BOL: Related items

Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data

Neel — Fri, 25 Feb 2022 04:42:09 -0600

This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc.

Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example:

Address of the bookmark: https://github.com/KamilSJaron/smudgeplot

Shinyheatmap

Jit — Fri, 21 Oct 2016 05:12:11 -0500

Background: Transcriptomics, metabolomics, metagenomics, and other various next-generation sequencing (-omics) fields are known for their production of large datasets. Visualizing such big data has posed technical challenges in biology, both in terms of available computational resources as well as programming acumen. Since heatmaps are used to depict high-dimensional numerical data as a colored grid of cells, efficiency and speed have often proven to be critical considerations in the process of successfully converting data into graphics. For example, rendering interactive heatmaps from large input datasets (e.g., 100k+ rows) has been computationally infeasible on both desktop computers and web browsers. In addition to memory requirements, programming skills and knowledge have frequently been barriers-to-entry for creating highly customizable heatmaps. Results: We propose shinyheatmap: an advanced user-friendly heatmap software suite capable of efficiently creating highly customizable static and interactive biological heatmaps in a web browser. shinyheatmap is a low memory footprint program, making it particularly well-suited for the interactive visualization of extremely large datasets that cannot typically be computed in-memory due to size restrictions. Conclusions: shinyheatmap is hosted online as a freely available web server with an intuitive graphical user interface: http://shinyheatmap.com. The methods are implemented in R, and are available as part of the shinyheatmap project at: https://github.com/Bohdan-Khomtchouk/shinyheatmap.

More at http://biorxiv.org/content/early/2016/09/21/076463

Address of the bookmark: http://shinyheatmap.com/

17 Marie Curie PhD position available immediately

Tue, 23 Jun 2015 06:52:06 -0500

Kindly look into following webpage:
http://medhealth.leeds.ac.uk/info/1450/scholarships/1795/marie_curie_phd_training_network

The closing date for application will be 26 June 2015.

ArrayGen Bioinformatics Genomics Group

Sun, 28 Sep 2014 14:09:55 -0500

ArrayGen is a global bioinformatics company which is a one stop solution for microarray designing and genomics data analysis. Our novel Array Design Approach Strategy (ADAS) aims to condense the time lag between demands of scientific community and manufacture industry, thereby expediting research processes.

ArrayGen specializes in Genomics data analysis and research, as we believe in the level of precision, predictability, benchmark-ability, and data analysis capability of genomics data over other forms of biological data. ArrayGen constantly strives to develop new solutions, and plug the existing gaps in the technological advancement of the field.

More http://www.arraygen.com/

Genetics, epigenetics and disease

Fri, 27 Sep 2013 11:32:55 -0500

Royal Society GlaxoSmithKline Prize Lecture given by Professor Adrian Bird CBE FMedSci FRS on Tuesday 22 January 2013. Adrian Bird CBE FMedSci FRS is the Buchanan Chair of Genetics at the University of Edinburgh. The human genome sequence has been available for more than a decade, but its significance is still not fully understood. While most human genes have been identified, there is much to learn about the DNA signals that control them. This lecture described an unusually short DNA sequence, just two base pairs long, CG, which occurs in several chemically different forms. Defects in signalling by CG are implicated in disease. For example, the autism spectrum disorder Rett syndrome is caused by loss of a protein that reads methylated CG and affects the activity of genes. The Royal Society GlaxoSmithKline Prize Lecture is awarded for original contributions to medical and veterinary sciences published within ten years from the date of the award.

Molecular Genetics Lecture

Rahul Agarwal — Fri, 27 Sep 2013 04:24:45 -0500

"Robert Sapolsky makes interdisciplinary connections between behavioral biology and molecular genetic influences. He relates protein synthesis and point mutations to microevolutionary change, and discusses conflicting theories of gradualism and punctuated equilibrium and the influence of epigenetics on development theories."

"Robert Sapolsky is an American neuroendocrinologist, professor of biology, neuroscience, and neurosurgery at Stanford University, researcher and author" ----Wikipedia

Address of the bookmark: http://www.youtube.com/watch?v=_dRXA1_e30o

Prof. Chandrasekhar Kanduri Laboratory

Fri, 24 Jun 2016 16:59:43 -0500

Our lab has been interested in understanding how long noncoding RNAs control tumor initiation and progression, in addition to use them as potential biomarkers in diagnosis and therapy. We have been using neuroblastoma, a childhood cancer, as a model system to understand the functional role of long noncoding RNAs in cancer development and progression. By using new RNA sequencing technology on neuroblastoma tumors from a large group of Swedish children including both high-risk and low-risk neuroblastomas (108), we have identified several long noncoding RNAs that could have potential role in diagnosis and therapy. We are currently exploring the functional role of these differentially expressed long noncoding RNA in nuroblastoma progression and development.

SocBiN Bioinformatics 2014

Tue, 03 Sep 2013 18:50:20 -0500

14th annual conference in Bioinformatics

Date : June 10-13

Organizers: The Society for Bioinformatics in Northern European countries (SocBiN) and the Norwegian Bioinformatics Platform / ELIXIR.NO

Venue: Department of Informatics, University of Oslo, Norway

Topics:
Tools and technologies for integrative bioinformatics
Metagenomics
Comparative genomics and phylogeny
Post-ENCODE bioinformatics
Gene regulation
Cancer genomes
Marine genomics

2 PhD Position-Bioinformatics Austria

Sun, 09 Feb 2020 03:13:05 -0600

1 position as a University Assistant for 3 years, 30 hours per week, starting as
soon as possible, at the Institute of Biomedical Informatics at Graz University of
Technology

A position for a doctoral candidate is available in Leila Taher’s new lab at the Institute for
Biomedical Informatics at Graz University of Technology (Austria, https://www.bioinfo.tugraz.at).
We develop and apply regulatory genomics and systems biology approaches to analyze large
genomic datasets. Our long-term goal is to gain novel insights into the mechanisms and
evolution of differential gene expression

Link:
https://www.tugraz.at/fileadmin/user_upload/tugrazExternal/1565e0f6-6c94-4077-a118-f84bc91c4b07/Stellenausschreibung_Bioinfo_FWF_Jan2020_EN.pdf

Ensembl comparative genomics resources

Jitendra Narayan — Sun, 28 Feb 2016 17:10:20 -0600

The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available.

Database URL: http://www.ensembl.org.

Address of the bookmark: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4761110/