ChiBE: interactive visualization and manipulation of BioPAX pathway models (2010)
Babur, Ozgun, Dogrusoz, Ugur, Demir, Emek, Sander, Chris
Summary: Representing models of cellular processes or pathways in a graphically rich form facilitates interpretation of biological observations and generation of new hypotheses. Solving biological...
Erratum: The Systems Biology Graphical Notation (2009)
Nicolas Le Novère, Michael Hucka, Huaiyu Mi, Stuart Moodie, Falk Schreiber, Anatoly Sorokin, ...
The Systems Biology Graphical Notation (2009)
Le Novère, Nicolas, Hucka, Michael, Mi, Huaiyu, Moodie, Stuart, Schreiber, Falk, Sorokin, Anatoly, ...
Circuit diagrams and Unified Modeling Language diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software...
Report on EU-USA workshop: how systems biology can advance cancer research. (2009)
Aebersold, Ruedi, Auffray, Charles, Baney, Erin, Barillot, Emmanuel, Brazma, Alvis, Brett, Catherine, ...
The main conclusion is that systems biology approaches can indeed advance cancer research, having already proved successful in a very wide variety of cancer-related areas, and are likely to prove...
Models from experiments: combinatorial drug perturbations of cancer cells (2008)
Sven Nelander, Weiqing Wang, Björn Nilsson, Qing-Bai She, Christine Pratilas, Neal Rosen, ...
Introducing meta-services for biomedical information extraction (2008)
Leitner, Florian, Krallinger, Martin, Rodriguez-Penagos, Carlos, Hakenberg, Jörg, Plake, Conrad, Kuo, Cheng-Ju, ...
Abstract We introduce the first meta-service for information extraction in molecular biology, the BioCreative MetaServer (BCMS; http://bcms.bioinfo.cnio.es/ ). This prototype platform is a joint...
A Specificity Map for the PDZ Domain Family (2008)
Raffi Tonikian, Yingnan Zhang, Stephen L. Sazinsky, Bridget Currell, Jung-Hua Yeh, Boris Reva, ...
PDZ domains are protein–protein interaction modules that recognize specific C-terminal sequences to assemble protein complexes in multicellular organisms. By scanning billions of random peptides,...
Introducing meta-services for biomedical information extraction (2008)
Leitner, Florian, Krallinger, Martin, Rodriguez-Penagos, Carlos, Hakenberg, Jorg, Plake, Conrad, Kuo, Cheng-Ju, ...
We introduce the first meta-service for information extraction in molecular biology, the BioCreative MetaServer (BCMS; http://bcms.bioinfo.cnio.es/). This prototype platform is a joint effort of 13...
Introducing meta-services for biomedical information extraction (2008)
Leitner, Florian, Krallinger, Martin, Rodriguez-Penagos, Carlos, Hakenberg, Jorg, Plake, Conrad, Kuo, Cheng-Ju, ...
We introduce the first meta-service for information extraction in molecular biology, the BioCreative MetaServer (BCMS; http://bcms.bioinfo.cnio.es/). This prototype platform is a joint effort of 13...
Predicting protein structure using hidden Markov models (2008)
Kevin Karplus Y, David Haussler, Kimmen Sjolander, Richard Hughey, Christian Barrett, Liisa Holm, ...
We discuss how methods based on hidden Markov models performed in the fold-recognition section of the CASP2 experiment. Hidden Markov models were built for a representative set of just over one...
Predicting cancer involvement of genes from heterogeneous data (2008)
Aragues, Ramon, Sander, Chris, Oliva, Baldo
Abstract Background Systematic approaches for identifying proteins involved in different types of cancer are needed. Experimental techniques such as microarrays are being used to characterize cancer,...
The microRNA.org resource: targets and expression (2008)
Betel, Doron, Wilson, Manda, Gabow, Aaron, Marks, Debora S., Sander, Chris
MicroRNA.org (http://www.microrna.org) is a comprehensive resource of microRNA target predictions and expression profiles. Target predictions are based on a development of the miRanda algorithm which...
Determinants of protein function revealed by combinatorial entropy optimization (2007)
Reva, Boris, Antipin, Yevgeniy, Sander, Chris
Abstract We use a new algorithm (combinatorial entropy optimization [CEO]) to identify specificity residues and functional subfamilies in sets of proteins related by evolution. Specificity residues...
