NIC Workshop 2006, From Computational Biophysics to Systems Biology, (2009)
Faruck Morcos, Mike Boxem, Niels Klitgord, Marc Vidal, Jesús A. Izaguirre, Jan Meinke, ...
published in
Janghoo Lim, Tong Hao, Chad Shaw, Akash J. Patel, Gábor Szabó, Jean-françois Rual, ...
Many human inherited neurodegenerative disorders are characterized by loss of balance due to cerebellar Purkinje cell (PC) degeneration. Although the disease-causing mutations have been identified...
An empirical framework for binary interactome mapping (2009)
Venkatesan, Kavitha, Rual, Jean-Francois, Vazquez, Alexei, Stelzl, Ulrich, Lemmens, Irma, Hirozane-Kishikawa, Tomoko, ...
Several attempts have been made to systematically map protein-protein interaction, or 'interactome', networks. However, it remains difficult to assess the quality and coverage of existing data sets....
Array MAPPIT: High-Throughput Interactome Analysis in Mammalian Cells (2009)
Lievens, Sam, Vanderroost, Nele, Van Der Heyden, José, Gesellchen, Viola, Vidal, Marc, Tavernier, Jan
Physical interactions between proteins play a key role in probably every cellular process. Efforts to chart the protein interaction networks are ongoing in a number of model organisms using a...
An experimentally derived confidence score for binary protein-protein interactions (2009)
Braun, Pascal, Tasan, Murat, Dreze, Matija, Barrios-Rodiles, Miriam, Lemmens, Irma, Yu, Haiyuan, ...
Information on protein-protein interactions is of central importance for many areas of biomedical research. At present no method exists to systematically and experimentally assess the quality of...
Simonis, Nicolas, Rual, Jean-Francois, Carvunis, Anne-Ruxandra, Tasan, Murat, Lemmens, Irma, Hirozane-Kishikawa, Tomoko, ...
Abstract: To provide accurate biological hypotheses and elucidate global properties of cellular networks, systematic identification of protein-protein interactions must meet high quality standards....
Shifted Transversal Design smart-pooling for high coverage interactome mapping (2009)
Xin, Xiaofeng, Rual, Jean-François, Hirozane-Kishikawa, Tomoko, Hill, David E., Vidal, Marc, Boone, Charles, ...
“Smart-pooling,” in which test reagents are multiplexed in a highly redundant manner, is a promising strategy for achieving high efficiency, sensitivity, and specificity in systems-level...
VirusMINT: a viral protein interaction database (2009)
Chatr-aryamontri, Andrew, Ceol, Arnaud, Peluso, Daniele, Nardozza, Aurelio, Panni, Simona, Sacco, Francesca, ...
Understanding the consequences on host physiology induced by viral infection requires complete understanding of the perturbations caused by virus proteins on the cellular protein interaction network....
A Biological Atlas of Functional Maps Review (2008)
responses at the cellular level. Thus, it is reasonable to Dana-Farber Cancer Institute and imagine that more integrative approaches will be needed
BMC Biology BioMed Central (2008)
Samuel Kerrien, Ra Orchard, Luisa Montecchi-palazzi, Bruno Ar, Antony F Quinn, Nisha Vinod, ...
Software Broadening the horizon – level 2.5 of the HUPO-PSI format for
Prediction of domain interactions in C. elegans (2008)
Faruck Morcos, Mike Boxem, Niels Klitgord, Marc Vidal, Jesús A. Izaguirre
High throughput experiments and computational methods allow the elucidation of networks of protein-protein interactions (PPI) in several organisms. Since about 80 % of all proteins consist of...
Annotation Transfer Between Genomes: (2008)
Protein–protein Interologs, Haiyuan Yu, Nicholas M. Luscombe, Hao Xin Lu, Xiaowei Zhu, ...
this paper, we present results from both approaches
A protein domain-based interactome network for C. elegans early embryogenesis (2008)
Boxem, Mike, Maliga, Zoltan, Klitgord, Niels, Li, Na, Lemmens, Irma, Mana, Miyeko, ...
