BOL: Related items

Anders Krogh Lab

Mon, 30 Sep 2013 19:07:40 -0500

In a lot of my work in bioinformatics, I have been using hidden Markov models (HMMs). As a postdoc with David Haussler at UCSC we developed the so-called profile HMMs (refs). Since then I have applied HMMs to membrane proteins (refs) and gene identification (refs) and have worked on methods for such things as discriminative estimation of HMMs (refs) and alternative decoding algorithms etc. (refs).

Now my main interests are in gene regulation, where we work on promoter analysis; non-coding RNA, where miRNAs and structure prediction are the main areas; and protein structure, where the group is working on methods for structure prediction from sequence. To read more about these topics, please see the research pages.

Lab page @ http://wiki.binf.ku.dk/User:Krogh

Paolo Ruggerone Lab

Tue, 01 Oct 2013 14:15:53 -0500

Efflux pumps (RND family)

Functioning of efflux systems in Gram-negative bacteria
Determinants of the compound-efflux system interactions
Action of inhibitors on efflux systems
Structural and dynamical features of the efflux systems

TatA
Assembly of the TatA system
Study of the dynamical features of the charge zipper

Methods
Setup of a kinetic Monte Carlo (KMC) scheme to study the flux of antibiotics through porins and efflux systems
Setup of protocol to integrate MD results in a ligand-based approach

Viral inhibitors
Interactions of selected compounds with RNA-dependent RNA polymerases (RdRps) of HCV and BVDV
Assessment of the role of mutations in RdRps
Antimicrobial peptides

Interactions of antimicrobial peptides with membranes: structure and dynamics
Interactions between antimicrobial peptides in the presence of different membranes
Protein-protein interactions
Effects of mutations

Lab Page
http://www.dsf.unica.it/~paolo/Site/Home.html

Shendure Lab

Wed, 09 Oct 2013 14:21:58 -0500

The Shendure Lab is part of the Department of Genome Sciences at the University of Washington (Seattle, WA). The mission of the lab is to develop and apply new technologies in genomics and molecular biology. Most projects in the lab exploit new DNA sequencing technologies (Shendure et al., Nature Reviews Genetics 2004; Shendure & Ji, Nature Biotechnology 2008; Shendure & Lieberman Aiden, Nature Biotechnology 2012), and generally fall into one of six areas: 1) next-generation human genetics; 2) genome contiguity & completeness; 3) massively parallel functional analysis; 4) molecular tagging; 5) synthetic biology; 6) translational genomics. Our interests in each of these areas are outlined briefly below, and a full list of publications is available via PubMed. http://www.ncbi.nlm.nih.gov/pubmed?cmd=search&term=shendure
More http://krishna.gs.washington.edu/research.html

Lab page @ http://krishna.gs.washington.edu/index.html

DbBrowser: Attwood Lab

Fri, 18 Oct 2013 10:48:19 -0500

DbBrowser: Attwood Lab research concerns protein sequence analysis, primarily using the method of protein 'fingerprinting'. DbBrowser: Attwood Lab maintain a diagnostic fingerprint database (PRINTS), one of the founding partner of InterPro. We also design software to display sequence and structural data in visually-striking ways (e.g., Ambrosia, CINEMA); DbBrowser: Attwood Lab are building re-usable software components to create semantically integrated bioinformatics applications through UTOPIA, including a 'smart' PDF reader that links bioinformatics databases and tools directly with scientific articles (Utopia Documents); and have developed a number of tools for automatic annotation and text mining (e.g., MINOTAUR, PRECIS, METIS).

More @ http://www.bioinf.manchester.ac.uk/dbbrowser/index.php

List of Bioinformatics Vacancy, Jobs, Opportunity websites

Jitendra Narayan — Tue, 12 Nov 2013 20:04:28 -0600

Bioinformatics cover wide area of biology, and indulge in almost all sort of science related work. Bioinformatician give strong emphasis on open access to biological information as well as Free and Open Source software!!

There are several jobs opening in bioinformatics all around the world, but many of them do not get proper attention due to lack of advertisements, or social connectivity. This bookmark is created for an academic, non-academic, scientists and budding researchers to help and updates the bioinformatics/computational biology jobs links of all know websites around the world.

I also love to stream the live bioinformatics or Computational biology jobs updates using Twitter https://twitter.com/search?q=bioinformatics%20jobs&src=typd

Find out here about exciting job opportunities in the life sciences.

Please add well known bioinformatics jobs websites below in comment section.

Address of the bookmark: http://www.nature.com/naturejobs/science/jobs?utf8=%E2%9C%93&q=bioinformatics&where=&commit=Find+Jobs

Molecular Bioinformatics Lab (MBL)

Tue, 19 Nov 2013 18:23:27 -0600

The main subject of interest in our laboratory is the study of the relationship among sequence, structure, and function in proteins and nucleic acids. Our research can be divided in two major topics:

the study of the sequence-structure relationship
(application -> structure prediction)
the study of the structure-function relationship
(application -> function prediction)

Therefore, anything related to the configuration (sequence) and conformation (structure) in atomic systems of proteins and nucleic acids, and the interaction of these with other elements (function) is of our major interest.