Computational Analysis of Mouse piRNA Sequence and Biogenesis (2007)
Doron Betel, Robert Sheridan, Debora S. Marks, Chris Sander
The recent discovery of a new class of 30-nucleotide long RNAs in mammalian testes, called PIWI-interacting RNA (piRNA), with similarities to microRNAs and repeat-associated small interfering RNAs...
Computational analysis of mouse piRNA sequence and biogenesis (2007)
Doron Betel, Robert Sheridan, Debora Marks, Chris Sander
The recent discovery of a new class of 30 nucleotide long RNAs in mammalian testes, called PIWI-interacting RNA (piRNAs), with similarities to microRNAs and rasiRNAs, has raised puzzling questions...
Cotignola, Javier, Reva, Boris, Mitra, Nandita, Ishill, Nicole, Chuai, Shaokun, Patel, Ami, ...
Abstract Background Cutaneous Malignant Melanoma causes over 75% of skin cancer-related deaths, and it is clear that many factors may contribute to the outcome. Matrix Metalloproteinases (MMPs) play...
Jomol P. Mathew, Barry S. Taylor, Gary D. Bader, Saiju Pyarajan, Marco Antoniotti, Arul M. Chinnaiyan, ...
CancerGenes: a gene selection resource for cancer genome projects (2007)
Higgins, Maureen E., Claremont, Martine, Major, John E., Sander, Chris, Lash, Alex E.
The genome sequence framework provided by the human genome project allows us to precisely map human genetic variations in order to study their association with disease and their direct effects on...
cPath: open source software for collecting, storing, and querying biological pathways (2006)
Cerami, Ethan G, Bader, Gary D, Gross, Benjamin E, Sander, Chris
Abstract Background Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220...
Signal Processing in the TGF-β Superfamily Ligand-Receptor Network (2006)
Jose M. G. Vilar, Ronald Jansen, Chris Sander
The TGF-β pathway plays a central role in tissue homeostasis and morphogenesis. It transduces a variety of extracellular signals into intracellular transcriptional responses that control a plethora...
Bmc Bioinformatics, Chris Sander
Software cPath: open source software for collecting, storing, and querying biological pathways
CancerGenes: a gene selection resource for cancer genome projects (2006)
Higgins, Maureen E., Claremont, Martine, Major, John E., Sander, Chris, Lash, Alex E.
The genome sequence framework provided by the human genome project allows us to precisely map human genetic variations in order to study their association with disease and their direct effects on...
Pathguide: a Pathway Resource List (2006)
Bader, Gary D., Cary, Michael P., Sander, Chris
Pathguide: the Pathway Resource List (http://pathguide.org) is a meta-database that provides an overview of more than 190 web-accessible biological pathway and network databases. These include...
CancerGenes: a gene selection resource for cancer genome projects (2006)
Higgins, Maureen E., Claremont, Martine, Major, John E., Sander, Chris, Lash, Alex E.
The genome sequence framework provided by the human genome project allows us to precisely map human genetic variations in order to study their association with disease and their direct effects on...
Signal processing in the TGF-β superfamily ligand-receptor network (2005)
Jose M. G. Vilar, Ronald Jansen, Chris Sander
The TGF-β pathway plays a central role in tissue homeostasis and morphogenesis. It transduces a variety of extracellular signals into intracellular transcriptional responses that control a plethora...
Signal processing in the TGF-beta superfamily ligand-receptor network (2005)
Vilar, Jose M. G., Jansen, Ronald, Sander, Chris
The TGF-beta pathway plays a central role in tissue homeostasis and morphogenesis. It transduces a variety of extracellular signals into intracellular transcriptional responses that control a...
MicroRNA profiling of the murine hematopoietic system (2005)
Monticelli, Silvia, Ansel, K Mark, Xiao, Changchun, Socci, Nicholas D, Krichevsky, Anna M, Thai, To-Ha, ...
Abstract Background MicroRNAs (miRNAs) are a class of recently discovered noncoding RNA genes that post-transcriptionally regulate gene expression. It is becoming clear that miRNAs play an important...
