BOL: Related items

Cáceres Lab

Sat, 02 Oct 2021 00:20:42 -0500

Lab are included within the Genomics, Bioinformatics and Evolution group of the UAB, and collaborate closely with other researchers in the Barcelona area, such as Xavier Estivill of the Centre for Genomic Regulation (CRG), Juan R González of the Centre for Research in Environmental Epidemiology (CREAL), and Tomàs Marqués-Bonet of the Institute of Evolutionary Biology (IBE), as well as with other international groups and projects.

https://grupsderecerca.uab.cat/cacereslab/

Postdoc at UBasel Comparative Single Cell Genomics

Fri, 13 Dec 2024 12:46:19 -0600

A fully funded 4-year Postdoc position is available in the lab of Patrick
Tschopp at the University of Basel, Switzerland, study the molecular and
tissue-scale dynamics during the embryonic formation of the vertebrate
skeleton and compare it across different vertebrate species with distinct
habitats.

We are looking for a highly motivated candidate with a PhD degree in
Bioinformatics or a related field. Candidates are expected to have a
strong background in evolutionary biology and/or comparative functional
genomics. Additional experiences in single cell functional genomics
analyses, statistics and computational data analyses are a plus, as is
an interest in comparative developmental (EvoDevo) questions.

We offer a dynamic and interactive research environment with state-of-the
art research facilities, good research funding and internationally
competitive salaries.

The Tschopp lab (www.evolution.unibas.ch/tschopp/research/)
studies the gene regulatory mechanisms of cell type
specification and evolution in vertebrates. See also our
preprints at https://doi.org/10.1101/2024.03.26.586769 and
https://doi.org/10.1101/2024.11.28.625862 Applications should include
a motivation letter, a CV, a list of publications, a statement about
research interests, as well as the names and contact details of at
least two referees. Applications (in the form of a single .pdf file)
should be sent to Patrick Tschopp (patrick.tschopp@unibas.ch); review
of applications will begin on January 1st 2025, and will continue until
the position is filled.

Shendure Lab

Wed, 09 Oct 2013 14:21:58 -0500

The Shendure Lab is part of the Department of Genome Sciences at the University of Washington (Seattle, WA). The mission of the lab is to develop and apply new technologies in genomics and molecular biology. Most projects in the lab exploit new DNA sequencing technologies (Shendure et al., Nature Reviews Genetics 2004; Shendure & Ji, Nature Biotechnology 2008; Shendure & Lieberman Aiden, Nature Biotechnology 2012), and generally fall into one of six areas: 1) next-generation human genetics; 2) genome contiguity & completeness; 3) massively parallel functional analysis; 4) molecular tagging; 5) synthetic biology; 6) translational genomics. Our interests in each of these areas are outlined briefly below, and a full list of publications is available via PubMed. http://www.ncbi.nlm.nih.gov/pubmed?cmd=search&term=shendure
More http://krishna.gs.washington.edu/research.html

Lab page @ http://krishna.gs.washington.edu/index.html

Shankar Lab

Wed, 16 Oct 2013 07:02:22 -0500

Research Interest:

(A) Regulatory System Analysis with respect to microRNAs

(B) Computational Epigenomics & Regulomics:

Department of Biotechnology,
Institute of Himalyan Bioresources Technology
CSIR, Palampur(Himachal Pradesh), India.
Email: ravishihbt.res.in; ravish9gmail.com

More @ http://scbb.ihbt.res.in/SCBB_dept/Lab_Member.php

DbBrowser: Attwood Lab

Fri, 18 Oct 2013 10:48:19 -0500

DbBrowser: Attwood Lab research concerns protein sequence analysis, primarily using the method of protein 'fingerprinting'. DbBrowser: Attwood Lab maintain a diagnostic fingerprint database (PRINTS), one of the founding partner of InterPro. We also design software to display sequence and structural data in visually-striking ways (e.g., Ambrosia, CINEMA); DbBrowser: Attwood Lab are building re-usable software components to create semantically integrated bioinformatics applications through UTOPIA, including a 'smart' PDF reader that links bioinformatics databases and tools directly with scientific articles (Utopia Documents); and have developed a number of tools for automatic annotation and text mining (e.g., MINOTAUR, PRECIS, METIS).

