BOL: Related items

Liberles Research Group

Wed, 12 Aug 2026 03:39:53 -0500

The Liberles Research Group works in the areas of computational comparative genomics, and molecular evolution. The central theme in the research group is the detection and characterization of the lineage-specific divergence of protein-encoding genes. Much of the work in the group is done in a phylogenetic context. Ultimately, we want to ask the question, “What makes each species unique at the genomic level?” and “what are the processes driving the functional divergence of genomes?”.

More at https://sites.temple.edu/liberles/

When Genes Leave Clues: Reading the Evolutionary Footprints of Life

LEGE — Fri, 11 Sep 2026 13:47:07 -0500

Imagine walking through a forest and finding two sets of footprints that always appear, disappear, and reappear together. You might wonder whether the animals are connected. In genomics, genes leave similar footprints across evolution. When two genes repeatedly occur together—or disappear together—across different species, their shared evolutionary history can provide clues about their function.

This idea, known as phylogenetic profiling, is the foundation of Profylo (https://github.com/MartinSchoenstein/Profylo), an open-source Python toolkit developed for comparing evolutionary profiles and discovering co-evolving genes. Profylo brings together seven profile-comparison methods and four approaches for identifying co-evolving gene clusters, making it easier to explore hidden functional relationships within genomes.

The study demonstrates that even a simple matrix of gene presence and absence can reveal meaningful biological patterns. By following these evolutionary footprints, researchers can generate new hypotheses about unknown genes, pathways, and molecular interactions. In a world where genomes are being sequenced faster than ever, tools like Profylo offer an exciting way to let evolution itself become a guide to understanding gene function.

More at https://link.springer.com/article/10.1007/s00239-025-10280-6

Compressive Genomics

Rahul Agarwal — Sun, 11 Aug 2013 11:13:58 -0500

The key to finding a solution is to notice that most genomicsequences differ by very little. It may well be that the number of complete genome sequences being stored is increasing rapidly, but the actual amount of new data is very small. In other words, a single DNA sequence isn't particularly compressible but a set of sequences shares so much in common that the redundancy can be used to store them in a much smaller storage space. (Source:e-article from Alex Armstrong)

http://www.i-programmer.info/news/181-algorithms/4537-a-new-dna-sequence-search-compressive-genomics.html

http://en.wikipedia.org/wiki/Compression_of_Genomic_Re-Sequencing_Data

http://www.nature.com/nbt/journal/v30/n7/full/nbt.2241.html

http://bioinformatics.oxfordjournals.org/content/29/13/i283.full

http://groups.csail.mit.edu/cb/cast/

Bioinformatics course and lectures

Rahul Agarwal — Tue, 03 Sep 2013 16:41:02 -0500

http://openwetware.org/wiki/User:Jarle_Pahr/Bioinformatics

Address of the bookmark: http://gtpb.igc.gulbenkian.pt/bicourses/index.html

Eivind Hovig's Lab

Tue, 03 Sep 2013 19:06:29 -0500

Bioinformatics relevant research topics are:

genomic scale studies
endogenous mechanisms of mutations, germ line and somatic
computational aspects of immunology in cancer
signalling networks
three-dimensional organization of information in the nucleus
gene silencing
metastatic cross-talk
kinase signaling
personalized medicine
detection of biomarkers in cancer
historical DNA variation

From : http://www.ous-research.no/hovig/

Group address:
Eivind Hovig, The Norwegian Radium Hospital, Montebello, 0310 Oslo,Norway
Email: ehovig@radium.uio.no

Computational Methods for the Analysis of the Diversity and Dynamics of Genomes

Sat, 09 Nov 2013 20:19:02 -0600

The German-Canadian international research training group

"Computational Methods for the Analysis of the Diversity and Dynamics of Genomes"

has currently open positions for graduate students, to study at Simon Fraser University (Vancouver, Canada) and
Bielefeld University (Germany), starting in the fall 2014.

This international graduate program is a close cooperation of:

Bielefeld University, Germany: Graduate progam "DiDy"
Simon Fraser University (SFU), Vancouver, Canada: Graduate program "MADD-Gen"

The available positions include six PhD positions at Bielefeld University, as well as PhD and MSc positions at SFU.

Application deadline: December 31st, 2013
Webpage: http://wiki.techfak.uni-bielefeld.de/didy/Announcement

Bioinformatics job in Genotypic Tech, India

Mon, 07 Apr 2014 08:20:54 -0500

Genotypic Technology, the first Genomics Company of India is poised to become the next generation life sciences company. We are hiring professionals for our high end Genomics Labs (Molecular Biology/ Microarray/NGS) and Bioinformatics groups.

Apply to Genotypic Technology if you are a PhD in Life Sciences/ Molecular Biology/ Biotechnology/ Human Genetics/ Bioinformatics with minimum 4-5 years post doctoral experience as well as publications in peer reviewed journals.

Source: http://www.genotypic.co.in/Careers/2/Current-Openings.aspx

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.

Epiviz: an interactive visualization tool for functional genomics data.

Jit — Mon, 09 Jul 2018 05:27:39 -0500

Epiviz is an interactive visualization tool for functional genomics data. It supports genome navigation like other genome browsers, but allows multiple visualizations of data within genomic regions using scatterplots, heatmaps and other user-supplied visualizations. It also includes data from the Gene Expression Barcode project for transcriptome visualization. It has a flexible plugin framework so users can addd3 visualizations. You can see a video tour here.

https://bioconductor.org/packages/release/bioc/html/epivizr.html

https://github.com/epiviz

https://github.com/epiviz/epiviz

Address of the bookmark: https://epiviz.github.io/

Nucleus: Python and C++ code for reading and writing genomics data.

Jit — Sun, 02 Feb 2020 08:14:19 -0600

Nucleus is a library of Python and C++ code designed to make it easy to read, write and analyze data in common genomics file formats like SAM and VCF. In addition, Nucleus enables painless integration with the TensorFlow machine learning framework, as anywhere a genomics file is consumed or produced, a TensorFlow tfrecords file may be used instead.

Address of the bookmark: https://github.com/google/nucleus