Correction: Human MicroRNA Targets (2005)
Bino John, Anton J. Enright, Alexei Aravin, Thomas Tuschl, Chris Sander, Debora S. Marks
Correction: Human MicroRNA Targets (2005)
Bino John, Anton J. Enright, Alexei Aravin, Thomas Tuschl, Chris Sander, Debora S. Marks
Identification of microRNAs of the herpesvirus family (2005)
Sébastien Pfeffer, Alain Sewer, Mariana Lagos-Quintana, Robert Sheridan, Chris Sander, Friedrich A Grässer, ...
The developmental miRNA profiles of zebrafish as determined by small RNA cloning (2005)
Chen, Po Yu, Manninga, Heiko, Slanchev, Krasimir, Chien, Minchen, Russo, James J., Ju, Jingyue, ...
MicroRNAs (miRNAs) represent a family of small, regulatory, noncoding RNAs that are found in plants and animals. Here, we describe the miRNA profile of the zebrafish Danio rerio resolved in a...
Bino John, Anton J. Enright, Alexei Aravin, Thomas Tuschl, Chris Sander, Debora S. Marks
This computational analysis provides evidence that as many as 10% of human genes are targets for regulation by small RNA molecules called microRNAs.
Bino John, Anton J. Enright, Alexei Aravin, Thomas Tuschl, Chris Sander, Debora S. Marks
MicroRNAs (miRNAs) interact with target mRNAs at specific sites to induce cleavage of the message or inhibit translation. The specific function of most mammalian miRNAs is unknown. We have predicted...
Henning Hermjakob, Luisa Montecchi-Palazzi, Gary Bader, Jérôme Wojcik, Lukasz Salwinski, Arnaud Ceol, ...
MicroRNA targets in Drosophila (2003)
Enright, Anton J, John, Bino, Gaul, Ulrike, Tuschl, Thomas, Sander, Chris, Marks, Debora S
Abstract Background The recent discoveries of microRNA (miRNA) genes and characterization of the first few target genes regulated by miRNAs in Caenorhabditis elegans and Drosophila melanogaster have...
The amino-acid mutational spectrum of human genetic disease (2003)
Vitkup, Dennis, Sander, Chris, Church, George M
Abstract Background Nonsynonymous mutations in the coding regions of human genes are responsible for phenotypic differences between humans and for susceptibility to genetic disease. Computational...
MicroRNA Targets in Drosophila (2003)
Enright, Anton, John, Bino, Gaul, Ulrike, Tuschl, Thomas, Sander, Chris, Marks, Debora
Abstract The recent discoveries of microRNAs (miRNAs) and characterization of the first few targets of their gene products in Caenorhabditis elegans and Drosophila melanogaster have set the stage for...
Characterizing gene sets with FuncAssociate (2003)
Berriz, Gabriel F., King, Oliver D., Bryant, Barbara, Sander, Chris, Roth, Frederick P.
Summary: FuncAssociate is a web-based tool to help researchers use Gene Ontology attributes to characterize large sets of genes derived from experiment. Distinguishing features of FuncAssociate...
Evaluation of annotation strategies using an entire genome sequence (2003)
Iliopoulos, Ioannis, Tsoka, Sophia, Andrade, Miguel A., Enright, Anton J., Carroll, Mark, Poullet, Patrick, ...
Motivation: Genome-wide functional annotation either by manual or automatic means has raised considerable concerns regarding the accuracy of assignments and the reproducibility of methodologies. In...
Kresse, Hans P., Czubayko, Martin, Nyakatura, Gerald, Vriend, Gerrit, Sander, Chris, Bloecker, Helmut
We converted the small homodimeric four-helix bundle repressor of primer protein (Rop) into a monomeric four-helix bundle by introduction of connecting loops. Both left- and right-handed four-helix...
Genome sequences and great expectations (2000)
Iliopoulos, Ioannis, Tsoka, Sophia, Andrade, Miguel A, Janssen, Paul, Audit, Benjamin, Tramontano, Anna, ...
Abstract To assess how automatic function assignment will contribute to genome annotation in the next five years, we have performed an analysis of 31 available genome sequences. An emerging pattern...
CAST: an iterative algorithm for the complexity analysis of sequence tracts (2000)
Promponas, Vasilis J., Enright, Anton J., Tsoka, Sophia, Kreil, David P., Leroy, Christophe, Hamodrakas, Stavros, ...
