NDLI: Creating the backbone for the virtual cell (abstract only): cell mapping projects on the run

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The sequence of the human genome (abstract only)

A new approach to sequence comparison: normalized sequence alignment

Context-specific Bayesian clustering for gene expression data

An optimal procedure for gap closing in whole genome shotgun sequencing

Class discovery in gene expression data

On the predictive power of sequence similarity in yeast

Algorithms for phylogenetic footprinting

Predicting the β-helix fold from protein sequence data

Information processing by cells and biologists (abstract only)

Finding motifs using random projections

Rapid significance estimation in local sequence alignment with gaps

Regulatory element detection using correlation with expression (abstract only)

Gene-finding via tandem mass spectrometry

Algorithms for identifying protein cross-links via tandem mass spectrometry

Hunger for new technologies, metrics, and spatiotemporal models in functional genomic (abstract only)

Fast recovery of evolutionary trees with thousands of nodes

Geometric algorithms for the analysis of 2D-electrophoresis gels

Analysis techniques for microarray time-series data

A structural EM algorithm for phylogenetic inference

Optimal sequencing by hybridization in rounds

Efficient algorithms for lateral gene transfer problems

The greedy path-merging algorithm for sequence assembly

Extracting structural information using time-frequency analysis of protein NMR data

Separating repeats in DNA sequence assembly

A NMR-spectra-based scoring function for protein docking

101 optimal PDB structure alignments: a branch-and-cut algorithm for the maximum contact map overlap problem

Comparative analysis of organelle genomes, a biologist's view of computational challenges (abstract only)

DNA segmentation as a model selection process

Edit distance between two RNA structures

Genetics and genemoics: impact on drug discovery and development

The role of computational chemistry in translating genomic information into bioactive small molecules (abstract only)

Comparing sequence scaffolds

Fast and simple character classes and bounded gaps pattern matching, with application to protein searching

Applications of generalized pair hidden Markov models to alignment and gene finding problems

Gene functional classification from heterogeneous data

A new approach to fragment assembly in DNA sequencing

Imposing specificity by regulated localization (abstract only)

Large scale sequencing by hybridization

RNA biology and the genome (abstract only)

Towards predicting coiled-coil protein interactions

Using motion planning to study protein folding pathways

Zinc finger gene clusters and tandem gene duplication

A Gibbs sampling method to detect over-represented motifs in the upstream regions of co-expressed genes

Creating the backbone for the virtual cell (abstract only): cell mapping projects on the run

Creating the backbone for the virtual cell: cell mapping projects on the run

Creating the backbone for the virtual cell (abstract only): cell mapping projects on the run

Content Provider	ACM Digital Library
Author	Wilm, Matthias
Abstract	The ability to identify proteins with mass spectrometry has a profound impact on biological research. Its long term effects can only be compared with the significance PCR enzyme had for the advancement of biological science.Suddenly proteins can be identified having only minute quantities available. The efforts invested in to the technology lead to a constant increase in throughput - comparable to the development of DNA sequencing technology.Biological mechanisms can be studied directly on the protein level. There are two research directions: protein expression based proteomics and cell mapping or functional proteomics.Protein expression based proteomics is focussing on the understanding of cellular states by analyzing the protein expression level of as many proteins as possible. In cell mapping experiments the protein - protein interaction network within a cell is analyzed.At the EMBL a protein complex purification technique, called tandem affinity purification (TAP), was developed which allows to rapidly purify very specifically non covalently interacting proteins which can be subsequently analyzed with mass spectrometry (cell mapping approach). The complexes assemble in vivo, are purified as such and characterized. The technique had been developed in yeast and efforts are under way to establish similar methods in higher eukaryotes. The comparison of this technique with similar experiments based on two hybrid screens demonstrate that the protein based approach is more specific and functional data suggest that it is more complete. This may be due to the fact that the complexes assemble first in their native environment and are then pulled out for characterization.The organization of all the proteins into groups of physically in teracting proteins is an important step towards understanding their functional role within a cell. To a large degree cellular processes organize themselves based on the non-covalent affinity of proteins. Protein based approaches as exemplified by the tandem affinity purification method in conjunction with mass spectrometry are very important in analyzing this functional infra structure. The identification of all the proteins involved in a particular biological mechanism and the characterization of their interaction constants may provide the physical data to simulate the process by a computer.
File Format	PDF
ISBN	1581133537
DOI	10.1145/369133.374565
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2001-04-22
Publisher Place	New York
Access Restriction	Subscribed
Content Type	Text
Resource Type	Article

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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