More @ http://www.bioinf.manchester.ac.uk/dbbrowser/index.php

Edwards Lab

Sun, 10 Nov 2013 15:07:08 -0600

We study the evolutionary biology of birds and relatives, combining field, museum and genomics approaches to understand the basis of avian diversity, evolution and behavior. Our guiding approaches include population genetics, which provides a quantitative framework for studying speciation, geographic variation and genome evolution; systematics, which acknowledges that the focal species of any study has relatives that are behaviorally and ecologically no less interesting; and natural history, which gives meaning to the genes and genomic patterns we study.

Lab page: http://www.oeb.harvard.edu/faculty/edwards/index.html

Courses to Get You Started with Bioinformatics

LEGE — Tue, 30 Sep 2025 13:07:19 -0500

Bioinformatics is now at the heart of modern biology and medicine. From decoding genomes and predicting antimicrobial resistance, to developing personalized medicine and advancing evolutionary research, computational skills are no longer optional — they are essential.

Yet, for many students, biologists, and even computer scientists, the question is: “Where do I begin?” With so many platforms, books, and tutorials available, it’s easy to feel overwhelmed.

To make it easier, I’ve compiled 10 excellent resources — ranging from beginner-friendly introductions to advanced computational genomics courses. Many of these are freely available, created by pioneers in the field, and widely used in classrooms and research labs worldwide.

Whether you are a complete beginner or looking to strengthen your foundations, these courses will help you build the skills needed to analyze biological data, design workflows, and think computationally about complex biological systems.

1. HarvardX Data Analysis for Genomics by Rafael Irizarry

From the almighty Rafa, this set of online courses (via edX/HarvardX) is a classic starting point for genomic data science and bioinformatics.

2. Applied Computational Genomics – Aaron Quinlan

Aaron Quinlan (creator of bedtools and many other tools) has made his course materials open. A practical, tool-driven genomics introduction.

3. Bioinformatics Algorithms (Coursera + Companion Book)

Find the highly visual video classes on Coursera, backed by the popular Bioinformatics Algorithms book.

4. The Biostar Handbook

Not a course per se, but a hands-on manual by Istvan (founder of Biostars.org) that’s even used in classes at Penn State.

5. Introduction to Bioinformatics and Computational Biology (by Shirley Liu)

A comprehensive introduction from Shirley Liu’s lab (Harvard DFCI). Covers both theory and computational practice.

6. Data Carpentry: Genomics Workshops

Community-driven training workshops that focus on practical, reproducible research. I was honored to serve as curriculum committee chair here.

7. Computational Genomics: Applied Comparative Genomics

From the Schatz Lab — applied comparative genomics with real-world data.

8. Introduction to Computational Biology (Mike Love, creator of DESeq2)

This course bridges statistics, biology, and computation — a solid primer for anyone entering computational biology.

9. MIT Computational Biology (6.047 / 6.878 / HST.507) by Manolis Kellis

Covers genomes, networks, evolution, and health. A deep-dive from MIT’s OpenCourseWare archive.

10. An Introduction to Applied Bioinformatics

An interactive textbook with Python code, designed for practical applied bioinformatics learning.

Oldest Hominin DNA Sequenced

Surajeet — Fri, 27 Dec 2013 19:58:31 -0600

Matthias Meyer and his team from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, have developed new techniques for retrieving and sequencing highly degraded ancient DNA. They then joined forces with Juan-Luis Arsuaga and applied the new techniques to a cave bear from the Sima de los Huesos site. After this success, the researchers sampled two grams of bone powder from a hominin thigh bone from the cave. They extracted its DNA and sequenced the genome of the mitochondria or mtDNA, a small part of the genome that is passed down along the maternal line and occurs in many copies per cell. The researchers then compared this ancient mitochondrial DNA with Neandertals, Denisovans, present-day humans, and apes.