Motivation: Sensitive detection and masking of low-complexity regions in protein sequences. Filtered sequences can be used in sequence comparison without the risk of matching compositionally biased...
The HSSP database of protein structure-sequence alignments and family profiles (1998)
Chris Dodge, Reinhard Schneider, Chris Sander
HSSP (http://www.sander.embl-ebi.ac.uk/hssp/ ) is a derived database merging structure (3-D) and sequence (1-D) information. For each protein of known 3D structure from the Protein Data Bank (PDB),...
Predicting protein structure using hidden Markov models (1997)
Kevin Karplus, Kimmen Sjölander, Christian Barrett, Melissa Cline, David Haussler, Richard Hughey, ...
We discuss how methods based on hidden Markov models performed in the fold-recognition section of the CASP2 experiment. Hidden Markov models were built for a representative set of just over one...
Predicting protein structure using hidden Markov models (1997)
Kevin Karplus Computer, Kevin Karplus, Kimmen Sjolander, Christian Barrett, Melissa Cline, David Haussler, ...
We discuss how methods based on hidden Markov models performed in the fold-recognition section of the CASP2 experiment. Hidden Markov models were built for a representative set of just over one...
Predicting protein structure using hidden Markov models (1997)
Kevin Karplus, Kimmen Sjölander, Christian Barrett, Melissa Cline, David Haussler, Richard Hughey, ...
We discuss how methods based on hidden Markov models performed in the fold-recognition section of the CASP2 experiment. Hidden Markov models were built for a representative set of just over one...
Objectively judging the quality of a protein structure from a Ramachandran plot (1997)
Hooft, Rob W.W., Sander, Chris, Vriend, Gerrit
Motivation Statistical methods that compare observed and expected distributions of experimental observables provide powerful tools for the quality control of protein structures. The distribution of...
Andrade, Miguel, Casari, Georg, De Daruvar, Antoine, Sander, Chris, Schneider, Reinhard, Tamames, Javier, ...
Errors in protein structures (1996)
Rob W. W. Hooft, Gert Vriend, Chris Sander, Enrique E. Abola
Genequiz II: Automatic Function Assignment For Genome Sequence Analysis (1996)
Georg Casari, Christos Ouzounis, Alfonso Valencia, Chris Sander, Embl Heidelberg
GeneQuiz II, the updated version of an integrated system for large-scale biological sequence analysis. The main improvement of the system consists of a module that allows a fully automatic evaluation...
Genequiz II: Automatic Function Assignment For Genome Sequence Analysis (1996)
Georg Casari, Christos Ouzounis, Alfonso Valencia, Chris Sander, Embl Heidelberg
n integrated system for large-scale biological sequence analysis. The main improvement of the system consists of a module that allows a fully automatic evaluation of results and function assignment....
The prediction of protein contacts from multiple sequence alignments (1996)
Thomas, David J., Casari, Georg, Sander, Chris
We have studied the question of how much extra predictive power the correlated mutational behaviour of pairs of amino acid residues separated along a sequence has concerning the likelihood of those...
Downloaded From, C. Ouzounis, P. Bork, G. Casari, C. Sander, Christos Ouzounis, ...
Article cited in:
Transmembrane helices predicted at 95% accuracy (1995)
Burkhard Rost, Rita Casadio, Piero Fariselli, Chris Sander
We describe a neural network system that predicts the locations of transmembrane helices in integral membrane proteins. By using evolutionary information as input to the network system, the method...
Novel protein families in archaean genomes (1995)
Ouzounis, Christos, Kyrpides, Nikos, Sander, Chris
In a quest for novel functions in archaea, all archaean hypothetical open reading frames (ORFs), as annotated in the Swiss-Prot protein sequence database, were used to search the latest databases for...
PHD-an automatic mail server for protein secondary structure prediction (1994)
Rost, Burkhard, Sander, Chris, Schneider, Reinhard
By the middle of 1993, >30 000 protein sequences had been listed. For 1000 of these, the three-dimensional (tertiary) structure has been experimentally solved. Another 7000 can be modelled by...
Holm, Liisa, Sander, Chris, Rüterjans, Heinz, Schnarr, Manfred, Fogh, Rasmus, Boelens, Rolf, ...
