LibGuides: Undergraduate Research Program (URP): Bioinformatics & Genomics @ CSHL

Databases

1000 Genomes Project This link opens in a new window
The goal of the 1000 Genomes Project is to find most genetic variants that have frequencies of at least 1% in the populations studied. This goal can be attained by sequencing many individuals lightly. To sequence a person's genome, many copies of the DNA are broken into short pieces and each piece is sequenced. The many copies of DNA mean that the DNA pieces are more-or-less randomly distributed across the genome. The pieces are then aligned to the reference sequence and joined together. To find the complete genomic sequence of one person with current sequencing platforms requires sequencing that person's DNA the equivalent of about 28 times (called 28X). If the amount of sequence done is only an average of once across the genome (1X), then much of the sequence will be missed, because some genomic locations will be covered by several pieces while others will have none. The deeper the sequencing coverage, the more of the genome will be covered at least once. Also, people are diploid; the deeper the sequencing coverage, the more likely that both chromosomes at a location will be included. In addition, deeper coverage is particularly useful for detecting structural variants, and allows sequencing errors to be corrected.
AceDB This link opens in a new window
AceDB is a genome database system developed since 1989 primarily by Jean Thierry-Mieg (CNRS, Montpellier) and Richard Durbin (Sanger Institute). It provides a custom database kernel, with a non-standard data model designed specifically for handling scientific data flexibly, and a graphical user interface with many specific displays and tools for genomic data. AceDB is used both for managing data within genome projects, and for making genomic data available to the wider scientific community.

AceDB was originally developed for the C.elegans genome project , from which its name was derived: AC. elegans DataBase. However, the tools in it have been generalized to be much more flexible and the same software is now used for many different genomic databases from bacteria to fungi to plants to man. It is also increasingly used for databases with non-biological content.
ACM Digital Library This link opens in a new window
The ACM Digital Library is a research, discovery and networking platform containing: The Full-Text Collection of all ACM publications, including journals, conference proceedings, technical magazines, newsletters and books. A collection of curated and hosted full-text publications from select publishers. The ACM Guide to Computing Literature, a comprehensive bibliographic database focused exclusively on the field of computing. A richly interlinked set of connections among authors, works, institutions, and specialized communities.
Allen Brain Atlas This link opens in a new window
The Allen Brain Atlas resources are a growing collection of online public resources integrating extensive gene expression and neuroanatomical data, complete with a novel suite of search and viewing tools. This portal gives you access to each of these resources by clicking on the button for a particular project or by clicking the project from the banner tab or drop-down menu.
ARTS This link opens in a new window
ARTS: Accurate Recognition of Transcription Starts in Human (now at cBio@mskcc)
arXiv.org This link opens in a new window
A document submission and retrieval system that is heavily used by the physics, mathematics and computer science communities. It has become the primary means of communicating cutting-edge manuscripts on current and ongoing research. Manuscripts are often submitted to the arXiv before they are published by more traditional means.
BAMS This link opens in a new window
The Brain Architecture Management System - an online resource for information about neural circuitry. This rapidly expanding set of inference engines currently has 5 interrelated modules: Brain Parts (gray matter regions, major fiber tracts, and ventricles), Cell Types, Molecules, Connections (between regions and cell types), and Relations (between parts identified different neuroanatomical atlases).
Berkeley Drosophila Genome Project (BDGP) at Lawrence Berkeley National Laboratory This link opens in a new window
The Berkeley Drosophila Genome Project (BDGP) is a consortium of the Drosophila Genome Center, funded by the National Human Genome Research Institute, National Cancer Institute, and Howard Hughes Medical Institute, through its support of work in the Gerald Rubin, Allan Spradling, Roger Hoskins, Hugo Bellen, Susan Celniker, and Gary Karpen laboratories.

The goals of the Drosophila Genome Center are to finish the sequence of the euchromatic genome of Drosophila melanogaster to high quality and to generate and maintain biological annotations of this sequence. In addition to genomic sequencing, the BDGP is 1) producing gene disruptions using P element-mediated mutagenesis on a scale unprecedented in metazoans; 2) characterizing the sequence and expression of cDNAs; and 3) developing informatics tools that support the experimental process, identify features of DNA sequence, and allow us to present up-to-date information about the annotated sequence to the research community.

