<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/13226?offset=1130 https://bioinformaticsonline.com/pages/view/1161/genomics-for-bioinformatician Sat, 20 Jul 2013 07:03:00 -0500 https://bioinformaticsonline.com/pages/view/1161/genomics-for-bioinformatician <![CDATA[Genomics for Bioinformatician]]> Genomics is the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of intragenomic phenomena such as heterosis, epistasis, pleiotropy and other interactions between loci and alleles within the genome. In contrast, the investigation of the roles and functions of single genes is a primary focus of molecular biology or genetics and is a common topic of modern medical and biological research. Research of single genes does not fall into the definition of genomics unless the aim of this genetic, pathway, and functional information analysis is to elucidate its effect on, place in, and response to the entire genome's networks.

Genomics was established by Fred Sanger when he first sequenced the complete genomes of a virus and a mitochondrion. His group established techniques of sequencing, genome mapping, data storage, and bioinformatic analyses in the 1970-1980s. A major branch of genomics is still concerned with sequencing the genomes of various organisms, but the knowledge of full genomes has created the possibility for the field of functional genomics, mainly concerned with patterns of gene expression during various conditions. The most important tools here are microarrays and bioinformatics. Study of the full set of proteins in a cell type or tissue, and the changes during various conditions, is called proteomics. A related concept is materiomics, which is defined as the study of the material properties of biological materials (e.g. hierarchical protein structures and materials, mineralized biological tissues, etc.) and their effect on the macroscopic function and failure in their biological context, linking processes, structure and properties at multiple scales through a materials science approach. The actual term 'genomics' is thought to have been coined by Dr. Tom Roderick, a geneticist at the Jackson Laboratory (Bar Harbor, ME) over beer at a meeting held in Maryland on the mapping of the human genome in 1986.

The outcome of almost two years of intense discussions with literally hundreds of scientists and members of the public, has three major areas of focus: Genomics to Biology, Genomics to Health, and Genomics to Society.

Genomics to Biology: 
The human genome sequence provides foundational information that now will allow development of a comprehensive catalog of all of the genome's components, determination of the function of all human genes, and deciphering of how genes and proteins work together in pathways and networks.

Genomics to Health:
Completion of the human genome sequence offers a unique opportunity to understand the role of genetic factors in health and disease, and to apply that understanding rapidly to prevention, diagnosis, and treatment. This opportunity will be realized through such genomics-based approaches as identification of genes and pathways and determining how they interact with environmental factors in health and disease, more precise prediction of disease susceptibility and drug response, early detection of illness, and development of entirely new therapeutic approaches.

Genomics to Society: 
Just as the HGP has spawned new areas of research in basic biology and in health, it has created new opportunities in exploring the ethical, legal, and social implications (ELSI) of such work. These include defining policy options regarding the use of genomic information in both medical and non-medical settings and analysis of the impact of genomics on such concepts as race, ethnicity, kinship, individual and group identity, health, disease, and "normality" for traits and behaviors.

This vision for the future of genomics is not just about the NHGRI. It encompasses the whole field of genomics, including the work of all the other Institutes and Centers at the NIH and of a number of other federal agencies. All of the NIH Institutes are already taking full advantage of the sequence and will apply its data to the better understanding of both rare and common diseases, almost all of which have a genetic component. A recent example of the way that the HGP and the knowledge and new technologies it has spawned are already facilitating science is the extremely rapid sequencing by groups in Canada and at the Centers for Disease Control and Prevention (CDC) in Atlanta of the genome of the virus that causes Severe Acute Respiratory Syndrome (SARS). The sequencing of the SARS virus genome provides insight into this new and deadly disease at a speed never before possible in science. In turn, this should lead to the rapid development of diagnostic tests and, in time, vaccines and effective treatments.

