BOL: Related items

DeCoSTAR - Detection of Co-evolution

Jit — Fri, 14 Apr 2017 06:27:25 -0500

DeCoSTAR is a software which aims at reconstructing ancestral gene or genome organizations, in the form of sets of neighborhood relations -adjacencies- between pairs of ancestral genes or gene domains.
Ancestral genes or domains are deduced from reconciled gene trees in a context of birth, speciation, duplication, loss, transfer, which are either given as input or computed with the ecceTERA package, to which DeCoSTAR is integrated. DeCoSTAR constructs parsimonious scenarios of gains and breakages of adjacencies, and contains in particular all the features of previous software DeCo, DeCoLT, ArtDeCo and DeClone. It provides statistical supports on ancestral adjacencies, or the possibility to handle badly assembled genomes.
DeCoSTAR is able to reconstruct the histories of domains inside genes, including gene fusion and fission events, as well as ancestral genome structures for dozens of whole genomes from all kingdoms of life in a few minutes.

Address of the bookmark: http://pbil.univ-lyon1.fr/software/DeCoSTAR/

List of GOI approved peer reviewed bioinformatics and computational biology journals

Jit — Tue, 25 Apr 2017 05:03:27 -0500

Unfortunately, we now live in a world where the integrity of peer-reviewed journals is being threatened by the rise of the academic version of fake news – something many call “predatory publishing". Mostly in academic publishing world, "predatory open access publishing" is an exploitative open-access publishing business model that involves charging publication fees to authors without providing the editorial and publishing services associated with legitimate journals (open access or not).

Nearly 20% of the such journals have a flashy impact factor and quick publication time, which are quick give-aways. Interestingly, under contact address, some journal websites do not even provide any address to contact. All of this has led to the emergence of a new and dark market of deceptive publishers that exploit the concept of open access and provide channels for “scientific journal” publication with little or no peer review. For a fee, they will publish almost anything – even if the study was fatally flawed. And these journals provide a forum that can be used as a channel to publish fraudulent “advocacy research.” You can find list of certain such publishers at "Beall's List" http://beallslist.weebly.com/

Keeping all these in mind, Government of India (GOI) decided to approved certain bioinformatics and computational biology journals for your research publication.

Following are the list of GOI validated and peer reviewed bioinformatics and computational biology journals:

NOTE:Each journal details are in following order Tittle\nSource\nSubject.
Point to remember: The list of journals are NOT sorted in any ascending or descending order.

If I missed any other GOI validated bioinformatics journal, then please report me in comment section.

Open Bioinformatics Journal
Scopus
Computer Science; Engineering; Medicine

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
WoS
BIOLOGY & BIOCHEMISTRY

Advances and Applications in Bioinformatics and Chemistry
Scopus
Biochemistry, Genetics and Molecular Biology Chemistry; Computer Science

Advances in Bioinformatics
Scopus
Biochemistry, Genetics and Molecular Biology; Computer Science; Engineering

Applied Bioinformatics
Scopus
Agricultural and Biological Sciences; Computer Science

BIOINFORMATICS
WoS & Scopus
COMPUTER SCIENCE

Bioinformatics and Biology Insights
Scopus
Biochemistry, Genetics and Molecular Biology; Computer Science; Mathematics

BMC BIOINFORMATICS
WoS & Scopus
COMPUTER SCIENCE

BRIEFINGS IN BIOINFORMATICS
WoS & Scopus
COMPUTER SCIENCE

Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference
Scopus
Medicine

Current Bioinformatics
WoS & Scopus
COMPUTER SCIENCE

Current Protocols in Bioinformatics
Scopus
Biochemistry, Genetics and Molecular Biology

JOURNAL OF COMPUTATIONAL INTELLIGENCE IN BIOINFORMATICS
ICI
BIOLOGICAL SCIENCE

Journal of integrative bioinformatics
Scopus
Medicine

Journal of Proteomics and Bioinformatics
Scopus
Biochemistry, Genetics and Molecular Biology; Computer Science

Mathematical Biology and Bioinformatics
Scopus
Engineering; Mathematics

Trends in Bioinfprmatics
Scopus
Computer Science

Eurasip Journal on Bioinformatics and Systems Biology
Scopus
General; Computer Science; Mathematics; Medicine

Evolutionary Bioinformatics
WoS & Scopus
COMPUTER SCIENCE

Genomics, Proteomics and Bioinformatics
Scopus
Biochemistry, Genetics and Molecular Biology;Mathematics

IEEE/ACM Transactions on Computational Biology and Bioinformatics
Scopus
Biochemistry, Genetics and Molecular Biology;Mathematics

IEEE-ACM Transactions on Computational Biology and Bioinformatics
WoS
COMPUTER SCIENCE

International Journal of Bioinformatics Research and Application
Scopus
Biochemistry, Genetics and Molecular Biology; Medicine, Health

International Journal o f Data M ining and Bioinformatics
WoS & Scopus
COMPUTER SCIENCE