BIOBASE Knowledge Library (BKL) Proteome

Cancer Genome Atlas This link opens in a new window
The Cancer Genome Atlas (TCGA), a collaboration between the National Cancer Institute (NCI) and National Human Genome Research Institute (NHGRI), has generated comprehensive, multi-dimensional maps of the key genomic changes in 33 types of cancer. The TCGA dataset, 2.5 petabytes of data describing tumor tissue and matched normal tissues from more than 11,000 patients, is publically available and has been used widely by the research community. The data have contributed to more than a thousand studies of cancer by independent researchers and to the TCGA research network publications.
Catalogue of Somatic Mutations in Cancer (COSMIC) This link opens in a new window
All cancers arise as a result of the acquisition of a series of fixed DNA sequence abnormalities, mutations, many of which ultimately confer a growth advantage upon the cells in which they have occurred. There is a vast amount of information available in the published scientific literature about these changes. COSMIC is designed to store and display somatic mutation information and related details and contains information relating to human cancers.
There are two types of data in COSMIC: Expert manual curation data and systematic screen data.
ChromDB This link opens in a new window
The broad mission of ChromDB is display, annotate, and curate sequences of two broad functional classes of biologically important proteins: chromatin-associated proteins (CAPs) and RNA interference-associated proteins. Plant proteins are the major focus of the work support by The Plant Genome Research Program (PGRP) of the National Science Foundation.
CoCoMac This link opens in a new window
Macaque macro connectivity at your fingertips
Cold Spring Harbor Mammalian Promoter Database This link opens in a new window
In the post-genome era, characterization of gene regulation networks has become an important part of genomic research. To succeed in such studies in any organism, a high-quality and comprehensive database of genes and their promoters, transcription factor binding sites, and other cis-regulatory elements is much desired if not a must.

Cold Spring Harbor Laboratory mammalian promoter database (CSHLmpd) used all known transcripts, integrating with predicted transcripts, to construct gene set of human, mouse and rat genomes. For promoter information, we collected known promoter information from multiple resources, together with predicted ones. These promoters were mapped to genome, and linked to related genes. We also compared promoters of orthologous gene groups to detect the sequence conservation in promoter regions.

We expect CSHLmpd to be helpful for research in gene regulation networks by providing guidance for experimental studies such as DNA microarray and chromatin IP. It will also facilitate the building of a foundation upon which we expand our insights into the structure of mouse genome through continued data collection, intelligent data analysis and integration.
Copy Number Variation Project This link opens in a new window
Database of Genomic Variants This link opens in a new window
The objective of the Database of Genomic Variants is to provide a comprehensive summary of structural variation in the human genome. We define structural variation as genomic alterations that involve segments of DNA that are larger than 50bp. The content of the database is only representing structural variation identified in healthy control samples.

The Database of Genomic Variants provides a useful catalog of control data for studies aiming to correlate genomic variation with phenotypic data. The database is continuously updated with new data from peer reviewed research studies. We always welcome suggestions and comments regarding the database from the research community.
Database of Transcriptional Start Sites This link opens in a new window
Supporting transcriptional regulation studies, the DBTSS (DataBase of Transcriptional Start Sites), which represents exact positions of transcriptional start sites (TSSs) in the genome based on our unique experimentally validated TSS sequencing method, TSS-seq.