Links for the addition material available on Net

Genomes and genomics:

Bioinformatics and Genomics:

Structural genomics tutorial:

Comparative Genomics Tutorial:

GENOME TUTORIAL:

Tools and resources for identifying protein families, domains and motifs

Bioinformatics Tools 
Tips, Tutorials, and Terminology for Using Selected Resources in Genome Database Guide:

A Web-Based Comparative Genomics Tutorial for Investigating Microbial Genomes:

Free Online Tutorials Teach Anyone How to Use Genome Databases:

Circos to create concise, explanatory, unique and print-ready visualizations of your data:

Genomics and Comparative Genomics Learning Module:

Computational Challenges in Comparative Genomics

A Tutorial:

A Comparative Genomics Resource for Grains:

PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants:

VISTA:

Software for Genomics

  1. Artemis Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation.
  2. Chromas It will display and prints chromatogram files from ABI automated DNA sequencers, and Staden SCF files which the analysis programs for ALF, Li-Cor and Visible Genetics OpenGene sequencers can create.
  3. Glimmer A system for finding genes in microbial DNA, especially the genomes of bacteria and archaea.Glimmer (Gene Locator and Interpolated Markov Modeler) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DN
  4. Glimmer HMM A fast and accurate gene finder based on a GHMM architecture, developed specifically for eukaryotes. It incorporates splice site models adapted from the GeneSplicer program and uses interpolated Markov models for evaluating the coding regions.
  5. Glimmer M A gene finder derived from Glimmer, but developed specifically for eukaryotes. It is based on a dynamic programming algorithm that considers all combinations of possible exons for inclusion in a gene model and chooses the best of these combinations. The d
  6. MUMmer MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form.
  7. pDRAW pDRAW32 is being developed as a free time hobby project. It is far from finished, but as it has reached a point where it could be helpful for many labs, it is now available to the scientific community.
  8. Sequin Sequin is a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank, EMBL, or DDBJ sequence databases. It is capable of handling simple submissions that contain a single short mRNA sequence, and complex submissio
  9. Staden The Staden Package consists of a series of tools for DNA sequence preparation (pregap4), assembly (gap4), editing (gap4) and DNA/protein sequence analysis (spin).

For more software @ http://bioinformaticsonline.com/bookmarks/view/926/list-of-popular-bioinformatics-softwaretools

]]> Jitendra Narayan https://bioinformaticsonline.com/blog/view/44762/stay-connected-and-productive-unlock-the-power-of-screen-tmux-and-mosh-for-bioinformatics Wed, 22 Jan 2025 00:29:52 -0600 https://bioinformaticsonline.com/blog/view/44762/stay-connected-and-productive-unlock-the-power-of-screen-tmux-and-mosh-for-bioinformatics <![CDATA[Stay Connected and Productive: Unlock the Power of Screen, Tmux, and Mosh for Bioinformatics]]> If you are a bioinformatician, chances are you have spent hours running long, complex analyses on remote servers only to lose your session because of an unstable connection. Frustrating, isnt it? Fear not! With tools like screen, tmux, and mosh, you can safeguard your workflow and stay productive, no matter where you are.

Why Remote Session Management is a Must-Have

In bioinformatics, tasks like genome assembly, RNA-seq analyses, and phylogenetic computations often take hours or days. A dropped SSH connection can result in:

  • Lost Progress: Restarting a job from scratch wastes valuable time.
  • Workflow Interruptions: Disruptions can derail your focus and productivity.
  • Corrupted Data: Interrupted processes may lead to incomplete or corrupted outputs.

By integrating screen, tmux, or mosh into your workflow, you can avoid these setbacks and ensure a seamless experience.

Screen: The Classic Workhorse

Screen is a terminal multiplexer that comes pre-installed on most Linux systems. It allows you to manage multiple terminal sessions and reconnect to them even after being disconnected.

Getting Started with Screen:

  1. Start a Session:
    screen
  2. Detach from a Session:
    Press Ctrl+A, then D.
  3. Reattach to a Session:
    screen -r

Pro Tip: Enhance your screen experience with a customized .screenrc configuration file. Download one here: Get .screenrc.

Tmux: A Modern Alternative

Tmux takes everything great about screen and adds modern features, including better key bindings and intuitive session management. It\u2019s perfect for bioinformaticians who want more control over their workflow.

Getting Started with Tmux:

  1. Start a Session:
    tmux
  2. Detach from a Session:
    Press Ctrl+B, then D.
  3. Reattach to a Session:
    tmux attach

Customize Your Tmux Experience:
Use a .tmux.conf file to personalize your setup. Grab one here: Download .tmux.conf.

