Reece K. Hart, Ajay K. Royyuru, Gustavo Stolovitzky, Andrea Califano
We present an efficient algorithm to systematically and automatically identify patterns in protein sequence families. The procedure is based on the Splash deterministic pattern discovery algorithm...
A Homogeneous Framework for Visual Recognition (2008)
Rick Kjeldsen, Ruud Ml Bolle, Andrea Califano, Russell W. Taylor
A homogeneous paradigm for evidence integration is presented, and a vision system to recognize 3D objects is demonstrated using this paradigm. A new concept called generalizedfeatures supports a...
Li, Zhong, Zheng, Tian, Califano, Andrea, Floratos, Aris
Abstract As genome-wide association studies grow in popularity for the identification of genetic factors for common and rare diseases, analytical methods to comb through large numbers of genetic...
Adam A. Margolin, Teresa Palomero, Pavel Sumazin, Andrea Califano, Adolfo Ferrando, Gustavo A. Stolovitzky
ChIP-on-chip has emerged as a powerful tool to dissect the complex network of regulatory interactions between transcription factors and their targets. However, most ChIP-on-chip analysis methods use...
Reece K. Hart, Gustavo Stolovitzky, Andrea Califano
We present an efficient algorithm to systematically and automatically identify patterns in protein sequence families. The procedure is based on the Splash deterministic pattern discovery algorithm...
ChIP-on-chip significance analysis reveals ubiquitous transcription factor binding (2007)
Margolin, Adam A, Palomero, Teresa, Ferrando, Adolfo A, Califano, Andrea, Stolovitzky, Gustavo
No abstract available.
A Pattern Discovery-Based Method for Detecting Multi-Locus Genetic Association (2007)
Li, Zhong, Floratos, Aris, Wang, David, Califano, Andrea
Methods to effectively detect multi-locus genetic association are becoming increasingly relevant in the genetic dissection of complex trait in humans. Current approaches typically consider a limited...
Margolin, Adam A, Nemenman, Ilya, Basso, Katia, Wiggins, Chris, Stolovitzky, Gustavo, Favera, Riccardo, ...
Abstract Background Elucidating gene regulatory networks is crucial for understanding normal cell physiology and complex pathologic phenotypes. Existing computational methods for the genome-wide...
Genome-wide discovery of modulators of transcriptional interactions in human B lymphocytes (2005)
Wang, Kai, Nemenman, Ilya, Banerjee, Nilanjana, Margolin, Adam, Califano, Andrea
Transcriptional interactions in a cell are modulated by a variety of mechanisms that prevent their representation as pure pairwise interactions between a transcription factor and its target(s). These...
Conditional Network Analysis Identifies Candidate Regulator Genes in Human B Cells (2004)
Wang, Kai, Banerjee, Nilanjana, Margolin, Adam, Nemenman, Ilya, Basso, Katia, Favera, Riccardo, ...
Cellular phenotypes are determined by the dynamical activity of networks of co-regulated genes. Elucidating such networks is crucial for the understanding of normal cell physiology as well as for the...
On The Reconstruction of Interaction Networks with Applications to Transcriptional Regulation (2004)
Margolin, Adam A., Nemenman, Ilya, Wiggins, Chris, Stolovitzky, Gustavo, Califano, Andrea
A novel information-theoretic method for reconstruction of interaction networks is introduced. We prove that the method is exact for some class of networks. Performance tests on large synthetic...
Margolin, Adam A., Nemenman, Ilya, Basso, Katia, Klein, Ulf, Wiggins, Chris, Stolovitzky, Gustavo, ...
Background: Elucidating gene regulatory networks is crucial for understanding normal cell physiology and complex pathologic phenotypes. Existing computational methods for the genome-wide ``reverse...
Pharmacogenetics: Ethical Issues and Policy Options (2002)
Califano, Andrea., Kahn, Jeffrey P., McPherson, Elizabeth., Brody, Baruch A.
Kennedy Institute of Ethics Journal - Volume 12, Number 1, March 2002
Agatha H. Liu, Andrea Califano
Given a functionally heterogeneous group of proteins, such as a large superfamily, or an entire database, two important problems in biology are the automated inference of subsets of functionally...
Analysis of gene expression microarrays for phenotype classification (2000)
Andrea Califano, Gustavo Stolovitzky, Yuhai Tu
Several microarray technologies that monitor the level of expression of a large number of genes have recently emerged. Given DNA-microarray data for a set of cells characterized by a given phenotype...
Systematic and automated discovery of patterns in PROSITE families (2000)
Reece Hart, Ajay K. Royyuru, Gustavo Stolovitzky, Andrea Califano
PROSITE is a method for protein classification which relies on a database of biologically significant sites and patterns in protein sequences. Most patterns in PROSITE have been gathered by a a labor...
SPLASH: structural pattern localization analysis by sequential histograms (2000)
Motivation: The discovery of sparse amino acid patterns that match repeatedly in a set of protein sequences is an important problem in computational biology. Statistically significant patterns, that...