Many protein-protein interactions are mediated through independently folding modular domains. Proteome-wide efforts to model protein-protein interaction or "interactome" networks have largely ignored...
Revisiting the Saccharomyces cerevisiae predicted ORFeome (2008)
Li, Qian-Ru, Carvunis, Anne-Ruxandra, Yu, Haiyuan, Han, Jing-Dong J., Zhong, Quan, Simonis, Nicolas, ...
Accurately defining the coding potential of an organism, i.e., all protein-encoding open reading frames (ORFs) or “ORFeome,” is a prerequisite to fully understand its biology. ORFeome annotation...
Marc Vidal, PhD Associate Professor of Genetics, Harvard Medical School presented a lecture at 11:00 AM, Tuesday, November 27, 2007, Klaus Advanced Computing Building, Room 1116W
Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions (2007)
Kerrien, Samuel, Orchard, Sandra, Montecchi-Palazzi, Luisa, Aranda, Bruno, Quinn, Antony F, Vinod, Nisha, ...
Abstract Background Molecular interaction Information is a key resource in modern biomedical research. Publicly available data have previously been provided in a broad array of diverse formats,...
Wang, Haidong, Segal, Eran, Ben-Hur, Asa, Li, Qian-Ru, Vidal, Marc, Koller, Daphne
Abstract We propose InSite, a computational method that integrates high-throughput protein and sequence data to infer the specific binding regions of interacting protein pairs. We compared our...
Confirmation of Organized Modularity in the Yeast Interactome (2007)
Nicolas Bertin, Nicolas Simonis, Denis Dupuy, Michael E. Cusick, Hunter B. Fraser, ...
Ceron, Julian, Rual, Jean-François, Chandra, Abha, Dupuy, Denis, Vidal, Marc, Van Den Heuvel, Sander
Abstract Background The retinoblastoma tumor suppressor (Rb) acts in a conserved pathway that is deregulated in most human cancers. Inactivation of the single Rb-related gene in Caenorhabditis...
Reece-Hoyes, John S., Shingles, Jane, Dupuy, Denis, Grove, Christian A., Walhout, Albertha J. M., Vidal, Marc, ...
BACKGROUND: The C. elegans Promoterome is a powerful resource for revealing the regulatory mechanisms by which transcription is controlled pan-genomically. Transcription factors will form the core of...
interaction binding sites on a proteome-wide scale (2007)
Haidong Wang, Eran Segal, Asa Ben-hur, Qian-ru Li, Marc Vidal, Daphne Koller
InSite: a computational method for identifying protein-protein
Intrinsic Disorder Is a Common Feature of Hub Proteins from Four Eukaryotic Interactomes (2006)
Chad Haynes, Christopher J. Oldfield, Fei Ji, Niels Klitgord, Michael E. Cusick, Predrag Radivojac, ...
Recent proteome-wide screening approaches have provided a wealth of information about interacting proteins in various organisms. To test for a potential association between protein connectivity and...
Intrinsic Disorder is a Common Feature of Hub Proteins from Four Eukaryotic Interactomes (2006)
Chad Haynes, Christopher J Oldfield, Fei Ji, Niels Klitgord, Michael E Cusick, Predrag Radivojac, ...
Recent proteome-wide screening approaches have provided a wealth of information about interacting proteins in various organisms. To test for a potential association between protein connectivity and...
From genome to proteome: developing expression clone resources for the human genome (2006)
Temple, Gary, Lamesch, Philippe, Milstein, Stuart, Hill, David E., Wagner, Lukas, Moore, Troy, ...
From genome to proteome: developing expression clone resources for the human genome (2006)
Temple, Gary, Lamesch, Philippe, Milstein, Stuart, Hill, David E., Wagner, Lukas, Moore, Troy, ...
cDNA clones have long been valuable reagents for studying the structure and function of proteins. With recent access to the entire human genome sequence, it has become possible and highly productive...