Comparison of structures can reveal surprising connections between protein families and provide new insights into the relationship between sequence, structure and function. The solution structure of...
A novel search method for protein sequence-structure relations using property profiles (1994)
Vriend, Gerrit, Sander, Chris, Stouten, F.W.
In protein engineering and design it is very important that residues can be inspected in their specific environment. A standard relational database system cannot serve this purpose adequately because...
Koonin, Eugene V., Bork, Peer, Sander, Chris
Using computer methods for database search, multiple alignment, protein sequence motif analysis and secondary structure prediction, a putative new RNA-binding motif was identified. The novel motif is...
Modeling of transmembrane seven helix bundles (1993)
Cronet, Philippe, Sander, Chris, Vriend, Gert
Transmembrane seven helix bundles form a large family of membrane inserted receptors and are responsible for a wide range of biological functions. Experimental data suggest that their overall...
Secondary structure prediction of all-helical proteins in two states (1993)
Can secondary structure prediction be improved by prediction rules that focus on a particular structural class of proteins? To help answer this question, we have assessed the accuracy of...
Sander, Chris, Vriend, Gerrit, Bazan, Fernando, Horovitz, Amnon, Nakamura, Haruki, Ribas, Luis, ...
What is the current state of the art in protein design? This question was approached in a recent two-week protein design workshop sponsored by EMBO and held at the EMBL in Heidelberg. The goals were...
Selection of representative protein data sets (1991)
Downloaded From, U. Hobohm, M. Scharf, R. Schneider, C. Sander, Email Alerting, ...
Article cited in:
We have performed computer searches in the database of known protein sequences for proteins similar in sequence to bacteriophage regulatory proteins of known 3-D structure. The searches are more...
Conservation of residue interactions in a family of Ca-binding proteins (1989)
In the TNC family of Ca-binding proteins (calmodulin, parvalbumin, intestinal calcium binding protein and troponin C) {small tilde} 70 well-conserved amino acid sequences and six crystal structures...
Genome sequences and great expectations
Iliopoulos, Ioannis, Tsoka, Sophia, Andrade, Miguel A, Janssen, Paul, Audit, Benjamin, Tramontano, Anna, ...
To assess how automatic function assignment will contribute to genome annotation in the next five years, we have performed an analysis of 31 available genome sequences. An emerging pattern is that...
The amino-acid mutational spectrum of human genetic disease
Vitkup, Dennis, Sander, Chris, Church, George M
The human disease spectrum is compared to the spectra of mutual amino-acid mutation frequencies, non-disease polymorphisms in human genes, and substitutions fixed between species.
MicroRNA targets in Drosophila
Enright, Anton J, John, Bino, Gaul, Ulrike, Tuschl, Thomas, Sander, Chris, Marks, Debora S
A computational method for whole-genome prediction of microRNA target genes is presented. Application of this method to the Drosophila melanogaster, Drosophila pseudoobscura and Anopheles gambiae...
John, Bino, Enright, Anton J, Aravin, Alexei, Tuschl, Thomas, Sander, Chris, Marks, Debora S
MicroRNAs (miRNAs) interact with target mRNAs at specific sites to induce cleavage of the message or inhibit translation. The specific function of most mammalian miRNAs is unknown. We have predicted...
The developmental miRNA profiles of zebrafish as determined by small RNA cloning
Chen, Po Yu, Manninga, Heiko, Slanchev, Krasimir, Chien, Minchen, Russo, James J., Ju, Jingyue, ...
MicroRNAs (miRNAs) represent a family of small, regulatory, noncoding RNAs that are found in plants and animals. Here, we describe the miRNA profile of the zebrafish Danio rerio resolved in a...
Correction: Human MicroRNA Targets
John, Bino, Enright, Anton J, Aravin, Alexei, Tuschl, Thomas, Sander, Chris, Marks, Debora S
MicroRNA profiling of the murine hematopoietic system
Monticelli, Silvia, Ansel, K Mark, Xiao, Changchun, Socci, Nicholas D, Krichevsky, Anna M, Thai, To-Ha, ...
The first report of systematic miRNA profiling in cells of the hematopoietic system suggests that, in addition to regulating commitment to particular cellular lineages, miRNAs might have a general...