This database includes TSS data of a major part of human adult and embryonic tissues are covered. DBTSS now contains 491 million TSS tag sequences for collected from a total of 20 tissues and 7 cell cultures. We also integrated our newly generated RNA-seq data of subcellular- fractionated RNAs and ChIP-seq data of histone modifications, RNA polymerase II and several transcriptional regulatory factors in cultured cell lines. We also included recently accumulating external epigenomic data, such as chromatin map of the ENCODE project.
dbCASE This link opens in a new window
dbCASE (database of classified alternative splicing events) is derived by high-quality transcript/genome sequence alignment. "Transcripts" means RefSeq, cDNA (or mRNA) and EST sequences. The alignments for each gene were then converted into a data structure directed acyclic graph (DAG) or splicing graph. This data structure is a natural representation of multiple transcripts, which are not linear any more. Splicing graph allows to detect AS patterns and the supporting evidence efficiently. We have several important extensions in splicing graph to, e.g., estimate exon inclusion rate and transcript coverages.
dbEST This link opens in a new window
dbEST (Nature Genetics 4:332-3;1993) is a division of GenBank that contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms.
ENCODE Project This link opens in a new window
The National Human Genome Research Institute (NHGRI) launched a public research consortium named ENCODE, the Encyclopedia Of DNA Elements, in September 2003, to carry out a project to identify all functional elements in the human genome sequence. The project started with two components - a pilot phase and a technology development phase.

The pilot phase tested and compared existing methods to rigorously analyze a defined portion of the human genome sequence (See: ENCODE Pilot Project). The conclusions from this pilot project were published in June 2007 in Nature and Genome Research [genome.org]. The findings highlighted the success of the project to identify and characterize functional elements in the human genome. The technology development phase also has been a success with the promotion of several new technologies to generate high throughput data on functional elements.

With the success of the initial phases of the ENCODE Project, NHGRI funded new awards in September 2007 to scale the ENCODE Project to a production phase on the entire genome along with additional pilot-scale studies. Like the pilot project, the ENCODE production effort is organized as an open consortium and includes investigators with diverse backgrounds and expertise in the production and analysis of data (See: ENCODE Participants and Projects). This production phase also includes a Data Coordination Center [genome.ucsc.edu] to track, store and display ENCODE data along with a Data Analysis Center to assist in integrated analyses of the data. All data generated by ENCODE participants will be rapidly released into public databases (See: Accessing ENCODE Data) and available through the project's Data Coordination Center.
Ensembl This link opens in a new window
The Ensembl project was started in 1999, some years before the draft human genome was completed. Even at that early stage it was clear that manual annotation of 3 billion base pairs of sequence would not be able to offer researchers timely access to the latest data. The goal of Ensembl was therefore to automatically annotate the genome, integrate this annotation with other available biological data and make all this publicly available via the web. Since the website's launch in July 2000, many more genomes have been added to Ensembl and the range of available data has also expanded to include comparative genomics, variation and regulatory data.

The number of people involved in the project has also steadily increased. Currently, the Ensembl group consists of between 40 and 50 people, divided in a number of teams. The Genebuild team creates the gene sets for the various species. The result of their work is stored in the core databases, which are taken care of by the Software team. This team also develops and maintains the BioMart data mining tool. The Compara, Variation and Regulation teams are responsible for the comparative and the variation and regulatory data, respectively. The Web team makes sure that all data are presented on the website in a clear and user-friendly way. Finally the Outreach team answers questions from users and gives workshops worldwide about the use of Ensembl. The Ensembl project is headed by Paul Flicek and receives input from an independent scientific advisory board.

Ensembl is a joint project between European Bioinformatics Institute (EBI), an outstation of the European Molecular Biology Laboratory (EMBL), and the Wellcome Trust Sanger Institute (WTSI). Both institutes are located on the Wellcome Trust Genome Campus in Hinxton, south of the city of Cambridge, United Kingdom.
Entrez-Gene This link opens in a new window
The Gene database provides detailed information for known and predicted genes defined by nucleotide sequence or map position. Currently, Gene contains more than 14 million entries and includes data from all major taxonomic groups. Each record in the database corresponds to a single gene and is derived from processing by the NCBI Reference Sequence and genome annotation groups. Gene data can be accessed on the web through the Gene home page, programmatically through the Entrez Programming Utilities, or by file transfer through its FTP site.
EPD - Eukaryotic Promoter Database This link opens in a new window
This resource allows the access to several databases of experimentally validated promoters: EPD and EPDnew databases. They differ by the validation technique used and the coverage. EPD is a collection of eukaryotic promoters derived from published articles. Instead, the EPDnew databases (HT-EPD) are the result of merging EPD promoters whith in-house analysis of promoter-specific high-throughput data for selected organisms only. This process gives EPDnew high precision and high coverage.