From the missing mutations in the old DNA sequences the researchers calculated that the Sima hominin lived about 400,000 years ago. They also found that it shared a common ancestor with the Denisovans, an extinct archaic group from Asia related to the Neandertals, about 700,000 years ago. "The fact that the mtDNA of the Sima de los Huesos hominin shares a common ancestor with Denisovan rather than Neandertal mtDNAs is unexpected since its skeletal remains carry Neandertal-derived features," says Matthias Meyer. Considering their age and Neandertal-like features, the Sima hominins were likely related to the population ancestral to both Neandertals and Denisovans. Another possibility is that gene flow from yet another group of hominins brought the Denisova-like mtDNA into the Sima hominins or their ancestors.

Reference

http://www.sciencedaily.com/releases/2013/12/131204132018.htm

Marie Curie PhD position available immediately

Fri, 24 Apr 2015 09:23:57 -0500

Sub-project 10: Development of bioinformatic tools for the analysis of MACE data
Host Organizations GenXPRO (Germany)
Objectives : The ESR will be in charge of standardising pipelines that will be used for RNA-seq and MACE analyses by all the participants. He will be involved in performing next generation sequencing to characterise environmental adaptation. A single pipeline to analyse listerial transcriptomic and proteomic data will be developed and implemented by each partner for the sake of uniformity of all the data produced within List_MAPS. The ESR will be involved in the interpretation of transcriptomic and proteomic data for which pathway analyses and good data visualization will be required. A cytoscape app will be developed as visualization tool.
Expected Results: MACE analysis pipeline. Database. Transcriptome comparisons in selected habitats. Data visualization tool.
Duration (months) 24
Contact Dr. Bjorn ROTTER: rotter@genxpro.de

11. Development of innovative tools for rapid phenotypic characterisation of intraspecific diversity of Listeria monocytogenes (Joint supervision PhD)
Host Organizations BioFilm Control (France) and GenXPRO (Germany)
Objectives
1. The ESR will develop an assay to test biofilm phenotype in a large array of food processing-related environmental conditions (salt, acides, disinfectants, preservatives) in BFC facilities. He will be in charge of the development and validation of an in silico virulence assay. This assay will target specific mRNAs in order to estimate the virulence potential of strains of L. monocytogenes. Transcript targets will be selected and tested by qPCR in GXP premises. In the process of validation, virulence results of several strains collected in a humanised mouse model will be compared with the in silico analysis. Once these innovative tools will be validated, intraspecific phenotypic diversity (biofilm and virulence) will be assessed on a collection of environmental and clinical isolates of L. monocytogenes. Genotypic diversity will be assessed under the supervision of GPX.
Expected Results : Adaptation of the BioFilm Ring test R to test food processing environmental conditions. Development of an innovative in silico virulence assay surrogate to animal models. Diversity results will inform stakeholders on the level of health hazard according to the strain. This in turn will help secure food safety all along the shelf life of foodstuff.
Duration (months) 36
Contact : Dr. Thierry BERNARDI: thbe@biofilmcontrol.com
Dr. Bjorn ROTTER: rotter@genxpro.de
ELIGIBLE CRITERIA of Marie Sklokowska Curie actions:
Researchers may be of any nationality
Candidates shall at the time of recruitment by the host organization, be in the first four years (full-time equivalent research experience) of their research careers. Full-time equivalent research experience is measured from the date when a researcher obtained the degree which would formally entitle him or her to embark on a doctorate, either in the co

Post doc in Computational Genetics and Genomics at CEINGE Biotecnologie Avanzate, Naples, Italy

Tue, 11 Feb 2014 08:06:47 -0600

We are seeking one motivated scientist to analyze genomics and transcriptomics data of a large collection of neuroblastoma tumors. The successful candidate will be part of a team of researchers with extensive expertise in genome cancer study. He/she will be involved in the analysis of DNA-seq, RNA-seq, ChIP-seq data using available methods running in R and UNIX environment.

Qualifications

PhD or Post-Graduated Master degree is required. Successful candidates will have some expertise in data analysis of NGS data by using methods running in R and UNIX environment. Familiarity with genome databases and browsers is required.

Application

Candidates should send a CV and a brief personal statement focusing on their skills and interests related to the research project.

Contacts

Start date: 1° April 2014
Salary on grant: 25,000 euros per year.
Contact Person (Referent): Mario Capasso
Ref. Email: mario.capasso@unina.it and achille.iolascon@unina.it
Tel: +39 081 3737889