Mosh: The Mobile Shell for Unreliable Connections

SSH works well for stable networks, but it struggles in areas with spotty connectivity. Enter Mosh, the Mobile Shell. Designed for intermittent networks, Mosh keeps your session alive even when the connection drops temporarily.

Why Mosh is a Game-Changer:

  • No lag over high-latency networks.
  • Automatically reconnects when the network is restored.
  • Ideal for working on the go, from cafes to trains.

Getting Started with Mosh:

  1. Install Mosh:
    sudo apt install mosh # For Debian/Ubuntu
  2. Connect to a Server:
    mosh username@server

Learn more at mosh.org.

Why This Matters for Bioinformatics

Every bioinformatician knows the value of time and data integrity. Tools like screen, tmux, and mosh provide a lifeline when running long analyses, enabling you to:

  • Safeguard your work against disconnections.
  • Easily manage multiple workflows in parallel.
  • Stay productive, even in challenging environments.

Quickstart Cheat Sheet

  • Screen:

    screen # Start a session Ctrl+A, D # Detach screen -r # Reattach

  • Tmux:

    tmux # Start a session Ctrl+B, D # Detach tmux attach # Reattach

  • Mosh:

    mosh username@server

Final Thoughts

As a bioinformatician, your time is too valuable to spend restarting analyses due to technical hiccups. With screen, tmux, and mosh in your toolkit, you can work smarter, protect your progress, and stay productive no matter where you are. Start using these tools today and transform the way you work with remote systems.

Let me know how these tools work for you, and don\u2019t forget to follow for more bioinformatics tips!

]]> BioStar https://bioinformaticsonline.com/news/view/1219/research-with-help-of-bioinformatics-helpful Fri, 02 Aug 2013 11:20:24 -0500 https://bioinformaticsonline.com/news/view/1219/research-with-help-of-bioinformatics-helpful <![CDATA[Research with help of bioinformatics helpful]]> Endocrinologist G.R. Sridhar says

Research with the help of bioinformatics with a trans-disciplinary approach is yielding good results.

http://www.thehindu.com/features/education/research/research-with-help-of-bioinformatics-helpful/article2295629.ece

]]> Jit https://bioinformaticsonline.com/blog/view/44908/top-journals-in-bioinformatics-how-to-choose-where-to-publish-why-it-matters Fri, 26 Sep 2025 06:49:02 -0500 https://bioinformaticsonline.com/blog/view/44908/top-journals-in-bioinformatics-how-to-choose-where-to-publish-why-it-matters <![CDATA[Top Journals in Bioinformatics: How to Choose Where to Publish & Why It Matters]]>

Bioinformatics is a rapidly growing field at the intersection of biology, computer science, mathematics, and statistics. As data volumes increase, as well as the diversity of data types (genomics, proteomics, metabolomics, imaging, single‑cell data, etc.), the need for robust computational methods, rigorous models, and reproducible tools has never been greater.


A key decision for researchers is: Where should I publish my work? The choice of journal impacts visibility, peer recognition, and long‑term influence of your research. Below I provide a guide to leading journals in bioinformatics, criteria for selecting the journal that best fits your work, and why these considerations matter.

Leading Journals in Bioinformatics

Journal

What it’s Known For / Strengths

Best Fit for What Kind of Work

Bioinformatics (Oxford Journals)

Strong for methods, computational biology, database papers, algorithm development.

New computational methods; tools with broad applicability; databases; methodological advances.

Briefings in Bioinformatics

High impact reviews, overviews, and synthesis articles.

Review‑style articles; comparative studies; widely used tools.

PLOS Computational Biology

Emphasis on method development plus biological insight; open access.

Interdisciplinary work; computational method with biological applications.

BMC Bioinformatics

Broad scope; good for software, pipelines, resources; open access.

Software development; pipelines; data resources; benchmarking.

IEEE Transactions on Computational Biology and Bioinformatics (TCBB)

Rigor in computation, algorithms, performance.

Algorithmic innovations; statistical/computational method work.

BioData Mining

Focused on data mining / ML in biology.

Machine learning / AI applied to biological datasets; predictive models.

