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 | [ image quantification software ] |
| Scanalyze | Stanford software used for processing fuorescent microarray images. Includes semi-automatic definition of grids and complex pixel and spot analyses. Outputs to tab-delimited text files for transfer to any database. |
| F-Scan | NIH software for quantifying fluorescent images. F-Scan requires MATLAB software and a UNIX account. Analyses include scatterplots, multiple image comparison, data merging. |
| P-Scan | NIH software for quantifying peak intensities from images generated from membranes scanned using a phosphoimager. P-Scan requires MATLAB software access and a UNIX account. |
| [ data analysis software ] |
| SAM: Significance Analysis of Microarrays | An excel add-in that supports supervised learning for genomic expression data mining (uses data permutations to provide estimate of False Discovery Rate for multiple testing). |
| BioConductor | Bioconductor is an open source and open development software project based primarily on the R programming language created to provide tools for the analysis and comprehension of genomic data. |
| dChip | DNA-Chip Analyzer (dChip) is a software package implementing model-based expression analysis of oligonucleotide arrays and several high-level analysis procedures (particularly useful for Affymetrix arrays). High-level analysis in dChip includes comparative analysis, hierarchical clustering, SNP analysis etc. (Li and Wong, 2001 [Pubmed]) |
| GenePattern | GenePattern is a software package from the Broad Institute for the analysis of molecular profiles, e.g., genome-wide microarray expression signatures. It includes a collection of analytic and visualization tools, interfaces for the easy construction of analytic pipelines and integration of new modules without additional programming |
| Expression Profiler | A collection of EBI web accessible microarray data analysis tools including clustering and gene ontology tools. |
| Cluster and TreeView | Classic cluster analysis and graphical visualization software from Eisen lab at Stanford. Currently includes hierarchical clustering, self-organizing maps (SOMs), k-means clustering, principal component analysis.Hierarchical clustering methods described in Eisen et al. (1998) PNAS 95:14863. |
| CAGED | CAGED (Cluster Analysis of Gene Expression Dynamics) is a computer program for the analysis of temporal gene expression data. CAGED is based on a method called Bayesian Clustering by Dynamics, which identifies the most probable set of clusters given a set of time series (it can be used as a Bayesian clustering program on a-temporal expression data). |
| Cyber-T | Cyber-T is a a microarray analysis web interface from UCI's Institute for Genomics and Bioinformatics. It accommodates both paired (2-dye) data and data in which control and experiment are on separate experiments (e.g. affymetrix based data). It also supports Bayesian statistical approaches and Bonferroni corrections for significance analysis of differentially expressed clones. GeneX database and analysis tools are written in R and can also be installed locally. |
| TM4 (TIGR) | A package of open source software programs for microarray analysis from J. Craig Venter Institute. The suite includes MIDAS (Microarray Data Analysis System), MADAM (MicroArray DAta Manager), MEV (MultiExperiment Viewer) and the image processing tool Spotfinder. |
| SNOMAD | A collection of algorithms written in R statistical language, directed at the normalization and standardization of DNA microarray data. Useful mostly for paired microarray data. |
| BRB Array Tools | Integrated microsoft excel add-in useful for visualization and statistical analysis of DNA microarray data. Genes can also be annotated by linking to NCBI databases using clone identifiers. |
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| [ functional analysis software ] |
| DAVID and EASE (NIH) |
DAVID (Database for Annotation, Visualization and Integrated Discovery) and EASE (the Expression Analysis Systematic Explorer)provide integrated solutions for the annotation and analysis of genome-scale datasets derived from high-throughput technologies such as microarray and proteomic platforms. |
| Cytoscape | Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. |
| Onto-Express | Onto-Express systematically translates genetic fingerprints into functional profiles. Using strings of accession or cluster identification numbers, Onto-Express searches the public databases and returns tables that correlate expression profiles with the cytogenetic gene locations, the biochemical and molecular functions, the biological processes, cellular components and cellular roles of the translated proteins. |
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| [ selected links to academic core facilities ] |
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Apr, 2013; Christopher E. Mason, Assistant Professor in PBSB Program, was featured in Reuters, Nature, Newsday, CBC news, Huffington Post, The New Yorker, The Washington Post, and other media outlets for his recent paper on gene patents published in Genome Medicine and also for his work as a scientific expert on gene patents for the AMP v. Myriad Genetics case before the US Supreme Court.
