattern discovery and top-down clustering of primary sequences. - Agatha H. Liu; Andrea Califano (IBM Syst. J., 2001)

CASTOR: Clustering Algorithm for Sequence Taxonomical Organization and Relationships. - Agatha H. Liu; Andrea Califano (J. Comput. Biol., 2003)

Transcription Factor Centric Discovery of Regulatory Elements in Mammalian Genomes Using Alignment-Independent Conservation Maps. - Nilanjana Banerjee; Andrea Califano (Comparative Genomics, 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 (Systems Biology and Computational Proteomics, 2006)

Genome-Wide Discovery of Modulators of Transcriptional Interactions in Human B Lymphocytes. - Kai Wang 045; Ilya Nemenman; Nilanjana Banerjee; Adam A. Margolin; Andrea Califano (RECOMB, 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 001; Gustavo Stolovitzky; Riccardo Dalla Favera; Andrea Califano (BMC Bioinform., 2006)

Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks. - Wei Keat Lim; Kai Wang 045; Céline Lefebvre; Andrea Califano (ISMB/ECCB (Supplement of Bioinformatics), 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)

Hui-Huang Hsu, Advanced Data Mining Technologies in Bioinformatics, Editors: Idea Group Publishing, pp 239. - Andrea Califano (J. Biomed. Informatics, 2007)

Master Regulators Used As Breast Cancer Metastasis Classifier. - Wei Keat Lim; Eugenia Lyashenko; Andrea Califano (Pacific Symposium on Biocomputing, 2009)

Dissecting the Interface Between Signaling and Transcriptional Regulation in Human B Cells. - Kai Wang 045; Mariano J. Alvarez; Brygida C. Bisikirska; Rune Linding; Katia Basso; Riccardo Dalla Favera; Andrea Califano (Pacific Symposium on Biocomputing, 2009)

New JBI emphasis on translational bioinformatics. - Edward H. Shortliffe; Andrea Califano; Lawrence Hunter (J. Biomed. Informatics, 2009)

geWorkbench: an open source platform for integrative genomics. - Aris Floratos; Kenneth Smith 001; Zhou Ji; John Watkinson; Andrea Califano (Bioinform., 2010)

Keynote: A systems biology approach to integrative cancer genomics. - Andrea Califano (ICCABS, 2011)

Preface. - Manolis Kellis; Andrea Califano; Ziv Bar-Joseph (J. Comput. Biol., 2011)

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)

Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2011 Special Issue. - Andrea Califano; Manolis Kellis; Gustavo Stolovitzky (J. Comput. Biol., 2012)

Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2012 Special Issue. - Andrea Califano; Manolis Kellis; Gustavo Stolovitzky (J. Comput. Biol., 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 002; Benjamin A. Sauerwine; Yishai Shimoni; Hans Kristian Moen Vollan; Brigham H. Mecham; Oscar M. Rueda; Jorg Tost; et al. (PLoS Comput. Biol., 2013)

RECOMB/ISCB Systems Biology, Regulatory Genomics, and DREAM 2013 Special Issue. - Andrea Califano; Manolis Kellis; Gustavo Stolovitzky (J. Comput. Biol., 2014)

DIGGIT: a Bioconductor package to infer genetic variants driving cellular phenotypes. - Mariano J. Alvarez; James C. Chen; Andrea Califano (Bioinform., 2015)

The Cyni framework for network inference in Cytoscape. - Oriol Guitart-Pla; Manjunath Kustagi; Frank Rügheimer; Andrea Califano; Benno Schwikowski (Bioinform., 2015)

Preface: RECOMB/ISCB Systems Biology, Regulatory Genomics, and DREAM 2014 Special Issue. - Andrea Califano; Manolis Kellis; Gustavo Stolovitzky (J. Comput. Biol., 2015)

Detection and removal of spatial bias in multiwell assays. - Alexander Lachmann; Federico M. Giorgi; Mariano J. Alvarez; 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)

ScreenBEAM: a novel meta-analysis algorithm for functional genomics screens via Bayesian hierarchical modeling. - Jiyang Yu; José Silva; Andrea Califano (Bioinform., 2016)

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 001; Jessica N. Mazerik; Zhou Ji; Benjamin E. Gross; Olga Nikolova; Nadia Jaber; Andrea Califano; Stuart L. Schreiber; Daniela S. Gerhard; Leandro Hermida; et al. (Database J. Biol. Databases Curation, 2017)

Accelerated parallel algorithm for gene network reverse engineering. - Jing He; Zhou Zhou; Michael Reed; Andrea Califano (BMC Syst. Biol., 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)

iterClust: a statistical framework for iterative clustering analysis. - Hongxu Ding; Wanxin Wang; Andrea Califano (Bioinform., 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)

SJARACNe: a scalable software tool for gene network reverse engineering from big data. - Alireza Khatamian; Evan O. Paull; Andrea Califano; Jiyang Yu (Bioinform., 2019)

NaRnEA: An Information Theoretic Framework for Gene Set Analysis. - Aaron T. Griffin; Lukas J. Vlahos; Codruta Chiuzan; Andrea Califano (Entropy, 2023)

How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities. - Charlotte Bunne; Yusuf H. Roohani; Yanay Rosen; Ankit Gupta 018; Xikun Zhang 001; Marcel Roed; Theo Alexandrov; Mohammed AlQuraishi; Patricia Brennan; Daniel B. Burkhardt; Andrea Califano; Jonah Cool; et al. (CoRR, 2024)