High throughput one-hybrid system (2005)
Walhout, Albertha J. M., Vidal, Marc, Deplancke, Bart
The invention relates to a new high throughput yeast one-hybrid screening system
BIOINFORMATICS ORIGINAL PAPER Systems biology Local modeling of global interactome networks (2005)
Denise Scholtens, Marc Vidal, Robert Gentleman
Motivation: Systems biology requires accurate models of protein complexes, including physical interactions that assemble and regulate these molecular machines. Yeast two-hybrid (Y2H) and affinity–...
Fernandez, Anita G., Gunsalus, Kristin C., Huang, Jerry, Chuang, Ling-Shiang, Ying, Nancy, Liang, Hsiao-lan, ...
Several RNA interference (RNAi)-based functional genomic projects have been performed in Caenorhabditis elegans to identify genes required during embryogenesis. These studies have demonstrated that...
Local modeling of global interactome networks (2005)
Scholtens, Denise, Vidal, Marc, Gentleman, Robert
Motivation: Systems biology requires accurate models of protein complexes, including physical interactions that assemble and regulate these molecular machines. Yeast two-hybrid (Y2H) and...
Local modeling of global interactome networks (2005)
Scholtens, Denise, Vidal, Marc, Gentleman, Robert
Motivation: Systems biology requires accurate models of protein complexes, including physical interactions that assemble and regulate these molecular machines. Yeast two-hybrid (Y2H) and...
A gateway-compatible yeast one-hybrid system (2004)
Deplancke, Bart, Dupuy, Denis, Vidal, Marc, Walhout, Albertha J. M.
Since the advent of microarrays, vast amounts of gene expression data have been generated. However, these microarray data fail to reveal the transcription regulatory mechanisms that underlie...
Annotation Transfer Between Genomes: Protein-Protein Interologs and Protein-DNA Regulogs (2004)
Yu, Haiyuan, Luscombe, Nicholas M., Lu, Hao Xin, Zhu, Xiaowei, Xia, Yu, Han, Jing-Dong J., ...
Proteins function mainly through interactions, especially with DNA and other proteins. While some large-scale interaction networks are now available for a number of model organisms, their...
Brasch, Michael A., Hartley, James L., Vidal, Marc
Together with metabolites, proteins and RNAs form complex biological systems through highly intricate networks of physical and functional interactions. Large-scale studies aimed at a molecular...
Academia-Industry Collaboration: An Integral Element for Building "Omic" Resources (2004)
Hill, David E., Brasch, Michael A., Del Campo, Anthony A., Doucette-Stamm, Lynn, Garrels, James I., Glaven, Judith, ...
Lamesch, Philippe, Milstein, Stuart, Hao, Tong, Rosenberg, Jennifer, Li, Ning, Sequerra, Reynaldo, ...
The first version of the Caenorhabditis elegans ORFeome cloning project, based on release WS9 of Wormbase (August 1999), provided experimental verifications for ∼55% of predicted protein-encoding...
Hope, Ian A., Stevens, Jonathan, Garner, Anna, Hayes, Josie, Cheo, David L., Brasch, Michael A., ...
The understanding of gene function increasingly requires the characterization of DNA segments containing promoters and their associated regulatory sequences. We describe a novel approach for linking...
A Gateway-Compatible Yeast One-Hybrid System (2004)
Deplancke, Bart, Dupuy, Denis, Vidal, Marc, Walhout, Albertha J.M.
Since the advent of microarrays, vast amounts of gene expression data have been generated. However, these microarray data fail to reveal the transcription regulatory mechanisms that underlie...
High-Throughput Expression of C. elegans Proteins (2004)
Luan, Chi-Hao, Qiu, Shihong, Finley, James B., Carson, Mike, Gray, Rita J., Huang, Wenying, ...
Proteome-scale studies of protein three-dimensional structures should provide valuable information for both investigating basic biology and developing therapeutics. Critical for these endeavors is...
Human ORFeome Version 1.1: A Platform for Reverse Proteomics (2004)
Rual, Jean-François, Hirozane-Kishikawa, Tomoko, Hao, Tong, Bertin, Nicolas, Li, Siming, Dricot, Amélie, ...
