BOL: Related items

Peng Lab

Tue, 18 Feb 2014 13:53:46 -0600

Peng Lab at Janelia Farm Research Campus, Howard Hughes Medical Institute focuses on data mining for bioinformatics and computational molecular biology, particularly, bioimage data mining and informatics. These bioimages include cellular and molecular images and related medical images.

* Analysis of Gene Expression Pattern Images: high-performance image analysis and mining for different model organisms, such as fruitfly, C. elegans, and mouse;
* Feature/Model Learning: developing algorithms and software

Location :Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA.

http://research.janelia.org/peng/

SALSA: A tool to scaffold long read assemblies with Hi-C

Jit — Fri, 15 Jun 2018 04:01:15 -0500

This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch. To use the latest version, first run the following commands: cd SALSA make To run the code, you will need Python 2.7, BOOST libraries and Networkx(version lower than 1.2). If you consider using this tool, please cite our publication which describes the methods used for scaffolding. Ghurye, J., Pop, M., Koren, S., Bickhart, D., & Chin, C. S. (2017). Scaffolding of long read assemblies using long range contact information. BMC genomics, 18(1), 527. Link Ghurye, J., Rhie, A., Walenz, B.P., Schmitt, A., Selvaraj, S., Pop, M., Phillippy, A.M. and Koren, S., 2018. Integrating Hi-C links with assembly graphs for chromosome-scale assembly. bioRxiv, p.261149 Link For any queries, please either ask on github issue page or send an email to Jay Ghurye (jayg@cs.umd.edu).

Address of the bookmark: https://github.com/machinegun/SALSA

Assistant Professor @ King Saud University Riyadh

Fri, 21 Feb 2014 05:57:18 -0600

Qualifications: Candidates must have a Ph.D. and a strong background in Molecular and Cellular Biology, protein expression, FACS, or computational biology, and ability to work collaboratively.

This position will have a significant focus on providing analytical support for next generation sequencing data analysis – Exome-sequencing, Targetted sequencing as well as high-throughput genotyping on Illumina platform.

Job location:

Genome Research Chair
King Saud University, Riyadh-11451
KSA

Interested candidate may forward their CV to grcksu@gmail.com

VGSC: A Web-Based Vector Graph Toolkit of Genome Synteny and Collinearity

Abhimanyu Singh — Tue, 30 Oct 2018 10:46:28 -0500

VGSC, the Vector Graph toolkit of genome Synteny and Collinearity, and its online service, to visualize the synteny and collinearity in the common graphical format, including both raster (JPEG, Bitmap, and PNG) and vector graphic (SVG, EPS, and PDF).

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4783527/

SRF position in Computational Systems Biology Computational biology Group, IIIT-Delhi

Sun, 23 Feb 2014 20:56:08 -0600

An opportunity to perform research in DST supported project that involves building of mathematical models to understand the functional relationship between circadian rhythms and memory formation under stressful condition. In this project, mathematical model of circadian rhythms based on gene regulatory mechanisms will be unified with the mathematical model of calcium signal transduction pathway to understand and predict the formation of fear memory under stressful conditions. The research scholar will spend full time on this project to build new models and expected to contribute significantly to prepare the results for publication and presentation, and to contribute to grant proposals.

Required Qualifications: Masters in physics/chemistry/mathematics (or) MTech in bioengineering, chemical (or) Masters in any traditional field of science with outstanding performance throughout the program. Candidate should have cleared GATE/UGC-CSIR examinations. Applicant should have done basic mathematics courses like calculus, differential equations, numerical analysis etc in their degree program and have obtained good grades in those courses. Knowledge of MATLAB and C or at least one traditional programming language is absolutely necessary. Strong inclination to understand biological concepts is a must for this research work as this project is about modeling biological systems.

Salary: A fixed salary of Rs 18000 PM including HRA will be paid.

Last date for application: This advertisement is open until suitable candidate is found for the project.

Preferred Qualifications: - Expertise in dynamical systems theory, bifurcation theory, numerical simulations, parameter estimation.

Independence and high motivation for carrying out interdisciplinary research. - Excellent communication skills and ability to work independently. - Good working habits.

Interested candidates should submit both curriculum vitae and statement of interest in PDF format to sriramk@iiitd.ac.in and should clearly mention in the subject "Application for SRF".

Genome Annotation using MAKER tutorial !

Shruti Paniwala — Thu, 20 Dec 2018 17:39:23 -0600

MAKER is a great tool for annotating a reference genome using empirical and ab initiogene predictions. GMOD, the umbrella organization that includes MAKER, has some nice tutorials online for running MAKER. However, these were quite simplified examples and it took a bit of effort to wrap my head completely around everything. Here I will describe a de novo genome annotation for Boa constrictor in detail, so that there is a record and that it is easy to use this as a guide to annotate any genome.

Address of the bookmark: https://www.biostars.org/p/261203/

Landry Lab

Thu, 17 Jul 2014 14:33:57 -0500

EVOLUTIONARY AND INTEGRATIVE CELL BIOLOGY

Our research is at the crossroad between cell biology, ecological genomics, systems biology, molecular evolution and population genetics. We study the architecture and evolution of protein and signalling networks.

More at http://landrylab.ibis.ulaval.ca/

Darwin-WGA: A Co-processor Provides Increased Sensitivity in Whole Genome Alignments with High Speedup

Jit — Sat, 13 Apr 2019 08:55:31 -0500

Darwin-WGA, is the first hardware accelerator for whole genome alignment and accelerates the gapped filtering stage. Darwin-WGA also employs GACT-X, a novel algorithm used in the extension stage to align arbitrarily long genome sequences using a small on-chip memory, that provides better quality alignments at 2× improvement in memory and speed over the previously published GACT algorithm. Implemented on an FPGA, Darwin-WGA provides up to 24× improvement (performance/$) in WGA over iso-sensitive software.

https://stanford.edu/~yatisht/pubs/darwin-wga.pdf

Address of the bookmark: https://github.com/gsneha26/Darwin-WGA

J. Aires de Sousa Research Group

Wed, 12 Mar 2014 09:57:25 -0500

We are involved in the development of methods and software in chemoinformatics. Current main projects are:

1.automatic learning of chemical reactivity and metabolism,
2.simulation of NMR spectra,
3.modelling of properties of ionic liquids, and
4.representation of molecular chirality.

More at http://joao.airesdesousa.com/

Genome Informatics Section Lab !

Sat, 25 Jan 2020 06:38:23 -0600

Our section develops and applies computational methods for the analysis of massive genomics datasets, focusing on the challenges of genome sequencing and comparative genomics. We aim to improve such foundational processes and translate emerging genomic technologies into practice.

The Genome Informatics Section is hiring! Come join our outstanding team at the NIH’s National Human Genome Research Institute and contribute to the development of new reference genomes and computational methods for DNA sequencing and analysis. Both postdoc and PhD students positions are available. More information and application instructions follow below.

More at https://genomeinformatics.github.io/