Criteria to Use When Choosing a Journal

  • Scope & Audience
  • Impact & Visibility
  • Review Time & Speed
  • Open Access
  • Cost / APCs
  • Reputation vs Practical Fit
  • Reproducibility, Data & Code Sharing Policies
  • Indexing & Reach
  • Quality of the field
  • Accelerating discovery
  • Fair access
  • Credibility & trust
  • Read recent papers in the journal
  • Tailor the manuscript
  • Check the author guidelines
  • Have backup journals ready
  • More emphasis on machine learning / AI
  • Single‑cell, spatial omics, multimodal data
  • Cloud workflows, reproducible pipelines
  • Preprints / open peer review
  • Alternative metrics (software use, downloads, community adoption)

Selecting where to publish in bioinformatics isn’t just about prestige; it’s about reaching the right audience, ensuring your work is usable, and contributing to the field responsibly.

]]> LEGE https://bioinformaticsonline.com/opportunity/view/45115/postdoctoral-fellow-in-genomics-and-comparative-genomics Thu, 09 Apr 2026 02:12:32 -0500 <![CDATA[Postdoctoral Fellow in Genomics and Comparative Genomics]]> Environnement de travail (Work environment):
The successful candidate will join a dynamic research group working
on the ecology and evolution of host'parasite'environment
interactions in non-model organisms, particularly snail vectors and
its trematode parasites. She/He will conduct genomic analyses aimed at
understanding host'parasite coevolution and the genetic architecture
of resistance in the invasive snail Pseudosuccinea columella to the
zoonotic parasite Fasciola hepatica. This thematic line is embedded
within the regional scientific project InvaSnail financed by the
ExposUM initiative from the Montpellier. The position is based in
Montpellier, a vibrant scientific hub in Southern France internationally
recognized for excellence in ecology and evolutionary biology. The IHPE
laboratory provides a collaborative research environment with access
to high-performance computing facilities, sequencing platforms, and
strong interdisciplinary interactions across research institutions in
the Montpellier area. University

Main mission:

Develop and implement strategies for whole-genome sequencing of non-model
species
Generate high-quality de novo genome assemblies using short- and long-read
sequencing technologies
Perform genome annotation and structural/functional characterization
Conduct comparative genomic analyses across related species or populations
Design and implement genome-wide association studies (GWAS) to identify
loci associated with phenotypic or adaptive traits
Integrate genomic, phenotypic, and environmental datasets
Contribute to the development of reproducible bioinformatics pipelines

Activités (Activities):

Lead the genomic component of the research project
High-molecular-weight DNA extraction optimization
Long-read genome assembly (PacBio HiFi / ONT)
Genome polishing and quality assessment (BUSCO, QUAST)
Structural and functional annotation
Variant discovery (SNPs, indels, SVs)
Population genomic analyses (FST, demographic inference)
Mixed-model GWAS accounting for structure
Workflow development (Snakemake/Nextflow)
HPC-based pipeline implementation
Publish results in peer-reviewed journals
Present findings at international conferences
Collaborate with experimental and computational team members
Contribute to project development
Mentor graduate students when appropriate

More at https://evol.mcmaster.ca/brian/evoldir/PostDocs//MontpellierU.ComparativeGenomics

]]> https://bioinformaticsonline.com/fun/view/4196/chemical-elements-of-bioinformatics Tue, 03 Sep 2013 16:35:39 -0500 https://bioinformaticsonline.com/fun/view/4196/chemical-elements-of-bioinformatics <![CDATA[Chemical Elements of Bioinformatics]]> You must be familiar with periodic table and colour pattern, but this time you are going to amaze by new elements table by Eagle genomics. Just check it out and have fun :)

http://elements.eaglegenomics.com/

]]> Rahul Agarwal https://bioinformaticsonline.com/opportunity/view/1491/2013-nextgen-genomics-bioinformatics-technologies-ngbt-conference-new-delhi-india Thu, 08 Aug 2013 16:21:16 -0500 <![CDATA[2013 NextGen Genomics & Bioinformatics Technologies (NGBT) Conference, New Delhi, INDIA]]> 2013 NextGen Genomics & Bioinformatics Technologies (NGBT) Conference

SciGenom Research Foundation (SGRF) and Institute of Genomics and Integrative Biology (IGIB) are pleased to host the Next-Generation Sequencing and Bioinformatics for Genomics & Healthcare conference.