IPSJ Transactions on Bioinformatics
Scopus
Biochemistry, Genetics and Molecular Biology;Computer Science

Journal of Bioinformatics and Computational Biology
WoS & Scopus
COMPUTER SCIENCE

Journal of Clinical Bioinformatics
Scopus
Medicine

PLoS Computational Biology
WoS & Scopus
BIOLOGY & BIOCHEMISTRY

Reviews in Computational Chemistry
WoS & Scopus
CHEMISTRY

RSC Theoretical and Computational Chemistry Series
Scopus
Chemistry; Computer Science

Annual Reports in Computational Chemistry
Scopus
Chemistry; Mathematics

Computational and Structural Biotechnology Journal
Scopus
Biochemistry, Genetics and Molecular Biology; Computer Science

Computational and Theoretical Chemistry
WoS & Scopus
CHEMISTRY

COMPUTATIONAL BIOLOGY AND CHEMISTRY
WoS & Scopus
COMPUTER SCIENCE

COMPUTATIONAL CHEMISTRY
WoS
CHEMISTRY

Journal of Theoretical and Computational Chemistry
Scopus
Chemistry; Computer Science

Theoretical and Computational Chemistry
Scopus
Chemistry

Wiley Interdisciplinary Reviews: Computational Molecular Science
Scopus
Biochemistry, Genetics and Molecular Biology;Chemistry; Computer Science; Materials Science; Mathematics

Wiley Interdisciplinary Reviews- Computational Molecular Science
WoS
CHEMISTRY

Interdisciplinary sciences, computational life sciences
Scopus
Medicine

Interdisciplinary Sciences-Computational Life Science
WoS
Biology and Biochemistry

International Journal of Computational Biology and Drug Design
Scopus
Computer Science; Pharmacology, Toxicology and Pharmaceutics

SSPACE

Jit — Fri, 05 May 2017 05:42:15 -0500

SSPACE standard is a stand-alone program for scaffolding pre-assembled contigs using NGS paired-read data. It is unique in offering the possibility to manually control the scaffolding process. By using the distance information of paired-end and/or matepair data, SSPACE is able to assess the order, distance and orientation of your contigs and combine them into scaffolds. Currently we offer this as a command-line tool in Perl. The input data is given by pre-assembled contig sequences (FASTA) and NGS paired-read data (Illumina/454/Solid FASTA or FASTQ). The final scaffolds are provided in FASTA format.

Address of the bookmark: https://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE

Bienko and Crosetto Labs

Fri, 12 May 2017 07:42:15 -0500

We are two groups of scientists doing frontier research in quantitative biology and biomedicine. The Bienko group is interested in exploring the fundamental design principles controlling how DNA is packed in the eukaryotic nucleus and its relation to gene expression regulation. The Crosetto group engineers new molecular methods for single-cell and spatially resolved omic measurements of DNA, RNA, and proteins, with a strong focus on tumor heterogeneity. By sharing ideas and resources, we work synergistically towards a more quantitative understanding of life’s processes in healthy and diseased conditions.

https://bienkocrosettolabs.org/

PhD positions in Genova at DIBRIS - Univ. of Genoa, Italy

Thu, 18 May 2017 00:04:07 -0500

PhD positions in Genova at DIBRIS - Univ. of Genoa (Italy)

http://www.disi.unige.it/person/MasulliF/ricerca/PhDinGenova2017.html

The call for some funded positions for the 3 years PhD studies at the Department of Informatics, Bioengineering, Robotics and System Engineering (DIBRIS) in Genova is available at

http://www.studenti.unige.it/postlaurea/dottorati/XXXIII/ENG/

The deadline for applications is June13, 2017 and the PhD courses and fellowships should start on Nov 2017.

Details for the application to the PhD Program in Computer Science and Systems Engineering (CODICE 6608) are at http://phd.dibris.unige.it/csse/index.php/how-to-apply

The research activity of my research group is focused on Computational Intelligence, Machine Learning, Bioinformatics, Systems Biology, and Positive Technology as described at http://www.disi.unige.it/person/MasulliF/ricerca/index.html

The research themes proposed by me and Prof. Stefano Rovetta are:

- Computational Intelligence and Machine Learning (see http://www.disi.unige.it/person/MasulliF/ricerca/Phd2017-T1.html)

- Computational Intelligence and Health and Wellbeing Support( see http://www.disi.unige.it/person/MasulliF/ricerca/Phd2017-T3.html)

You can also propose a different research theme belonging to the research activity of my group.

Looking for self-motivated PhD candidates, interested to the mathematical aspects of their research and to the development of new algorithms for intelligent data analysis, and skilled in programming and in thorough experimental data analysis. They will be part of my research group and will collaborate to our research projects and publications.

Italian and international students interested to work are invited to send their cv and the name/email-addresses of 3 referees to my email address francesco.masulli@unige.it A.S.A.P.