Califano A: Statistical significance of patterns in biosequences (1998)
Gustavo Stolovitzky, Andrea Califano
Several algorithms for pattern discovery in sequences have recently emerged, such as Pratt, Teiresias, Splash, and Meme. These are proving useful in biological sequences analysis, as the presence of...
Transcriptional analysis of the B cell germinal center reaction
Klein, Ulf, Tu, Yuhai, Stolovitzky, Gustavo A., Keller, Jeffrey L., Haddad, Joseph, Miljkovic, Vladan, ...
The germinal center (GC) reaction is crucial for T cell-dependent immune responses and is targeted by B cell lymphomagenesis. Here we analyzed the transcriptional changes that occur in B cells during...
Identification of Hodgkin and Reed-Sternberg cell-specific genes by gene expression profiling
Küppers, Ralf, Klein, Ulf, Schwering, Ines, Distler, Verena, Bräuninger, Andreas, Cattoretti, Giorgio, ...
Hodgkin lymphoma (HL) is a malignancy of unknown pathogenesis. The malignant Hodgkin and Reed/Sternberg (HRS) cells derive from germinal center B cells (or rarely, T cells) but have a heterogeneous...
Transcriptional analysis of the B cell germinal center reaction
Klein, Ulf, Tu, Yuhai, Stolovitzky, Gustavo A., Keller, Jeffrey L., Haddad, Joseph, Miljkovic, Vladan, ...
The germinal center (GC) reaction is crucial for T cell-dependent immune responses and is targeted by B cell lymphomagenesis. Here we analyzed the transcriptional changes that occur in B cells during...
Identification of Hodgkin and Reed-Sternberg cell-specific genes by gene expression profiling
Küppers, Ralf, Klein, Ulf, Schwering, Ines, Distler, Verena, Bräuninger, Andreas, Cattoretti, Giorgio, ...
Hodgkin lymphoma (HL) is a malignancy of unknown pathogenesis. The malignant Hodgkin and Reed/Sternberg (HRS) cells derive from germinal center B cells (or rarely, T cells) but have a heterogeneous...
Piccaluga, Pier Paolo, Agostinelli, Claudio, Califano, Andrea, Rossi, Maura, Basso, Katia, Zupo, Simonetta, ...
Peripheral T cell lymphoma, unspecified (PTCL/U), the most common form of PTCL, displays heterogeneous morphology and phenotype, poor response to treatment, and poor prognosis. We demonstrate that...
Margolin, Adam A, Nemenman, Ilya, Basso, Katia, Wiggins, Chris, Stolovitzky, Gustavo, Favera, Riccardo Dalla, ...
Palomero, Teresa, Lim, Wei Keat, Odom, Duncan T., Sulis, Maria Luisa, Real, Pedro J., Margolin, Adam, ...
The NOTCH1 signaling pathway directly links extracellular signals with transcriptional responses in the cell nucleus and plays a critical role during T cell development and in the pathogenesis over...
Sosinsky, Alona, Honig, Barry, Mann, Richard S., Califano, Andrea
The functional annotation of the nonprotein-coding DNA of eukaryotic genomes is a problem of central importance. Phylogenetic footprinting methods, which attempt to identify functional regulatory...
Basso, Katia, Liso, Arcangelo, Tiacci, Enrico, Benedetti, Roberta, Pulsoni, Alessandro, Foa, Robin, ...
Hairy cell leukemia (HCL) is a chronic B cell malignancy characterized by the diffuse infiltration of bone marrow and spleen by cells displaying a typical “hairy” morphology. However, the nature...
Mani, Kartik M, Lefebvre, Celine, Wang, Kai, Lim, Wei Keat, Basso, Katia, Dalla-Favera, Riccardo, ...
The computational identification of oncogenic lesions is still a key open problem in cancer biology. Although several methods have been proposed, they fail to model how such events are mediated by...
Klein, Ulf, Tu, Yuhai, Stolovitzky, Gustavo A., Mattioli, Michela, Cattoretti, Giorgio, Husson, Hervé, ...
B cell–derived chronic lymphocytic leukemia (B-CLL) represents a common malignancy whose cell derivation and pathogenesis are unknown. Recent studies have shown that >50% of CLLs display...
Pattern-based mining strategy to detect multi-locus association and gene × environment interaction
Li, Zhong, Zheng, Tian, Califano, Andrea, Floratos, Aris
As genome-wide association studies grow in popularity for the identification of genetic factors for common and rare diseases, analytical methods to comb through large numbers of genetic variants...
Dinov, Ivo D., Rubin, Daniel, Lorensen, William, Dugan, Jonathan, Ma, Jeff, Murphy, Shawn, ...
The advancement of the computational biology field hinges on progress in three fundamental directions – the development of new computational algorithms, the availability of informatics resource...
Margolin, Adam A., Palomero, Teresa, Sumazin, Pavel, Califano, Andrea, Ferrando, Adolfo A., Stolovitzky, Gustavo
ChIP-on-chip has emerged as a powerful tool to dissect the complex network of regulatory interactions between transcription factors and their targets. However, most ChIP-on-chip analysis methods use...