The advent of systems biology necessitates the cloning of nearly entire sets of protein-encoding open reading frames (ORFs), or ORFeomes, to allow functional studies of the corresponding proteomes....
Toward Improving Caenorhabditis elegans Phenome Mapping With an ORFeome-Based RNAi Library (2004)
Rual, Jean-François, Ceron, Julian, Koreth, John, Hao, Tong, Nicot, Anne-Sophie, Hirozane-Kishikawa, Tomoko, ...
The recently completed Caenorhabditis elegans genome sequence allows application of high-throughput (HT) approaches for phenotypic analyses using RNA interference (RNAi). As large phenotypic data...
A First Version of the Caenorhabditis elegans Promoterome (2004)
Dupuy, Denis, Li, Qian-Ru, Deplancke, Bart, Boxem, Mike, Hao, Tong, Lamesch, Philippe, ...
An important aspect of the development of systems biology approaches in metazoans is the characterization of expression patterns of nearly all genes predicted from genome sequences. Such...
Generation of the Brucella melitensis ORFeome Version 1.1 (2004)
Dricot, Amélie, Rual, Jean-François, Lamesch, Philippe, Bertin, Nicolas, Dupuy, Denis, Hao, Tong, ...
The bacteria of the Brucella genus are responsible for a worldwide zoonosis called brucellosis. They belong to the α-proteobacteria group, as many other bacteria that live in close association with...
WorfDB: the Caenorhabditis elegans ORFeome Database (2003)
Vaglio, Philippe, Lamesch, Philippe, Reboul, Jérôme, Rual, Jean-François, Martinez, Monica, Hill, David, ...
WorfDB (Worm ORFeome DataBase; http://worfdb.dfci.harvard.edu) was created to integrate and disseminate the data from the cloning of complete set of ∼19 000 predicted protein-encoding Open...
WorfDB: the Caenorhabditis elegans ORFeome Database (2002)
Jérôme Reboul, Jean-françois Rual, Monica Martinez, David Hill, Marc Vidal
WorfDB (Worm ORFeome DataBase;
Structural genomics: A pipeline for providing structures for the biologist (2002)
Chance, Mark R., Bresnick, Anne R., Burley, Stephen K., Jiang, Jian-Sheng, Lima, Christopher D., Sali, Andrej, ...
A Roadmap-based Algorithm for Planning Object Handling in Changing Industrial Plants (1999)
Cherif, Moez, Vidal, Marc, Laugier, Christian
This paper addresses the problem of planning collision-free motions for a fleet of mobile robots moving in a cluttered and changing workspace. We focus on the problem of planning handling operations...
A Roadmap-based Algorithm for Planning Object Handling in Changing Industrial Plants (1999)
Cherif, Moez, Vidal, Marc, Laugier, Christian
This paper addresses the problem of planning collision-free motions for a fleet of mobile robots moving in a cluttered and changing workspace. We focus on the problem of planning handling operations...
Planning Handling Operations in Changing Industrial Plants (1998)
This paper addresses the problem of planning collision-free paths for a fleet of robots moving in a cluttered and changing workspace. We focus on the problem of planning handling operations in an...
Mammalian homologs of seven in absentia regulate DCC via the ubiquitin-proteasome pathway (1997)
Hu, Gang, Zhang, Sheng, Vidal, Marc, Baer, Joshua La, Xu, Tian, Fearon, Eric R.
Kim, Sung-Su, Chen, Yung-Ming, O’Leary, Eileen, Witzgall, Ralph, Vidal, Marc, Bonventre, Joseph V.
The Krüppel-associated box A (KRAB-A) domain is an evolutionarily conserved transcriptional repressor domain present in approximately one-third of zinc finger proteins of the Cys2-His2 type. Using...
Kennedy, Brian K., Liu, Oliver W., Dick, Fred A., Dyson, Nick, Harlow, Ed, Vidal, Marc
We have developed a yeast model system to address transcriptional repression by the retinoblastoma protein (pRB). When fused to the DNA-binding domain of Gal4p (DB-pRB), pRB can repress transcription...
