BOL: Related items

Ancestor at work !!!

Jit — Sun, 25 Aug 2013 19:45:28 -0500

When they will learn Bioinformatics :)

MGRA: Breakpoint graphs and ancestral genome reconstructions

Jit — Tue, 25 Jul 2017 08:48:25 -0500

MGRA (Multiple Genome Rearrangements and Ancestors) is a tool for reconstruction of ancestor genomes and evolutionary history of extant genomes.

It takes as an input a set of genomes represented as sequences of genes (or synteny blocks) and produces such sequences for ancestral genomes at the internal nodes of the phylogenetic tree.

The phylogenetic tree may be also specified completely or partially, in the latter case MGRA can reconstruct conserved ancestral regions (CARs) of the ancestral genome of interest.

Since version 2 MGRA supports gene insertion and deletions in addition to genome rearrangements and allows the input genomes to have different gene content.

It also can reconstruct most plausible phylogenetic tree based on the rearrangement characters.

Address of the bookmark: http://mgra.cblab.org/

Chang lab

Tue, 24 Sep 2013 17:25:49 -0500

The Chang lab is focused on how the activities of hundreds or even thousands of genes (gene parties) are coordinated to achieve biological meaning. We have pioneered methods to predict, dissect, and control large-scale gene regulatory programs; these methods have provided insights into human development, cancer, and aging. A particular interest is how cells know and remember their locations in the body, particularly with the help of long noncoding RNAs.

More at http://changlab.stanford.edu/index.html

Genomicus: genome browser that enables users to navigate in genomes in several dimensions

Jit — Sat, 18 Nov 2017 16:10:16 -0600

Genomicus is a genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.

Once a query gene has been entered, it is displayed in its genomic context in parallel to the genomic context of all its orthologous and paralogous copies in all the other sequenced metazoan genomes. Moreover, Genomicus stores and displays the predicted ancestral genome structure in all the ancestral species within the phylogenetic range of interest.

All the data on extant species displayed in this browser are from Ensembl.

Address of the bookmark: http://genomicus.biologie.ens.fr/genomicus-90.01/cgi-bin/search.pl

Genetics for Fun and Profit: Andrew Hessel at TEDxVilnius

Sun, 01 Sep 2013 19:15:06 -0500

Andrew Hessel co-chairs the Bioinformatics and Biotechnology track at the Singularity University, an institution founded by futurist Ray Kurzweil and X Prize Foundation CEO Peter Diamandis, with sponsorship from world-leading organizations that include Google, Autodesk, and NASA. He is also the founder of the Pink Army Cooperative, a venture aiming to make open source personalized cancer therapies. His work has been featured in The New York Times, Futurist Magazine, H+, and Wired News. In the spirit of ideas worth spreading, TEDx is a program of local, self-organized events that bring people together to share a TED-like experience. At a TEDx event, TEDTalks video and live speakers combine to spark deep discussion and connection in a small group. These local, self-organized events are branded TEDx, where x = independently organized TED event. The TED Conference provides general guidance for the TEDx program, but individual TEDx events are self-organized.* (*Subject to certain rules and regulations)

Mugsy: multiple whole genome alignment tool

Jit — Fri, 08 Dec 2017 17:41:14 -0600

Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive multiple alignment strategy from Seqan::TCoffee. Mugsy accepts draft genomes in the form of multi-FASTA files and does not require a reference genome.

To cite Mugsy, use:

Angiuoli SV and Salzberg SL. Mugsy: Fast multiple alignment of closely related whole genomes.Bioinformatics 2011 27(3):334-4

Address of the bookmark: http://mugsy.sourceforge.net/

PostDocs positions in computer science in HELSINKI, FINLAND

Fri, 06 Sep 2013 10:11:19 -0500

Several university departments in the Helsinki region, Finland, are looking for postdoctoral researchers in the field of computer science and information technology. Jobs are available at:
· Helsinki Institute for Information Technology HIIT, Aalto University and University of Helsinki, http://www.hiit.fi
· Department of Computer Science, University of Helsinki, http://www.cs.helsinki.fi
· Department of Information and Computer Science, Aalto University, http://ics.aalto.fi
· Department of Computer Science and Engineering, Aalto University, http://cse.aalto.fi
· Department of Mathematics and Statistics, University of Helsinki, http://mathstat.helsinki.fi/english/

Why Helsinki?
The collaborating Aalto University and University of Helsinki form a leading hub of computer science and modelling, including Machine learning, Data mining, Algorithms, Computational Logic, Cloud computing, Distributed computing, Human-centric ubiquitous ICT, Bioinformatics, etc.
Helsinki region is a safe, pleasant and attractive place to live in, with well-functioning services such as public transport etc. Finland has a comprehensive social security and health care system, including exceptionally good parental leaves, and children's day care services.