The Eukaryotic Promoter Database is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. This database contains 4806 promoters from several species.

EPDnew is a new collection of experimentally validated promoters in human, mouse, D. melanogaster and zebrafish genomes. Evidence comes from TSS-mapping from high-throughput expreriments such as CAGE and Oligocapping. ChIP-seq experiments on H2AZ, H3K4me3, Pol-II and DNA methylation are also taken into account during the analysis. The resulting database contains 23360 promoters for the human (H. sapiens) collection, 21239 promoters for the mouse (M. musculus) collection, 15073 promoters for the D. melanogaster collection, 10728 promoters for the zebrafish (D. rerio) collection, 7120 promoters for the worm (C. elegans) collection and 10229 promoters for the A. thaliana collection.
European Conditional Mouse Mutagenesis Programme This link opens in a new window
EUCOMM - The European Conditional Mouse Mutagenesis Program is founder member and European cornerstone of the International Knockout Mouse Consortium (IKMC).
EUCOMM contributes the largest fraction of conditionally trapped and targeted genes in mouse C57BL/6N embryonic stem (ES) cells to the IKMC.
EUCOMM vectors, mutant ES cells and mutant mice are distributed worldwide, enabling functional genomics research in a standardized and cost-effective manner by a much wider biomedical research community than has been possible previously.
EUCOMM mutant ES cells and vectors can be obtained from the European Mouse Mutant Cell Repository (EuMMCR).
FANTOM Functional Annotation of the Mammalian Genome This link opens in a new window
FANTOM is an international research consortium established by Dr. Hayashizaki and his colleagues in 2000 to assign functional annotations to the full-length cDNAs that were collected during the Mouse Encyclopedia Project at RIKEN. FANTOM has since developed and expanded over time to encompass the fields of transcriptome analysis. The object of the project is moving steadily up the layers in the system of life, progressing thus from an understanding of the ‘elements’ - the transcripts - to an understanding of the ‘system’ - the transcriptional regulatory network, in other words the ‘system’ of an individual life form.
Fantom Functional Annotation of Mouse This link opens in a new window
The FANTOM is a collection of functional annotations for the RIKEN full-length cDNA clones and provides not simply the gene functions themselves, but also many other informative and useful data describing functional information about the clones.
Fgenesh This link opens in a new window
FGENESH - Program for predicting multiple genes in genomic DNA sequences