WorfDB: the Caenorhabditis elegans ORFeome Database
Vaglio, Philippe, Lamesch, Philippe, Reboul, Jérôme, Rual, Jean-François, Martinez, Monica, Hill, David, ...
WorfDB (Worm ORFeome DataBase; http://worfdb.dfci.harvard.edu) was created to integrate and disseminate the data from the cloning of complete set of ∼19 000 predicted protein-encoding Open Reading...
Matthews, Lisa R., Vaglio, Philippe, Reboul, Jérôme, Ge, Hui, Davis, Brian P., Garrels, James, ...
Protein interaction maps have provided insight into the relationships among the predicted proteins of model organisms for which a genome sequence is available. These maps have been useful in...
Mammalian homologs of seven in absentia regulate DCC via the ubiquitin–proteasome pathway
Hu, Gang, Zhang, Sheng, Vidal, Marc, Baer, Joshua La, Xu, Tian, Fearon, Eric R.
DCC (deleted in colorectal cancer) is postulated to function as transmembrane receptor for the axon and cell guidance factor netrin-1. We report here that the DCC cytoplasmic domain binds to proteins...
Ronco, Lucienne V., Karpova, Alla Y., Vidal, Marc, Howley, Peter M.
Interferon regulatory factor-3 (IRF-3) was found to specifically interact with HPV16 E6 in a yeast two-hybrid screen. IRF-3 is activated by the presence of double-stranded RNA or by virus infection...
Safi, Alexias, Vandromme, Marie, Caussanel, Sabine, Valdacci, Laure, Baas, Dominique, Vidal, Marc, ...
In this work, we report the implication of the pleckstrin homology (PH) domain-containing protein CKIP-1 in phosphatidylinositol 3-kinase (PI3-K)-regulated muscle differentiation. CKIP-1 is...
Annotation Transfer Between Genomes: Protein–Protein Interologs and Protein–DNA Regulogs
Yu, Haiyuan, Luscombe, Nicholas M., Lu, Hao Xin, Zhu, Xiaowei, Xia, Yu, Han, Jing-Dong J., ...
Proteins function mainly through interactions, especially with DNA and other proteins. While some large-scale interaction networks are now available for a number of model organisms, their...
Combining biological networks to predict genetic interactions
Wong, Sharyl L., Zhang, Lan V., Tong, Amy H. Y., Li, Zhijian, Goldberg, Debra S., King, Oliver D., ...
Genetic interactions define overlapping functions and compensatory pathways. In particular, synthetic sick or lethal (SSL) genetic interactions are important for understanding how an organism...
Lamesch, Philippe, Milstein, Stuart, Hao, Tong, Rosenberg, Jennifer, Li, Ning, Sequerra, Reynaldo, ...
The first version of the Caenorhabditis elegans ORFeome cloning project, based on release WS9 of Wormbase (August 1999), provided experimental verifications for ∼55% of predicted protein-encoding...
Hope, Ian A., Stevens, Jonathan, Garner, Anna, Hayes, Josie, Cheo, David L., Brasch, Michael A., ...
The understanding of gene function increasingly requires the characterization of DNA segments containing promoters and their associated regulatory sequences. We describe a novel approach for linking...
A Gateway-Compatible Yeast One-Hybrid System
Deplancke, Bart, Dupuy, Denis, Vidal, Marc, Walhout, Albertha J.M.
Since the advent of microarrays, vast amounts of gene expression data have been generated. However, these microarray data fail to reveal the transcription regulatory mechanisms that underlie...
High-Throughput Expression of C. elegans Proteins
Luan, Chi-Hao, Qiu, Shihong, Finley, James B., Carson, Mike, Gray, Rita J., Huang, Wenying, ...
Proteome-scale studies of protein three-dimensional structures should provide valuable information for both investigating basic biology and developing therapeutics. Critical for these endeavors is...