Apr, 2013; Sheng Li, a PBSB graduate student in Dr. Christopher E. Mason's lab, won a National Science Foundation Travel Fellowship and was invited to give a speech at the 17th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2013) held at the Tsinghua University for her paper on "An optimized algorithm for detecting and annotating regional differential methylation".
Mar, 2013; Two Graduate Students working with PBSB faculty were awarded competitive graduate research fellowships: (1) Lenore Pipes, a graduate student in the Tri-Institutional Graduate Program in Computational Biology and Medicine, working in the laboratories of Dr. Christopher E. Mason and Dr. Adam Siepel, won a 2013 National Science Foundation (NSF) Graduate Research Fellowship Program (GRFP) Fellowship for her work on de novo transcriptome assembly and genome assembly. Her fellowship will last from 2013-2016. (2) Michael LeVine, a PBSB graduate student working in the lab of Dr. Harel Weinstein was awarded a National Research Service Award (NRSA - F31) to work on "Ligand-Specific Allosteric Modulation by Drugs of Abuse" for the next 4 years, starting June 1, 2013.
Jan, 2013; Dr. Olivier Elemento was awarded a five-year Irma T. Hirschl Career Scientist Award.
Dec, 2012; Mr. Vaja Liluashvili, a visiting graduate student in the Gumus laboratory was awarded a Sao Paulo Research Foundation (FAPESP) full fellowship to present at the international meeting SPAS: Advances in Molecular Oncology: Translating Molecular Biology into Cancer Treatment in Sao Paulo, Brazil 3-8th February 2013. Mr. Liluashivili will present his research with Dr. Zeynep H. Gumus, titled "iCAVE: immersive 3D visualization of complex biomolecular interaction networks".
Sept, 2012; The Campagne laboratory was awarded the best poster award for "Compression of high-throughput sequencing data" at the Wellcome Trust's Genome Informatics 2012 meeting in Cambridge, UK.
May, 2012; Dr. Christopher Mason was featured in a two part profile by the New York Genome Center for his work on non-human primate genomics, gene patenting policy, and other activities.
March, 2012; Michelle Sahai, Ph.D., a Postdoctoral Associate in Harel Weinstein's lab, was awarded a three year Canadian Institutes of Health Research (CIHR) Fellowship for her research on Molecular Mechanisms of the Dopamine Transporter Function: The effects of drugs of abuse.
Feb, 2012; Sayan Mondal, a student in Harel Weinstein's lab, won the Student Research Achievement Award at the Biophysical Society's 2012 Annual Meeting for his poster on the interaction of GPCRs with the membrane.
Jan, 2012; Jan Dlabal, a student from the Lycée Français de New York, was selected as a semi-finalist in the 2012 Intel Science Talent Search, for work on the determination of large-scale genomic structure performed in the lab of Olivier Elemento.
Oct, 2011; Sheila Nirenberg presented a talk, "Can we speak the language of the brain?", at the TEDMED 2011 conference.
A Q & A session followed.
Nov, 2011; GobyWeb binary release. The Campagne laboratory has just released a binary distribution of GobyWeb. This first public release of GobyWeb makes it possible to install the tool locally for non-commercial use. Detailled installation instructions are available on the download page.
Apr, 2011; Dr. Olivier Elemento was awarded an NSF CAREER Grant, the National Science Foundation's most prestigious award in support of junior faculty who exemplify the role of teacher-scholars through outstanding research, excellent education and the integration of education and research.
Nov, 2010; Dr. Sheila Nirenberg's work on artificial retinas has been featured in Technology Review, Wired, Scientific American, and the New Scientist.
Jul, 2009; ChIPseeqer, a comprehensive framework for analysis of ChIP-seq data developed in the Elemento lab, is now available for download. [More]
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