BOL: Related items

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/

Edanchin Lab

Thu, 19 Nov 2020 08:00:07 -0600

My main topics of interest are:

The impact of non tree-like evolution such as horizontal gene transfers and hybridization on species biology
Evolution and adaptation of animals in the absence of sexual reproduction and the underlying mechanisms
Genomic signatures of adaptation to a parasitic life-style

More at https://edanchin.org/

Postdoctoral Scholar in Bacterial Evolution at Pathogen and Microbiome Institute at Northern Arizona University

Fri, 13 Dec 2024 12:49:16 -0600

We are pleased to announce a Postdoctoral Scholar position to study
bacterial evolution at the Pathogen and Microbiome Institute at
Northern Arizona University with Professor Paul Keim. The scholar
will have the opportunity also work with Professor Sam Sheppard at
The University of Oxford on joint projects. See our recent paper
on interspecific gene flow in Campylobacter. (DOI:
https://doi.org/10.1128/mbio.00581-24)

The job description: "This research position focuses on the science
of bacterial evolution. It will consist of researching theoretical
principles, but could include translational applications. Phylogenomic
and bioinformatic analysis of bacterial populations in nature or
in laboratory experiments will be a key component of the work. Prior
experience is an asset though training will be possible at PMI.
Likewise, laboratory microbiological, molecular, and biochemical
skills are an asset though not essential. Communication and critical
thinking skills are essential for performing the work and for
communicating to the local and international scientific communities.
Participating in team or independent grant writing to obtain research
funding will be required. Student mentoring is a part of the NAU
mission and is a partial expectation."

https://hr.peoplesoft.nau.edu/psp/ph92prta/EMPLOYEE/HRMS/c/HRS_HRAM.HRS_APP_SCHJOB.GBL?Page=HRS_APP_JBPST&Action=U&FOCUS=Applicant&SiteId=1&JobOpeningId=608024&PostingSeq=1

Northern Arizona University is located in Flagstaff, Arizona, a
beautiful mountain town with a surprisingly vibrant restaurant
scene. Located a little over an hour from the Grand Canyon and ~45
min from Sedona, Flagstaff is a hiker's paradise. In fact, the city
of Flagstaff operates more than 50 miles of unpaved trails and there
are, on average, 266 sunny days per year with which to enjoy them.
At 7000 ft in elevation, Flagstaff experiences all four seasons,
but thesummers are mild and, in the winter, you can be on the ski
slopes within 30 min! https://www.flagstaffarizona.org/

As mentioned, joint projects with Professor Sheppard at Oxford
University are possible, including travel to his laboratory in the
United Kingdom. https://www.biology.ox.ac.uk/people/samuel-sheppard

Contact Information:
Paul.Keim@nau.edu

Paul S. Keim, Ph.D.
Regents Professor, &
Cowden Endowed Chair of Microbiology
Northern Arizona University
Flagstaff, AZ 86011-4073

Paul S Keim

Mulan: Multiple-sequence local alignment and visualization for studying function and evolution

Jit — Fri, 24 Aug 2018 09:50:01 -0500

Mulan: Multiple-sequence local alignment and visualization for studying function and evolution

Mulan (http://mulan.dcode.org/), a novel method and a network server for comparing multiple draft and finished-quality sequences to identify functional elements conserved over evolutionary time. Mulan brings together several novel algorithms: the TBA multi-aligner program for rapid identification of local sequence conservation, and the multiTF program for detecting evolutionarily conserved transcription factor binding sites in multiple alignments. In addition, Mulan supports two-way communication with the GALA database; alignments of multiple species dynamically generated in GALA can be viewed in Mulan, and conserved transcription factor binding sites identified with Mulan/multiTF can be integrated and overlaid with extensive genome annotation data using GALA.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC540288/

The Rogers Lab

Mon, 15 Jul 2019 08:07:44 -0500

The Rogers lab studies evolution of genome structure. We explore the ways that complex mutations like duplications, deletions, rearrangements, and retrogenes can create new genetic material. We study how these new mutations are important for adaptation. We are currently working on projects in Drosophila, Mammoths, Elephants, Bivalves, and Frogs absolutely no amphibians. This multi-organism approach can help us understand when and why complex mutations are important for organism fitness.

More at http://evolscientist.com/

P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads

BioStar — Fri, 07 Sep 2018 05:19:06 -0500

P_RNA_scaffolder is a novel scaffolding tool using Pair-end RNA-seq to scaffold genome fragments. The method is suitable for most genomes. The program could utilize Illumina Paired-end RNA-sequencing reads from target speciesies. Our method provides another practical alternative to existing mate-pair_based approaches or other Protein-based approaches (for instance, PEP_scaffolder ) for scaffolding genome sequences. The most important feature of this method is to improve the completeness of gene regions and long-coding gene regions (for instance, circRNA).

Address of the bookmark: http://www.fishbrowser.org/software/P_RNA_scaffolder/#

LTR_Finder: an efficient program for finding full-length LTR retrotranspsons in genome sequences.

Neel — Sun, 13 Jan 2019 07:05:53 -0600

LTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome sequences.

The Program first constructs all exact match pairs by a suffix-array based algorithm and extends them to long highly similar pairs. Then Smith-Waterman algorithm is used to adjust the ends of LTR pair candidates to get alignment boundaries. These boundaries are subject to re-adjustment using supporting information of TG..CA box and TSRs and reliable LTRs are selected. Next, LTR_FINDER tries to identify PBS, PPT and RT inside LTR pairs by build-in aligning and counting modules. RT identification includes a dynamic programming to process frame shift. For other protein domains, LTR_FINDER calls ps_scan (from PROSITE, http://www.expasy.org/prosite/) to locate cores of important enzymes if they occur.

Address of the bookmark: https://github.com/xzhub/LTR_Finder

AirLift, a methodology and tool for comprehensively moving mappings and annotations from one genome to another similar genome

Jit — Mon, 23 Dec 2019 10:20:13 -0600

We propose AirLift, a methodology and tool for comprehensively moving mappings and annotations from one genome to another similar genome while maintaining the accuracy of a full mapper.

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

Calling variants in non-diploid systems

Neel — Sat, 26 Jun 2021 15:37:49 -0500

The main challenge associated with non-diploid variant calling is the difficulty in distinguishing between the sequencing noise (abundant in all NGS platforms) and true low frequency variants. Some of the early attempts to do this well have been accomplished on human mitochondrial DNA although the same approaches will work equally good on viral and bacterial genomes (Rebolledo-Jaramillo et al. 2014, Li et al. 2015).

Address of the bookmark: https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/non-dip/tutorial.html

Monkeypox virus isolate MPXV_USA_2022_MA001, complete genome

Jit — Tue, 26 Jul 2022 06:21:07 -0500

LOCUS       ON563414              197205 bp    DNA     linear   VRL 30-MAY-2022
DEFINITION  Monkeypox virus isolate MPXV_USA_2022_MA001, complete genome.
ACCESSION   ON563414
VERSION     ON563414.3
KEYWORDS    .
SOURCE      Monkeypox virus (monkeypox)
  ORGANISM  Monkeypox virus
            Viruses; Varidnaviria; Bamfordvirae; Nucleocytoviricota;
            Pokkesviricetes; Chitovirales; Poxviridae; Chordopoxvirinae;
            Orthopoxvirus.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/nuccore/ON563414