FGENESH is the fastest (50-100 times faster than GenScan) and most accurate gene finder available - see the figure and the table below. In recent rice genome sequencing projects, it was cited "the most successful (gene finding) program (Yu et al. (2002) Science 296:79) and was used to produce 87% of all high-evidence predicted genes (Goff et al. (2002) Science 296:79).
FirstEF This link opens in a new window
FirstEF* (First Exon Finder) is a 5' terminal exon and promoter prediction program. It consists of different discriminant functions structured as a decision tree. The probabilistic models are optimized to find potential first donor sites and CpG-related and non-CpG-related promoter regions based on discriminant analysis. For every potential first donor site (GT) and an upstream promoter region, FirstEF decides whether or not the intermediate region can be a potential first exon, based on a set of quadratic discriminant functions.
FlyBase This link opens in a new window
A Database of Drosophila Genes & Genomes
GenBank This link opens in a new window
GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42). GenBank is part of the International Nucleotide Sequence Database Collaboration , which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NCBI. These three organizations exchange data on a daily basis.
TASSEL - Analysis of crop genomic diversity This link opens in a new window
TASSEL primary function continues to be providing tools to investigate the relationship between phenotypes and genotypes (Bradbury et al 2007). TASSEL has functionality for association study, evaluating evolutionary relationships, analysis of linkage disequilibrium, principal component analysis, cluster analysis, missing data imputation and data visualization. TASSEL development has been led by a group focused on maize genetics and genomics, and for these reasons that software has design and computational optimizations that account for the biology found in many plants and breeding situations. Compared to human genetics, many crops are highly diverse both at the nucleotide level and structural variations (10-50X greater than humans), inbreeding is common, large families are common, and whole genome prediction is being applied daily to real world problems.
GMOD - Generic Model Organism Database This link opens in a new window
Human Gene Mutation Database (HGMD) - Public Version This link opens in a new window
PGSB Repeat Element Database (PGSB-REdat) and Catalog (PGSB-REcat) This link opens in a new window
PGSB-REdat was initially started as a compilation of publicly available plant repeat sequences from TREP, TIGR repeats, PlantSat and Genbank. It was rapidly expanded with a bulk of de novo detected LTR-retrotransposon sequences (~37.000 by LTR_STRUC) from the genomes presented in PGSB PlantsDB. PGSB-REdat provides not only sequences, but if available also additional information regarding source (institution, Genbank ID), literature (Pubmed ID), organism (NCBI tax ID), sequence completeness and most important classification keys linking the repeat sequences to PGSB-REcat, a generic and detailed ontology for repeat elements.
PGSB Repeat Element Catalog (PGSB-REcat)
PGSB-REcat integrates existing classifications for repetitive elements ( 3-letter code, Repbase, Repeatmasker, TIGR and tandem repeats VNTRs ) into a more detailed hierarchical tree structure.
NCBI Structure Group
Developed databases:
Molecular Modeling Database (MMDB)
Conserved Domain Database (CDD)
Biological ctivities of small molecules( PubChem)
NCBI BioSystems Database
International Mouse Phenotype Consortium (IMPC) This link opens in a new window
The goal of the International Mouse Phenotyping Consortium (IMPC) is to discover functional insight for every gene by generating and systematically phenotyping 20,000 knockout mouse strains.
OMIM This link opens in a new window
OMIM is a comprehensive, authoritative compendium of human genes and genetic phenotypes that is freely available and updated daily. OMIM is authored and edited at the McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, under the direction of Dr. Ada Hamosh.
Oryza Map Alighment Project This link opens in a new window
The long term goal of this project is to develop an experimentally tractable and closed model system to globally unravel and understand the evolution, physiology and biochemistry of the genus Oryza.
Panzea This link opens in a new window
Panzea is an NSF-funded project called "Biology of Rare Alleles in Maize and its Wild Relatives". We are investigating the connection between phenotype (what we see) and genotype (the genes underlying the phenotype) - of complex traits in maize and its wild relative, teosinte, and specifically in how rare genetic variations contribute to overall plant function.
Reactome This link opens in a new window
Reactome is a free, open-source, curated and peer reviewed pathway database. Our goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modeling, systems biology and education.
RefSeq This link opens in a new window
The Reference Sequence (RefSeq) collection provides a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins. RefSeq sequences form a foundation for medical, functional, and diversity studies. They provide a stable reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis (especially RefSeqGene records), expression studies, and comparative analyses.
Repbase This link opens in a new window
Repbase Update (RU) is a database of prototypic sequences representing repetitive DNA from different eukaryotic species. RU is being used in genome sequencing projects worldwide as a reference collection for masking and annotation of repetitive DNA (e.g. by RepeatMasker or CENSOR).
Rice Annotation Project (RAP) Database This link opens in a new window
The Rice Annotation Project (RAP) was conceptualized in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project with the aim of providing the scientific community with an accurate and timely annotation of the rice genome sequence. One of the major objectives of this project is to facilitate a comprehensive analysis of the genome structure and function of rice on the basis of the annotation.
SumsDB This link opens in a new window
SumsDB (the Surface Management System DataBase) provides access to a growing body of neuroimaging and related data. WebCaret software provides online data visualization for datasets in SumsDB.
UniProtKB This link opens in a new window
The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. Contains UniProtKB, Swiss-Prot, TrEMBL, UniRef, UniParc, Proteomes.
TAIR - The Arabidopsis Information Resource This link opens in a new window
The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana . Data available from TAIR includes the complete genome sequence along with gene structure, gene product information, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every week from the latest published research literature and community data submissions. TAIR also provides extensive linkouts from our data pages to other Arabidopsis resources.
TCat: The Catalog of Tissue-Specific Regulatory Motifs This link opens in a new window
The catalog of tissue-specific regulatory motifs is a resource that contains cis-regulatory motifs and cis-regulatory modules that drive tissue-specific expression in mammalian tissues.

