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Resource Center
The resource center is here to serve as a portal to useful information in
computational biomedicine. New resources offered by the Institute or
external sources are quickly introduced and links to further information
are available for readers interested in a particular topic.
Bioinformatics Walk-in Clinics: To answer your bioinformatics questions, a member of the ICB will be available for consultation and advice
every Thursday between 2:00 pm and 3:00 pm in the Institute for Computational Biomedicine Conference Room, Y.13.01 (1305 York Avenue, at 70th Street 13th Floor).
 | [ services ] |
[Note: The ICB intranet is available only to ICB personnel and requires username and password authentication]
| [ tutorials and training ] |
The institute offers workshops and tutorials for our bioinformatics resources. Please visit our education section for more information. We also offer individualized training. This is appropriate if you would like somebody in your lab to learn a specific bioinformatics method. The hourly fees for training are listed under our fee schedule.
| [ tools developed at the ICB ] |
| Twease |
Search MedLine at the Sentence level. Twease is a new web-based tool to search for information in MedLine.
Twease indexes every word of Medline and offers innovative features which improve precision while maintaining
a good level of recall. Check out the tutorials on Twease.org.
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| SigPath | A prototype of an information system to integrate qualitative
and quantitative information about signaling networks.
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| Arcadia | A repository of mutants of GPCR and transporter proteins, and associated information.
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| Textractor | A software framework to support the development of tools that mine full text scientific articles to extract information.
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| TissueInfo | A series of tools and a curated database to predict
the tissue distribution of genes and EST (knowledge-based prediction).
TissueInfo can be applied to complete genomes and produces records
suitable for data mining.
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| Crover | A software framework to support the development
of Bioinformatics tools and applications. |
| RbDe | A web service allowing the iterative construction of
residue-based diagrams of proteins. The constructed
diagrams can be annotated to show experimental
results (directed mutagenesis, accessibility, etc.)
or to present key properties of the protein in the context
of its secondary structure. |
| RbDg | RbDg is a program that generates residue-based diagrams of proteins. RbDg can be thought of as a batch version of RbDe with added features. |
| ProperTM | ProperTM is a web service that calculates properties associated with positions in a sequence alignment. The methods employed in this program are designed to analyze membrane proteins (and G-protein coupled receptors (GPCRs) in particular) but some of the options (i.e the calculation of a conservation index) could be useful for the analysis of sequences of non-membrane proteins too. |
| Real-time eXperiment Interface | A software system for scientific experimentation. Experimenters can use this system to design their own hard real-time data acquisition and control applications. Applications are split into two parts: the user interface and the real-time control module. The user interfaces are written as Qt C++ plugins which get loaded into the DAQSystem program. Real-time control modules, which use RTLinux or RTAI, are written as C code that gets loaded into the kernel and is executed by the rtlab.o kernel module. |
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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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