RA Bioinformatics at NATIONAL INSTITUTE OF BIOMEDICAL GENOMICS, INDIA

Wed, 26 Jul 2017 03:49:52 -0500

NATIONAL INSTITUTE OF BIOMEDICAL GENOMICS
(An Autonomous Institution of the Government of India)
P.O.: N.S.S., Kalyani 741251, West Bengal

Advertisement No. 137/ESTB/NIBMG/17-18

Position available Project Description: Several positions are available for the project titled: “A unified web-portal for analysis, integration and visualization of multi-omics data”. The goal of this project is to develop a user-accessible resource for integrated analysis and visualization of multi-OMICs data sets (including gene expression, genotype, methylation, microRNA, etc.). Data sets generated on various platforms shall be maintained in a stable database, accessed through standard querying mechanisms, and the results shall be displayed via user-friendly interface. The analysis engine shall run on open-source software (such as R/Bioconductor) developed in-house. All positions are contractual.

Appointment will be initially given for a period of one year which is extendable depending upon performance, availability of funds and requirements of the institute.

Project Code: 20275 Position: (No. of positions available)

Research Associate (3)

Position 1: Ph.D. or equivalent in statistics, computer science, mathematics, bioinformatics, or related subject.
Position 1: Those with experience in database management shall be preferred. Experience with UNIX or GNU/Linux operating system.
Position 1: Creation and maintenance of a database for population- and diseaseassociated variation resource. Development of programmatic interface for querying the database, filtering of the results and identification of genes of interest.

Rs. 36000/- + 10% HRA

Please apply online via web link http://apply.nibmg.ac.in/ (no other form of application will be accepted). The last date of application is 14-08-2017. All letters to attend screening test and /or interview will be sent only to the short-listed candidates by Email only. No correspondence will be made with applicants who are not shortlisted /not called for screening test and /or interview. No TA/DA will be paid for attending the screening test and /or interview.
Detail information at http://www.nibmg.ac.in/academic/Advt_20275.pdf

More Info: http://www.nibmg.ac.in/?q=Project%20Linked%20Personnel

Bioinformatics lectures !

Jit — Wed, 29 Nov 2017 05:39:54 -0600

Computational Biology is a huge field of study, that touches upon many distinct algorithmic and biological areas of study. What we are able to cover in this course will depend, in part, on the pace at which we move, which I will attempt to adjust as appropriate. However, here is a tentative list of topics I hope to cover this semester (not necessarily in order).

Optimal sequence alignment (global, local, and glocal alignment &mdash with constant & affine gap penalties
Algorithms and data structures for efficient text indexing and exact search
Heuristics for read alignment and mapping &mdash mapping DNA-seq and RNA-seq reads
Genome assembly &mdash k-mers, De Brujin graph construction and representation, long-read technology and read-overlap graph assembly
Motif finding via Gibbs sampling
Gene finding &mdash statistical models for ab initio and evidence-guided prediction of genes
RNA-seq and transcriptomics &mdash transcript assembly, abundance estimation and differential expression testing
Phylogenetics &mdash The small and large phylogeny problem; parsimony, maximum likelihood and Bayesian methods

Address of the bookmark: https://rob-p.github.io/CSE549F16/lectures/

Assembly Course

Shruti Paniwala — Mon, 10 Jul 2017 09:38:05 -0500

https://ocw.mit.edu/courses/biology/7-91j-foundations-of-computational-and-systems-biology-spring-2014/lecture-slides/MIT7_91JS14_Lecture6.pdf

Address of the bookmark: https://ocw.mit.edu/courses/biology/7-91j-foundations-of-computational-and-systems-biology-spring-2014/lecture-slides/MIT7_91JS14_Lecture6.pdf

Eugene V. Koonin Lab

Tue, 09 Jan 2018 05:01:15 -0600

Interested in understanding the evolution of life. To obtain glimpses of such understanding, we employ existing and new methods of computational biology to perform research in several major areas.

https://www.ncbi.nlm.nih.gov/research/groups/koonin/

Rectangle Graph for Repeat Resolution in Genome Assembly

Rahul Nayak — Thu, 28 Dec 2017 09:43:03 -0600

Ultimate tool for resolving repeats in genome assemblies.

Though the specific implementation of the idea of the rectangle graph approach is already included into the current SPAdes distribution, we're also releasing the Rectangle Graph Module (RGM) as the separate code which can be run independently of SPAdes. Although RGM differs from the current implementation of the rectangle graph approach in SPAdes, in the future we plan to integrate RGM in SPAdes. RGM can be run with other genome assemblers if they use the graph format as SPAdes files.

For more details see: Nikolay Vyahhi, Son K. Pham, Pavel Pevzner. From de Bruijn Graphs to Rectangle Graphs for Genome Assembly, Lecture Notes in Bioinformatics 7534 (2012), pp. 249-261.

Address of the bookmark: http://bioinf.spbau.ru/en/rectangles