BOL: Related items

Assistant Professor - Genetics, Genomics, Evolution, and Development - Molecular & Cell Biology

Fri, 14 Aug 2026 09:54:00 -0500

Salary range: The current salary range for this position is $84,100 - $132,900 (9-month academic year salary), however, off-scale salary and other components of pay, which would yield compensation that is higher than this range, are offered to meet competitive conditions.
Anticipated start: July 1, 2027
Application Window
Open date: July 27, 2026
Next review date: Monday, Oct 19, 2026 at 11:59pm (Pacific Time)
Apply by this date to ensure full consideration by the committee.
Final date: Monday, Oct 19, 2026 at 11:59pm (Pacific Time)
Applications will continue to be accepted until this date.
The Department of Molecular and Cell Biology (MCB) at the University of California, Berkeley invites applications for a tenure-track faculty position in the Genetics, Genomics, Evolution, and Development (GGED) Division, at the Assistant Professor level.

More at https://evoldir.net/brian/evoldir/Jobs//UC-Berkeley.Tenure_track_faculty_in_genetics_genomics_evolution_and_development

PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.

BioStar — Fri, 21 Sep 2018 10:19:52 -0500

Development packages for zlib and libbz2 are needed, as well as a standard compiler environment. On Ubuntu, this can be installed via:

sudo apt-get install build-essential libtool automake zlib1g-dev libbz2-dev pkg-config

On MacOS, the Apple Developer tools and Fink (or MacPorts or Brew) must be installed, then:

sudo fink install bzip2-dev pkgconfig

Address of the bookmark: https://github.com/neufeld/pandaseq

ANGES: reconstructing ANcestral GEnomeS maps

Abhimanyu Singh — Thu, 18 May 2017 05:27:08 -0500

This page contains the software ANGES 1.01, that aims at reconstucting ancestral genome maps from homologous markers in extant related genomes.

Download

Program, version 1.01 (July 10, 2012, documentation updated in August 2014)
Examples with results (featured ancestors: boreoeutherian, amniote, yeasts, Burkholderia, monocots); please refer to the documentation of the distribution above.

Address of the bookmark: http://paleogenomics.irmacs.sfu.ca/ANGES/

DESCHRAMBLER

Jit — Thu, 29 Jun 2017 11:54:59 -0500

DESCHRAMBLER is shown to produce highly accurate reconstructions using data simulation and by benchmarking it against other reconstruction tools

You can find the detail of reconstructed data at http://bioinfo.konkuk.ac.kr/DESCHRAMBLER/

Address of the bookmark: https://github.com/jkimlab/DESCHRAMBLER

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

Jit — Mon, 28 Feb 2022 23:27:37 -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.

Summary statistics of Genomicus version 105.01: (view species tree in pdf or newick)


Number of extant species	200
Number of extant genes	4303993
Number of ancestral species	196
Number of ancestral genes	4624213
Number of ancestral synteny blocks	83342

Address of the bookmark: https://www.genomicus.bio.ens.psl.eu/genomicus-105.01/cgi-bin/search.pl

Manolis Kellis Lab

Sun, 31 Jan 2016 20:51:06 -0600

A major focus of our lab is understanding the effects of genetic variation on molecular phenotypes and human disease. We develop methods for integrating diverse functional genomic datasets of transcription, chromatin modifications, regulator binding, and their changes across multiple conditions to interpret genetic associations, identify causal variants, and predict the effects of genetic perturbations.

More at http://compbio.mit.edu

Andi

Jit — Fri, 13 May 2016 05:16:35 -0500

This is the andi program for estimating the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because andi does not compute full alignments, it is so efficient that it scales even up to thousands of bacterial genomes.

This readme covers all necessary instructions for the impatient to get andi up and running. For extensive instructions please consult the manual.

More at https://github.com/evolbioinf/andi/

Address of the bookmark: http://bioinformatics.oxfordjournals.org/content/early/2015/01/13/bioinformatics.btu815.full

Sequence Viewer: Download Transcripts, Exons and Proteins

Mon, 15 Sep 2014 17:30:36 -0500

How to download FASTA sequence for certain gene features while in the NCBI's Sequence Viewer. Sequence Viewer homepage: www.ncbi.nlm.nih.gov/projects/sviewer/ Sequence Viewer playlist: https://www.youtube.com/playlist?list=PL76D7EE6A6A8AC1C3

WEGO : simple but useful tool for visualizing, comparing and plotting GO (Gene Ontology) annotation results

BioStar — Sun, 12 Apr 2020 10:02:22 -0500

WEGO (Web Gene Ontology Annotation Plot) is a simple but useful tool for visualizing, comparing and plotting GO (Gene Ontology) annotation results. As the GO vocabulary became more and more popular, WEGO was widely adopted and used in many researches. Therefore we have updated WEGO 2.0 in 2018. Here are some changes we’ve made:
1. The limit of input file numbers was cancelled. Now the users could upload as many files as they want with one operation.
2. We have added the reference data of 9 species for users selection.
3. Besides the traditional WEGO histogram, WEGO 2.0 outputs an additional type of bar graph showing GO terms with significant gene number differences.

Address of the bookmark: http://wego.genomics.org.cn/

RAVEN: a software suite for Matlab that allows for semi-automated reconstruction of genome-scale models

Jit — Wed, 24 Oct 2018 22:38:05 -0500

The RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox 2 is a software suite for Matlab that allows for semi-automated reconstruction of genome-scale models (GEMs). It makes use of published models and/or KEGG, MetaCyc databases, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. The software is a useful tool for system-wide data analysis in a metabolic context and for streamlined reconstruction of metabolic networks based on protein homology.

Address of the bookmark: https://github.com/SysBioChalmers/RAVEN