BOL: Related items

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/

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/

RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs

BioJoker — Wed, 17 Apr 2019 19:45:22 -0500

Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC: Fast and accurate reference-guided scaffolding of draft genomes. bioRxiv 2019.

RaGOO is a tool for coalescing genome assembly contigs into pseudochromosomes via minimap2 alignments to a closely related reference genome. The focus of this tool is on practicality and therefore has the following features:

Good performance. On a MacBook Pro using Arabidopsis data, pseudochromosome construction takes less than a minute and the whole pipeline with SV calling takes ~2 minutes.
Intact ordering and orienting of contigs.
Chimeric contig correction
GFF lift-over
Structural variant calling with and integrated version of Assemblytics
Confidence scores associated with the grouping, localization, and orientation for each contig.

Address of the bookmark: https://github.com/malonge/RaGOO

Bioinformatics postdoctoral position at inStem

Tue, 13 Feb 2018 03:18:54 -0600

One postdoctoral position is available in the area of Bioinformatics. This position is available through a highly collaborative project involving multiple labs.

The primary focus here would be to analyse and integrate high throughput data from various aspects of translation regulation including non-coding RNAs, mRNAs and modification of ribosomal RNA. We request the interested candidates to approach either

Dasaradhi Palakodeti (dasaradhip@instem.res.in)
Or
Ravi Muddashetty (ravism@instem.res.in)

Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm

BioStar — Mon, 16 Mar 2020 10:09:26 -0500

Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a single run and polish the assemblies of genomes of any size. Described by Firtina et al. (preliminary version at https://arxiv.org/pdf/1902.04341.pdf

More at https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa179/5804978?rss=1

Address of the bookmark: https://github.com/CMU-SAFARI/Apollo

Bioinformatics postdoctoral position at CSIR - Institute of Himalayan Bioresource Technology, Palampur (H.P.)

Thu, 05 Apr 2018 06:57:17 -0500

Walk-in-Interview is scheduled to be held on the date as mentioned below for selection of Suitable candidates in the following areas under the DBT sponsored projecT on purely temporary basis for the duration of the project(s) or till completion of projects whichever is earlier:

Project Title:
"Exploration of RBP-RNA interactions to reveal the post-transcriptional regulatory impact, and development of related tools and resource server".

Position: Research Associate (1 position)
Age : 35 years as on 02.05.2018
Salary : Rs.36,000/- P.M. + H.R.A.

as per the funds provisions in the respective projects.

Eligibility Criteria :
Essential Qualifications: Ph.D. in any area of Bioinformatics/ Computational Biology/ Life Sciences.
Desirable: Candidate having experience in Bioinformatics will be preferred.

Essential Qualifications: M.Tech. in Bioinformatics/ Computation Biology/ Computer Science or any related area with 3 years of research experience.

Selection Procedure : Walk In Interview

Date : 02 May, 2018
Time : 9:30 A.M.
Venue : CSIR-IHBT Palampur (H.P.)

For more info refer to following doc:

http://ihbt.res.in/components/com_chronoforms5/chronoforms/uploads/Recruitment/20180404125233_AdvtNo11_2018.pdf

MitoFinder

Neel — Tue, 29 Aug 2023 02:13:01 -0500

Allio, R., Schomaker-Bastos, A., Romiguier, J., Prosdocimi, F., Nabholz, B., & Delsuc, F. (2020) Mol Ecol Resour. 20, 892-905. (publication link)

Mitofinder is a pipeline to assemble mitochondrial genomes and annotate mitochondrial genes from trimmed read sequencing data.

MitoFinder is also designed to find and annotate mitochondrial sequences in existing genomic assemblies (generated from Hifi/PacBio/Nanopore/Illumina sequencing data...)

MitoFinder is distributed under the license.

Address of the bookmark: https://github.com/RemiAllio/MitoFinder

Bioinformatics Project Assistant Level II position at CSIR - Institute of Himalayan Bioresource Technology, Palampur (H.P.)

Thu, 17 May 2018 01:53:17 -0500

Walk-in-Interview is scheduled to be held on the date as mentioned below for selection of Suitable candidates in the following areas under the DBT sponsored project on purely temporary basis for the duration of the project(s) or till completion of projects whichever is earlier:

Project Title:
"Exploration of RBP-RNA interactions to reveal the post-transcriptional regulatory impact, and development of related tools and resource server".

Position: Project Assistant Level II (1 position)
Age : 28 years as on 14.06.2018
Salary : Rs.25,000/- P.M.

as per the funds provisions in the respective projects.

Eligibility Criteria :
Essential Qualifications: M.Sc. in Bioinformatics / Computational Biology or any area of Bioinformatics with 55% marks.

Essential Qualifications: M.Sc. in any area of Life Sciences with 55% marks with Diploma in any area of Bloinformatics.

Essential Qualifications: B.Tech. / M.Tech. in Bioinformatics / Computer Science with 55% marks.

Selection Procedure : Walk In Interview

Date : 14 June, 2018
Time : 9:30 A.M.
Venue : CSIR-IHBT Palampur (H.P.)

For more info refer to following doc:

http://ihbt.res.in/components/com_chronoforms5/chronoforms/uploads/Recruitment/20180516114701_Advt15_2018.pdf

Peregrine & SHIMMER Genome Assembly Toolkit

Abhi — Thu, 16 Dec 2021 02:50:19 -0600

Peregrine is a fast genome assembler for accurate long reads (length > 10kb, accuracy > 99%). It can assemble a human genome from 30x reads within 20 cpu hours from reads to polished consensus. It uses Sparse HIereachical MimiMizER (SHIMMER) for fast read-to-read overlaping without quadratic comparisions used in other OLC assemblers.

Address of the bookmark: https://github.com/cschin/Peregrine

Applied Statistics for Bioinformatics using R

Neel — Thu, 30 Aug 2018 03:45:39 -0500

The purpose of this book is to give an introduction into statistics in order to solve some problems of bioinformatics. Statistics provides procedures to explore and visualize data as well as to test biological hypotheses. The book intends to be introductory in explaining and programming elementary statistical concepts, thereby bridging the gap between high school levels and the specialized statistical literature