Positions are offered in:
Algorithm engineering (String Algorithms group)
Algorithmic bioinformatics (Genome-Scale Algorithmics group)
Automated reasoning and search, especially propositional logic (Computational Logic group)
Computational astrophysics and/or data analysis (Computational Methods and Data Analysis for Astrophysics group)
Computational biology and statistical methods in bioinformatics (Computational Systems Biology group)
Computational creativity and data mining (Discovery group)
Dynamic and large-scale networked systems (Data Communications Software group)
Intelligent multimodal information access (Content-Based Image and Information Retrieval Group)
Machine learning and neuroscience (Statistical Machine Learning group)
Machine learning for structured data (Kernel Machines, Pattern Analysis and Computational Biology group)
Machine learning methods for infectious disease epidemiology (Bayesian Statistics Group)
Probabilistic modeling and machine learning (Complex Systems Computation group)
Statistical machine learning (Statistical Machine Learning group)
Analysing ubiquitous sensor data (HIIT-Wide Focus Area)
Interactive visualization (HIIT-Wide Focus Area)
Affective computing and BCI (HIIT-Wide Focus Area)
Intelligent user interfaces and/or recommender systems (HIIT-Wide Focus Area)
Information retrieval and HCI (HIIT-Wide Focus Area)
Machine learning and data analysis, especially information retrieval, HCI, text and context data (HIIT-Wide Focus Area)
Probabilistic modeling and data analysis for bioinformatics (HIIT-Wide Focus Area)

More at http://www.hiit.fi/postdoc-call-2013

AliTV—interactive visualization of whole genome comparisons

Jit — Wed, 10 Jan 2018 07:08:17 -0600

AliTV, which provides interactive visualization of whole genome alignments. AliTV reads multiple whole genome alignments or automatically generates alignments from the provided data. Optional feature annotations and phylo- genetic information are supported. The user-friendly, web-browser based and highly customizable interface allows rapid exploration and manipulation of the visualized data as well as the export of publication-ready high-quality figures. AliTV is freely available at https://github.com/AliTVTeam/AliTV

https://alitvteam.github.io/AliTV/

Address of the bookmark: https://github.com/AliTVTeam/AliTV

CPCRI Kasaragod Bioinformatics PA

Sat, 07 Sep 2013 14:15:53 -0500

CENTRAL PLANTATION CROPS RESEARCH INSTITUTE
(Indian Council of Agricultural Research)
KASARAGOD -671 124, KERALA

WALK-IN-INTERVIEW

Walk-in-test cum interview for selection to the following temporary assignments sanctioned under the DBT sponsored adhoc time bound research scheme entitled "Establishment of a Sub-DIC" will be held at CPCRl, Kudlu PO, Kasaragod District, Kerala -6711 24 on the date and time indicated against each:

Project Assistant

Qualification: Essential: Masters Degree in Bioinformatics / B.Tech Degree in Bioinformatics

Desirable: 1. Experience in the field of bioinformatics
2. M.Phil / Doctoral degree in the field

Date of interview 24.09.2013 at 10.00 a.m.

Trainee – 2 Posts

Essential: Masters Degree in Bioinformatics or B.Tech Degree in Bioinformatics.

Date of interview 25.09.2013 at 10.00 a.m.

Studentship – 2 Posts

Essential Final Year/Semester students of MSc Bioinformatics or B.Tech Bioinformatics

Date of Interview 25.09.2013 at 10.00 a.m.

The candidates fulfilling the above eligibility criteria for Item No.1 & II shall apply online and walk-in for a written test and interview at CPCRI, Kasaragod on the respective dates at 10.00 a.m. The candidates for Studentship should submit the application through their Head of the Department. They shall also bring with them a set of bio data and original certificates in proof of age, educational qualifications, experience etc. Candidates who fail to produce the original of the Degree/PO certificates OR provisional certificate will not be allowed to attend the test / interview. Those who are qualified in written test will only be permitted to attend the interview.

No TA will be paid for the journey for attending the interview.

Advertisement: http://www.cpcri.gov.in/images/images/opportunity/sep4_opp.pdf

ARCS: scaffolding genome drafts with linked reads

Rahul Nayak — Tue, 06 Mar 2018 16:35:26 -0600

ARCS, an application that utilizes the barcoding information contained in linked reads to further organize draft genomes into highly contiguous assemblies. We show how the contiguity of an ABySS H.sapiensgenome assembly can be increased over six-fold, using moderate coverage (25-fold) Chromium data. We expect ARCS to have broad utility in harnessing the barcoding information contained in linked read data for connecting high-quality sequences in genome assembly drafts.

Address of the bookmark: https://github.com/bcgsc/ARCS/