Pathguide: a Pathway Resource List
Bader, Gary D., Cary, Michael P., Sander, Chris
Pathguide: the Pathway Resource List () is a meta-database that provides an overview of more than 190 web-accessible biological pathway and network databases. These include databases on metabolic...
Signal Processing in the TGF-β Superfamily Ligand-Receptor Network
Vilar, Jose M. G, Jansen, Ronald, Sander, Chris
The TGF-β pathway plays a central role in tissue homeostasis and morphogenesis. It transduces a variety of extracellular signals into intracellular transcriptional responses that control a plethora...
cPath: open source software for collecting, storing, and querying biological pathways
Cerami, Ethan G, Bader, Gary D, Gross, Benjamin E, Sander, Chris
Genome sequences and great expectations
Iliopoulos, Ioannis, Tsoka, Sophia, Andrade, Miguel A, Janssen, Paul, Audit, Benjamin, Tramontano, Anna, ...
To assess how automatic function assignment will contribute to genome annotation in the next five years, we have performed an analysis of 31 available genome sequences. An emerging pattern is that...
The amino-acid mutational spectrum of human genetic disease
Vitkup, Dennis, Sander, Chris, Church, George M
The human disease spectrum is compared to the spectra of mutual amino-acid mutation frequencies, non-disease polymorphisms in human genes, and substitutions fixed between species.
MicroRNA targets in Drosophila
Enright, Anton J, John, Bino, Gaul, Ulrike, Tuschl, Thomas, Sander, Chris, Marks, Debora S
A computational method for whole-genome prediction of microRNA target genes is presented. Application of this method to the Drosophila melanogaster, Drosophila pseudoobscura and Anopheles gambiae...
John, Bino, Enright, Anton J, Aravin, Alexei, Tuschl, Thomas, Sander, Chris, Marks, Debora S
MicroRNAs (miRNAs) interact with target mRNAs at specific sites to induce cleavage of the message or inhibit translation. The specific function of most mammalian miRNAs is unknown. We have predicted...
The developmental miRNA profiles of zebrafish as determined by small RNA cloning
Chen, Po Yu, Manninga, Heiko, Slanchev, Krasimir, Chien, Minchen, Russo, James J., Ju, Jingyue, ...
MicroRNAs (miRNAs) represent a family of small, regulatory, noncoding RNAs that are found in plants and animals. Here, we describe the miRNA profile of the zebrafish Danio rerio resolved in a...
Correction: Human MicroRNA Targets
John, Bino, Enright, Anton J, Aravin, Alexei, Tuschl, Thomas, Sander, Chris, Marks, Debora S
MicroRNA profiling of the murine hematopoietic system
Monticelli, Silvia, Ansel, K Mark, Xiao, Changchun, Socci, Nicholas D, Krichevsky, Anna M, Thai, To-Ha, ...
The first report of systematic miRNA profiling in cells of the hematopoietic system suggests that, in addition to regulating commitment to particular cellular lineages, miRNAs might have a general...
Pathguide: a Pathway Resource List
Bader, Gary D., Cary, Michael P., Sander, Chris
Pathguide: the Pathway Resource List () is a meta-database that provides an overview of more than 190 web-accessible biological pathway and network databases. These include databases on metabolic...
Signal Processing in the TGF-β Superfamily Ligand-Receptor Network
Vilar, Jose M. G, Jansen, Ronald, Sander, Chris
The TGF-β pathway plays a central role in tissue homeostasis and morphogenesis. It transduces a variety of extracellular signals into intracellular transcriptional responses that control a plethora...
cPath: open source software for collecting, storing, and querying biological pathways
Cerami, Ethan G, Bader, Gary D, Gross, Benjamin E, Sander, Chris
CancerGenes: a gene selection resource for cancer genome projects
Higgins, Maureen E., Claremont, Martine, Major, John E., Sander, Chris, Lash, Alex E.
The genome sequence framework provided by the human genome project allows us to precisely map human genetic variations in order to study their association with disease and their direct effects on...
From Bytes to Bedside: Data Integration and Computational Biology for Translational Cancer Research
Mathew, Jomol P, Taylor, Barry S, Bader, Gary D, Pyarajan, Saiju, Antoniotti, Marco, Chinnaiyan, Arul M, ...