Human ORFeome Version 1.1: A Platform for Reverse Proteomics
Rual, Jean-François, Hirozane-Kishikawa, Tomoko, Hao, Tong, Bertin, Nicolas, Li, Siming, Dricot, Amélie, ...
The advent of systems biology necessitates the cloning of nearly entire sets of protein-encoding open reading frames (ORFs), or ORFeomes, to allow functional studies of the corresponding proteomes....
Toward Improving Caenorhabditis elegans Phenome Mapping With an ORFeome-Based RNAi Library
Rual, Jean-François, Ceron, Julian, Koreth, John, Hao, Tong, Nicot, Anne-Sophie, Hirozane-Kishikawa, Tomoko, ...
The recently completed Caenorhabditis elegans genome sequence allows application of high-throughput (HT) approaches for phenotypic analyses using RNA interference (RNAi). As large phenotypic data...
A First Version of the Caenorhabditis elegans Promoterome
Dupuy, Denis, Li, Qian-Ru, Deplancke, Bart, Boxem, Mike, Hao, Tong, Lamesch, Philippe, ...
An important aspect of the development of systems biology approaches in metazoans is the characterization of expression patterns of nearly all genes predicted from genome sequences. Such...
Generation of the Brucella melitensis ORFeome Version 1.1
Dricot, Amélie, Rual, Jean-François, Lamesch, Philippe, Bertin, Nicolas, Dupuy, Denis, Hao, Tong, ...
The bacteria of the Brucella genus are responsible for a worldwide zoonosis called brucellosis. They belong to the α-proteobacteria group, as many other bacteria that live in close association with...
Walhout, Albertha J.M., Vidal, Marc
Large-scale sequencing projects have predicted high numbers of gene products for which no functional information is yet available. Hence, large-scale projects, such as gene knockouts, gene expression...
New genes with roles in the C. elegans embryo revealed using RNAi of ovary-enriched ORFeome clones
Fernandez, Anita G., Gunsalus, Kristin C., Huang, Jerry, Chuang, Ling-Shiang, Ying, Nancy, Liang, Hsiao-lan, ...
Several RNA interference (RNAi)-based functional genomic projects have been performed in Caenorhabditis elegans to identify genes required during embryogenesis. These studies have demonstrated that...
Closing in on the C. elegans ORFeome by cloning TWINSCAN predictions
Wei, Chaochun, Lamesch, Philippe, Arumugam, Manimozhiyan, Rosenberg, Jennifer, Hu, Ping, Vidal, Marc, ...
The genome of Caenorhabditis elegans was the first animal genome to be sequenced. Although considerable effort has been devoted to annotating it, the standard WormBase annotation contains thousands...
A gene expression fingerprint of C. elegans embryonic motor neurons
Fox, Rebecca M, Von Stetina, Stephen E, Barlow, Susan J, Shaffer, Christian, Olszewski, Kellen L, Moore, Jason H, ...
A protein–protein interaction map of the Caenorhabditis elegans 26S proteasome
Davy, Anne, Bello, Paul, Thierry-Mieg, Nicolas, Vaglio, Philippe, Hitti, Joseph, Doucette-Stamm, Lynn, ...
The ubiquitin-proteasome proteolytic pathway is pivotal in most biological processes. Despite a great level of information available for the eukaryotic 26S proteasome—the protease responsible for...
Davison, Ewa M., Harrison, Melissa M., Walhout, Albertha J. M., Vidal, Marc, Horvitz, H. Robert
Ras-mediated vulval development in C. elegans is inhibited by the functionally redundant sets of class A, B, and C synthetic Multivulva (synMuv) genes. Three of the class B synMuv genes encode an...
Intrinsic Disorder Is a Common Feature of Hub Proteins from Four Eukaryotic Interactomes
Haynes, Chad, Oldfield, Christopher J, Ji, Fei, Klitgord, Niels, Cusick, Michael E, Radivojac, Predrag, ...
Recent proteome-wide screening approaches have provided a wealth of information about interacting proteins in various organisms. To test for a potential association between protein connectivity and...