In the ten years since the first human reference genome was completed for US$3 billion the sequencing technologies have radically changed leading to great reduction in sequencing cost. Today a human genome can be sequenced for under US$ 5000 in less than two weeks. It is expected that by the end of 2015 the cost of sequencing a human genome will drop to below thousand dollars. The next generation sequencing technologies over the past five years have enabled a large number of genomic studies that impact human health and disease. Also, this has made possible the growth of microbial, animal and plant genomics studies. While the data production has increased at a rapid pace challenges remain in analyzing and understanding the data. The conference will cover the next generation sequencing (NGS) technologies, bioinformatics for NGS and applications of NGS in many areas including personalized medicine.

For more info : http://www.scigenomconferences.com/2013/default.php

]]> https://bioinformaticsonline.com/pages/view/3889/bioinformatics-and-sequencing-courses-and-workshops Sat, 24 Aug 2013 16:41:26 -0500 https://bioinformaticsonline.com/pages/view/3889/bioinformatics-and-sequencing-courses-and-workshops <![CDATA[Bioinformatics and Sequencing Courses and Workshops]]> Swiss Institute of Bioinformatics (SIB) organises lots of bioinformatics courses covering wide range of topics:

http://www.isb-sib.ch/education/training-courses.html

Canadian bioinformatics also organises various bioinformatics and sequencing courses:

http://bioinformatics.ca/workshops

In addition to above two, EMBI Europe, EMBO Europe, Cold Spring Harbour USA, Wellcome Trust UK and NOVA Europe also organise bioinformatics and sequencing courses annually:

http://www.embl.de/training/events/index.php?p_outstation=ALL

http://www.embo.org/funding-awards/courses-workshops

http://meetings.cshl.edu/courses.html

http://www.wellcome.ac.uk/Education-resources/Courses-and-conferences/Advanced-Courses-and-Scientific-Conferences/Advanced-Courses/index.htm

http://www.nova-university.org/pagetop.cfm?MenySidorTop_id=2&open=7

]]> Rahul Agarwal https://bioinformaticsonline.com/opportunity/view/1720/postdoctoral-associate-bioinformatics-at-duke-university-medical-center Sat, 10 Aug 2013 18:38:38 -0500 <![CDATA[Postdoctoral Associate - Bioinformatics at Duke University Medical Center]]> The Department of Biostatistics and Bioinformatics at Duke University Medical Center is seeking a Postdoctoral Associate for a one year appointment to work on several high-dimensional research projects. The specific goals of the project are to identify genes or molecular markers that are predictive of clinical outcomes in renal and prostate cancer.

Candidates must have: a PhD degree in statistics, biostatistics or bioinformatics, extensive experience in analyzing high-dimensional data (microarray, SNP, CNVs) and of validation approaches. In addition, experience in penalized regression methods, data base manipulation; and strong programming skills in order to conduct Monte Carlo studies and applications (R). Candidate must have excellent communication skills (verbal, written and presentation), a strong proficiency in Linux system.

This position is available immediately and will be filled as soon as possible. Appointment could be extended beyond the first year based on additional funding.

For more information about the Department of Biostatistics and Bioinformatics, please visit our website: http://www.biostat.duke.edu.

For more info: http://biostat.duke.edu/sites/biostat.duke.edu/files/Halabi%20-%20Postdoc%20Job%20Posting%202013%20updated.pdf

Duke University is an Equal Opportunity/Affirmative Action Employer.

]]> https://bioinformaticsonline.com/researchlabs/view/5401/the-minerva-research-group-for-bioinformatics-janet-kelso Wed, 09 Oct 2013 12:57:45 -0500 <![CDATA[The Minerva Research Group for Bioinformatics (Janet Kelso)]]> The focus of this group is to use computational approaches to gain an insight into genome evolution in primates.

PNAS papers:
http://www.pnas.org/search?author1=Janet+Kelso&sortspec=date&submit=Submit

Jobs:
http://www.eva.mpg.de/genetics/bioinformatics/jobs.html

Contact:
Kelso Group
Department of Evolutionary Genetics
Max Planck Institute for Evolutionary Anthropology
Deutscher Platz 6
04103 Leipzig
Germany
Email: kelso@eva.mpg.de

]]>