The catalog contains information on both experimentally characterized binding site motifs, taken from the TRANSFAC database, as well as novel patterns identified as being significantly overrepresented in promoters of tissue-specific transcripts. Motifs are represented using position-weight matrices.
TGI This link opens in a new window
The software tools that enabled the TGI are still available through the DFCI Gene Indices Software Tools (ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/) page. The entire data sets, including the raw, trimmed sequences, Tensus Consensus (TC) sequences, and other data are available by FTP at ftp://occams.dfci.harvard.edu/pub/bio/tgi/data/.
TRANSFAC This link opens in a new window
TRANSFAC® is a database on eukaryotic cis-acting regulatory DNA elements and trans-acting factors. It covers the whole range from yeast to human. This documentation explains the contents of the tables and individual fields, the criteria applied on acquisition of the data as well as some technical information.
TRED This link opens in a new window
In order to understand gene regulation, accurate and comprehensive knowledge of transcriptional regulatory elements is essential. Transcriptional Regulatory Element Database (TRED) has been built in response to increasing needs of an integrated repository for both cis- and trans- regulatory elements in mammals, and the lack of such resources at present.
Distinguishing features of TRED include:
relatively complete genome wide promoter annotation for human, mouse and rat
availability of transcription factor binding and regulation information
data accuracy is ensured by curation, which continues to expand
easy and flexible data retrieval
availability of on-the-fly sequence analysis tools
UCSC Genome Browser This link opens in a new window
The UCSC Genome Browser site contains the reference sequence and working draft assemblies for a large collection of genomes. It also provides portals to ENCODE data at UCSC (2003 to 2012) and to the Neandertal project. You may download or purchase the Genome Browser source code, or the Genome Browser in a Box (GBiB) at our online store.
We encourage you to explore these sequences with our tools. The Genome Browser zooms and scrolls over chromosomes, showing the work of annotators worldwide. The Gene Sorter shows expression, homology and other information on groups of genes that can be related in many ways. Blat quickly maps your sequence to the genome. The Table Browser provides convenient access to the underlying database. VisiGene lets you browse through a large collection of in situ mouse and frog images to examine expression patterns. Genome Graphs allows you to upload and display genome-wide data sets.
Wormbase This link opens in a new window
WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematodes.

Bioinformatics and Genomics Researchers at CSHL

Gurinder Atwal - Population genetics; bioinformatics; cancer; stochastic processes; statistical mechanics and information theory

Jesse Gillis - Gene networks; gene function prediction; guilt by association; neuropsychiatric; hub genes; multifunctionality; computational genomics

Thomas Gingeras - Genome-wide organization of transcription and the functional roles of non-protein coding RNAs

Christopher Hammell - Post-transcriptional gene regulation; control of animal developmental timing; RNA biology

Molly Hammell - bioinformatics, integrated genomic analysis, small RNAs, gene regulatory networks

Gregory Hannon - Growth control in mammalian cells; post-transcriptional gene silencing

Ivan Iossifov - Computational biology; molecular networks; human genetics; human disease; applied statistical and machine learning; biomedical text-mining; molecular evolution

David Jackson - Plant development; stem cell signaling; genomics and imaging

Alexander Krasnitz - Genomics of cancer; machine learning for biology;inference from noisy biological data; large-scale numerical computing

Dan Levy - Human genetics; mathematical modeling; algorithm development

Zachary Lippman - Plant development, genetics; molecular mechanisms of phase transitions for flowering time and inflorescence branching; heterosis

Gholson Lyon - Human genetics, neuropsychiatric diseases, whole genome sequencing, ethics