Reece-Hoyes, John S, Shingles, Jane, Dupuy, Denis, Grove, Christian A, Walhout, Albertha JM, Vidal, Marc, ...
Kritikou, Ekaterini A., Milstein, Stuart, Vidalain, Pierre-Olivier, Lettre, Guillaume, Bogan, Erica, Doukoumetzidis, Kimon, ...
During oocyte development in Caenorhabditis elegans, approximately half of all developing germ cells undergo apoptosis. While this process is evolutionarily conserved from worms to humans, the...
Ceron, Julian, Rual, Jean-François, Chandra, Abha, Dupuy, Denis, Vidal, Marc, Van Den Heuvel, Sander
Confirmation of Organized Modularity in the Yeast Interactome
Bertin, Nicolas, Simonis, Nicolas, Dupuy, Denis, Cusick, Michael E, Han, Jing-Dong J, Fraser, Hunter B, ...
Epstein–Barr virus and virus human protein interaction maps
Calderwood, Michael A., Venkatesan, Kavitha, Xing, Li, Chase, Michael R., Vazquez, Alexei, Holthaus, Amy M., ...
A comprehensive mapping of interactions among Epstein–Barr virus (EBV) proteins and interactions of EBV proteins with human proteins should provide specific hypotheses and a broad perspective on...
Goh, Kwang-Il, Cusick, Michael E., Valle, David, Childs, Barton, Vidal, Marc, Barabási, Albert-László
A network of disorders and disease genes linked by known disorder–gene associations offers a platform to explore in a single graph-theoretic framework all known phenotype and disease gene...
Fas-activated serine/threonine phosphoprotein (FAST) is a regulator of alternative splicing
Simarro, Maria, Mauger, David, Rhee, Kirsten, Pujana, Miguel A., Kedersha, Nancy L., Yamasaki, Satoshi, ...
Fas-activated serine/threonine phosphoprotein (FAST) is a survival protein that is tethered to the outer mitochondrial membrane. In cells subjected to environmental stress, FAST moves to stress...
Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions
Kerrien, Samuel, Orchard, Sandra, Montecchi-Palazzi, Luisa, Aranda, Bruno, Quinn, Antony F, Vinod, Nisha, ...
Wang, Haidong, Segal, Eran, Ben-Hur, Asa, Li, Qian-Ru, Vidal, Marc, Koller, Daphne
InSite is a computational method that integrates high-throughput protein and sequence data to infer the specific binding regions of interacting protein pairs.
Structural genomics: A pipeline for providing structures for the biologist
Chance, Mark R., Bresnick, Anne R., Burley, Stephen K., Jiang, Jian-Sheng, Lima, Christopher D., Sali, Andrej, ...
Yeast Two-Hybrid Systems and Protein Interaction Mapping Projects for Yeast and Worm
Walhout, Albertha J. M., Boulton, Simon J., Vidal, Marc
The availability of complete genome sequences necessitates the development of standardized functional assays to analyse the tens of thousands of predicted gene products in high-throughput...
Revisiting the Saccharomyces cerevisiae predicted ORFeome
Li, Qian-Ru, Carvunis, Anne-Ruxandra, Yu, Haiyuan, Han, Jing-Dong J., Zhong, Quan, Simonis, Nicolas, ...
Accurately defining the coding potential of an organism, i.e., all protein-encoding open reading frames (ORFs) or “ORFeome,” is a prerequisite to fully understand its biology. ORFeome annotation...
VirusMINT: a viral protein interaction database
Chatr-aryamontri, Andrew, Ceol, Arnaud, Peluso, Daniele, Nardozza, Aurelio, Panni, Simona, Sacco, Francesca, ...
Understanding the consequences on host physiology induced by viral infection requires complete understanding of the perturbations caused by virus proteins on the cellular protein interaction network....
Tonikian, Raffi, Xin, Xiaofeng, Toret, Christopher P., Gfeller, David, Landgraf, Christiane, Panni, Simona, ...
A genome-scale specificity and interaction map for yeast SH3 domain-containing proteins reveal how family members show selective binding to target proteins and predicts the dynamic localization of...