Lab page @ http://melolab.org/mbl/

Bioinformatics group at Boku University

Thu, 12 Dec 2013 17:53:10 -0600

The Bioinformatics group at Boku University has two main areas of interest, underpinning a common goal, the study of complex systems in living organisms. To overcome the engineered redundancies and combinatorial effects prevalent in higher eukaryotes, novel views augmenting the classical gene by gene approaches are required. We combine

1. Work to establish improved quantitative experimental assays (such as microarrays or differential in-gel electrophoresis) and
2. Development of modern computational methods (such as hierarchical probabilistic models or integration of heterogeneous data sources)

Lab page @ http://bioinf.boku.ac.at/

List of Bioinformatics and Computational Biology Journals

Jitendra Narayan — Wed, 17 Jul 2013 02:36:53 -0500

Hi Bioinformatician and Computational Biologist, this is the comprehensive list of all (?) the bioinformatics and computational biology journals. Please update me if you know any other good journals related with our domains. Feel free to add your comments and suggestions. You comments will be helpful for others...

*The journals are not listed in any ascending, descending, or impact factors oders.

Bioinformatics

Journal of Computational Biology

Briefings in Bioinformatics

Protein Engineering

Nucleic Acids Research

Trends in Biotechnology

Proceedings of the National Academy of Sciences

Folding and Design

Genome Biology

Journal of Biomedical Informatics

Bioinformation

Journal of Computational Intelligence in Bioinformatics

Journal of Structural and Functional Genomics

Journal of Molecular Graphics and Modelling

Metabolic Engineering

Computers & Chemistry

Artificial Intelligence in Medicine

Journal of Biomedical Science

Artificial Intelligence

Machine Learning

Applied Bioinformatics

Applied Genomics and Proteomics

BMC Bioinformatics

Online Journal of Bioinformatics (OJB)

PSB On-Line Proceedings

Bioinformatics: Information Technology & Systems (BITS)

Data Mining and Knowledge Discovery

The EMBO Journal

Current Opinions in Structural Biology

Journal of Molecular Microbiology and Biotechnology

Nature

Nature Structural Biology

Journal of Machine Learning Research

Nature Genetics

Current Opinion in Genetics & Development

Nature Biotechnology

Trends in Biochemical Sciences

Proteins: Structure, Function, and Genetics

Nature Cell Biology

Trends in Genetics

ChemBioChem

Trends in Molecular Medicine

Journal of Molecular Modelling

Trends in Pharmacological Sciences

Drug Discovery Today

Others Free Online Full-text Journals

Update Genome Workbench 2.7.15 released

Surabhi Chaudhary — Wed, 26 Feb 2014 16:12:17 -0600

NCBI Genome Workbench is an integrated application for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix this data with your own private data.

Genome Workbench can display sequence data in many ways, including graphical sequence views, various alignment views, phylogenetic tree views, and tabular views of data. It can also align your private data to data in public databases, display your data in the context of public data, and retrieve BLAST results.

Genome Workbench is built on the NCBI C++ ToolKit and uses cross-platform APIs for graphics. It runs on your local machine, and is available for Windows 2000/XP, Linux, MacOS X, and various flavors of Unix.

NCBI Genome Workbench is an integrated application for viewing and analyzing sequence data. Genome Workbench was developed entirely in-house at NCBI and makes use of the NCBI C++ ToolKit. The C++ ToolKit provides a convenient and flexible cross-platform API for managing system internals, database connections, network sockets, and the NCBI data model. In addition, the C++ ToolKit provides the Object Manager, which abstracts handling of sequences and sequence-related objects.

New Features in Genome Workbench 2.7.15

Multiple Alignment View: implemented adaptive feature display when zooming in
Active Objects Inspector replaces Selection Inspector. New View should offer an improved selection context examination. See Using Active Objects Inspector tutorial for more details.
Binary packages for Linux OpenSUSE 13.1 are now available

Bug Fixes and Improvements in Genome Workbench 2.7.15

Fixed major issue with OpenGL overlay/scrolling. Could cause crashes or view scrolling irregularities
Multiple Pane View: fixed crash on loading BLAST results
Graphical Sequence View: fixed crash on zooming in and out, related to SNP track
Graphical Sequence View: fixed Go To Position dialog to give better diagnostics in case of a user error
Graphical Sequence View: PDF export fixed rendering of Markers with commas in the name
Text View / Flat File: fixed Mac OS rendering issues
Text View / Flat File: performance optimization, extended capabilities of real-time rendering of molecules to tens of thousands
File Import: optimization improvement to speed up load of files containing multiple project items
File Import: remapping stage now shows accession.version and description of molecules, instead of plain GI numbers
Mac OS: improved tooltips for toolbar buttons
Phylogenetic Tree Builder Tool: improved diagnostics of errors
Multiple Alignment View: optimizations to avoid main GUI freezes
Open Dialog: removed duplicate elements in table of genomes (load Genome)
PDF export: fixed issue with XREF table errors
Tree View: fixed issues with showing Force Layout progress on Mac OS
Tree View: PDF export fixed issues for showing labels of collapsed nodes
Tree View: added an option to stop layout
Tree View: broadcasting mechanism fixed not to accumulate selected nodes

Reference:

NCBI news

http://www.ncbi.nlm.nih.gov/tools/gbench/

Roth Lab

Tue, 11 Mar 2014 17:43:45 -0500

The Roth Lab seeks insight into biological systems through genome- and proteome-scale experimentation and analysis.

Current computational interests:

Systematic analysis of genetic epistasis to identify redundant or compensatory systems and to reveal order of action in genetic pathways.
Using knockout, knockdown, or overexpression, or other perturbation experiments in combinations of genes in S. cerevisiae, C. elegans or mouse.
Using genome-scale genotyping of natural polymorphisms in S. cerevisiae and human populations.
Alternative splicing and its relationship to protein interaction networks.
Integrating large-scale studies including phenotype, genetic epistasis, protein-protein and transcription-regulatory interactions and sequence patterns to quantitatively assign function to genes and guide experimentation.

More at http://llama.mshri.on.ca/index.html