Matrix Metalloproteinase-9 (MMP-9) polymorphisms in patients with cutaneous malignant melanoma
Cotignola, Javier, Reva, Boris, Mitra, Nandita, Ishill, Nicole, Chuai, Shaokun, Patel, Ami, ...
Computational Analysis of Mouse piRNA Sequence and Biogenesis
Betel, Doron, Sheridan, Robert, Marks, Debora S, Sander, Chris
The recent discovery of a new class of 30-nucleotide long RNAs in mammalian testes, called PIWI-interacting RNA (piRNA), with similarities to microRNAs and repeat-associated small interfering RNAs...
Cellular cofactors affecting hepatitis C virus infection and replication
Randall, Glenn, Panis, Maryline, Cooper, Jacob D., Tellinghuisen, Timothy L., Sukhodolets, Karen E., Pfeffer, Sebastien, ...
Recently identified hepatitis C virus (HCV) isolates that are infectious in cell culture provide a genetic system to evaluate the significance of virus–host interactions for HCV replication. We...
The microRNA.org resource: targets and expression
Betel, Doron, Wilson, Manda, Gabow, Aaron, Marks, Debora S., Sander, Chris
MicroRNA.org (http://www.microrna.org) is a comprehensive resource of microRNA target predictions and expression profiles. Target predictions are based on a development of the miRanda algorithm which...
Determinants of protein function revealed by combinatorial entropy optimization
Reva, Boris, Antipin, Yevgeniy, Sander, Chris
A new algorithm is presented allows protein specificity residues to be assigned from multiple sequence alignments alone. This information can be used, amongst other things, to infer protein functions.
Functional Copy-Number Alterations in Cancer
Taylor, Barry S., Barretina, Jordi, Socci, Nicholas D., DeCarolis, Penelope, Ladanyi, Marc, Meyerson, Matthew, ...
Understanding the molecular basis of cancer requires characterization of its genetic defects. DNA microarray technologies can provide detailed raw data about chromosomal aberrations in tumor samples....
A Specificity Map for the PDZ Domain Family
Tonikian, Raffi, Zhang, Yingnan, Sazinsky, Stephen L, Currell, Bridget, Yeh, Jung-Hua, Reva, Boris, ...
PDZ domains are protein–protein interaction modules that recognize specific C-terminal sequences to assemble protein complexes in multicellular organisms. By scanning billions of random peptides,...
Introducing meta-services for biomedical information extraction
Leitner, Florian, Krallinger, Martin, Rodriguez-Penagos, Carlos, Hakenberg, Jörg, Plake, Conrad, Kuo, Cheng-Ju, ...
We introduce the first meta-service for information extraction in molecular biology, the BioCreative MetaServer (BCMS; ). This prototype platform is a joint effort of 13 research groups and provides...
Models from experiments: combinatorial drug perturbations of cancer cells
Nelander, Sven, Wang, Weiqing, Nilsson, Björn, She, Qing-Bai, Pratilas, Christine, Rosen, Neal, ...
We present a novel method for deriving network models from molecular profiles of perturbed cellular systems. The network models aim to predict quantitative outcomes of combinatorial perturbations,...
Pratilas, Christine A., Taylor, Barry S., Ye, Qing, Viale, Agnes, Sander, Chris, Solit, David B., ...
Tumors with mutant BRAF and those with receptor tyrosine kinase (RTK) activation have similar levels of phosphorylated ERK, but only the former depend on ERK signaling for proliferation. The...
Veeriah, Selvaraju, Brennan, Cameron, Meng, Shasha, Singh, Bhuvanesh, Fagin, James A., Solit, David B., ...
Tyrosine phosphorylation plays a critical role in regulating cellular function and is a central feature in signaling cascades involved in oncogenesis. The regulation of tyrosine phosphorylation is...
DGCR8-dependent microRNA biogenesis is essential for skin development
Yi, Rui, Pasolli, H. Amalia, Landthaler, Markus, Hafner, Markus, Ojo, Tolulope, Sheridan, Robert, ...
MicroRNAs play important roles in animal development. Numerous conditional knockout (cKO) studies of Dicer have been performed to interrogate the functions of microRNA during mammalian development....