Rob Martienssen - Epigenetics; DNA methylation; chromatin and chromosome biology; transposable elements; RNA interference; stem cells; germline specification; plant genomics; plant evolution; aquatic plants

W. Richard McCombie - Genomics of psychiatric disorders; genomics of cancer; computational genomics; plant genomics

Scott Powers - Cancer genome; molecular targets and therapeutics; functional genomics; cancer biology

Michael Schatz - Genomics; Genome Assembly & Validation; Sequence Alignment; High Performance and Multicore Computing; Parallel Algorithms; Cloud Computing

Marja Timmermans - Plant development; epigenetic regulation of stem cell fate; pattern formation via small RNAs

Doreen Ware - Computational biology; comparative genomics; genome evolution; diversity; gene regulation; plant biology

Michael Wigler - Human genetic disorders; population genetics; cancer genomics

New York Genome Center

New York Genome Center Website

GenomeWeb Daily News Feed

Tools, Websites, and Other Resources

AB-BLAST This link opens in a new window
Basic Local Alignment Search Tool from Advanced Biocomputing, LLC
AB-BLAST is a powerful software package for gene and protein identification, using sensitive, selective and rapid similarity searches of protein and nucleotide sequence databases. The feature list for AB-BLAST is long and continues to expand, while performance is improved. Much of this is outlined below. A complete suite of BLAST search programs (blastp, blastn, blastx, tblastn and tblastx) is provided in the package, along with several database management and support programs that include nrdb, patdb, xdformat, xdget, seg, dust and xnu.
Biocatalogue This link opens in a new window
BioDAS This link opens in a new window
BioGPS This link opens in a new window
A free extensible and customizable gene annotation portal, a complete resource for learning about gene and protein function.
BioWorks This link opens in a new window
BLAST This link opens in a new window
ClustalW2 This link opens in a new window
Cluster-Buster This link opens in a new window
Comprehensive Perl Archive Network (CPAN) This link opens in a new window
CPAN is the Comprehensive Perl Archive Network, a large collection of Perl software and documentation. (CPAN is also the name of a Perl module, CPAN.pm, which is used to download and install Perl software from the CPAN archive.)
Consed This link opens in a new window
COREBOOST This link opens in a new window
DME-B This link opens in a new window
edgeR This link opens in a new window
Eponine This link opens in a new window
Exonerate This link opens in a new window
ExonHunter This link opens in a new window
ExPASY This link opens in a new window
GeneCards This link opens in a new window
Genevestigator This link opens in a new window
GeneWise (Wise2) This link opens in a new window
Gibbs Motif Sampler This link opens in a new window
HDMFinder This link opens in a new window
HMMER This link opens in a new window
IHMC CMap This link opens in a new window
JASPAR This link opens in a new window
JMP 3.1 This link opens in a new window
LAGAN This link opens in a new window
Look-Align This link opens in a new window
Match --> Align This link opens in a new window
MatCompare This link opens in a new window
MATLAB This link opens in a new window
MatrixREDUCE This link opens in a new window
McPromoter This link opens in a new window
MDScan This link opens in a new window
MedicCyc This link opens in a new window
MIPS Mammalian Protein-Protein Interaction Database This link opens in a new window
The MIPS Mammalian Protein-Protein Interaction Database is a collection of manually curated high-quality PPI data collected from the scientific literature by expert curators. We took great care to include only data from individually performed experiments since they usually provide the most reliable evidence for physical interactions.
Network Analysis Tools This link opens in a new window

PATSER

PROBER This link opens in a new window
PSORT This link opens in a new window
R This link opens in a new window
Reduce This link opens in a new window
Regulatory Sequence Analysis Tools This link opens in a new window
RepeatMasker This link opens in a new window
s+ (S-PLUS) This link opens in a new window
SAMtools This link opens in a new window
ScaLAPACK This link opens in a new window
SolCyc This link opens in a new window
SpliceRack This link opens in a new window
STADEN This link opens in a new window
TBLASTN This link opens in a new window
tinyURL This link opens in a new window
TwinScan/N-SCAN This link opens in a new window
Vmatch This link opens in a new window