This also includes:

• A2Amapper: ATAC, Assembly to Assembly Comparision tool:
  • Comparative mapping between two genome assemblies (same species), or between two different genomes (cross species).

• Sim4db:
  • Spliced alignment of cDNA and genomic sequences, from the same (sim4) or related (sim4cc) species. Optimized for high-throughput batched alignment.

• LEAFF:
  • LEAFF (ahem, Let's Extract Anything From Fasta) is a utility program for working with multi-fasta files. In addition to providing random access to the base level, it includes several analysis functions.

• Meryl:
  • An out-of-core k-mer counter. The amount of sequence that can be processed for any size k depends only on the amount of free disk space.

Address of the bookmark: https://help.rc.ufl.edu/doc/Kmer

Address of the bookmark: https://github.com/sib-swiss/training-collection

More at https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0611-3

Address of the bookmark: http://www.interactivenn.net/

More at https://www.nibmg.ac.in/uploads/3c5d4da3fb31bef490a218805408c858.pdf

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.

Reference: http://www.unitedformedicalresearch.com/wp-content/uploads/2013/06/The-Impact-of-Genomics-on-the-US-Economy.pdf

Here’s a curated list of the top websites offering bioinformatics job opportunities and postdoctoral fellowships worldwide.

1. General Bioinformatics Job Portals

These platforms are ideal for bioinformaticians seeking jobs in diverse sectors:

• Nature Careers: A trusted resource for job seekers in the sciences, Nature Careers offers bioinformatics roles globally. Their specialized search function allows you to filter jobs by keyword, location, and more.

  • Explore Bioinformatics Jobs on Nature Careers

• Science Careers: A job board from the AAAS, this site focuses on STEM jobs, including numerous bioinformatics opportunities in academia and industry.

• Euraxess: Euraxess is the go-to platform for researchers looking for jobs, fellowships, and funding across Europe and beyond. It lists both bioinformatics roles and research grants.

  • Search Bioinformatics Jobs on Euraxess

• ResearchGate Jobs: ResearchGate is widely known as a platform for researchers to share publications, but it also has a robust job board featuring bioinformatics positions globally.

• FindAPostDoc: This site is dedicated to helping postdoctoral researchers find positions, with bioinformatics being a popular category.

• Academic Positions: Targeting academic roles worldwide, Academic Positions lists bioinformatics jobs at universities and research institutions.

• PostdocJobs.com: Specializing in postdoctoral roles, this platform is a great resource for early-career researchers looking for bioinformatics-related positions.

• Scholarship Positions: In addition to jobs, Scholarship Positions provides information on scholarships, fellowships, and grants related to bioinformatics.

2. Fellowship and Training Opportunities in Bioinformatics

For those seeking fellowships or specialized training, these organizations offer postdoctoral programs, grants, and research opportunities:

• NIH Office of Intramural Training and Education: The National Institutes of Health offer extensive research training programs for postdocs, including those in bioinformatics.

• NSF Research Opportunity Awards: The National Science Foundation funds bioinformatics research at predominantly undergraduate institutions, providing fellowships and grants.

• Top U.S. Universities: Many prestigious U.S. institutions, including Harvard, Berkeley, Yale, MIT, Johns Hopkins, UCSD, and Cornell, offer postdoctoral opportunities in bioinformatics.

3. Country-Specific Job and Fellowship Resources

If you're targeting a specific region, these platforms offer bioinformatics opportunities tailored to their respective countries:

Canada

• CAPS/ACPP: The Canadian Association of Postdoctoral Scholars provides a job board, including bioinformatics roles in academia.
• Banting Postdoctoral Fellowships: A prestigious fellowship program for postdocs in bioinformatics and related fields.
• Mitacs Elevate: A Canadian initiative offering fellowships to connect postdoctoral researchers with industry partners.

United Kingdom

• UKRI: The UK Research and Innovation body funds bioinformatics research and offers various grants.
• The Royal Society: Provides funding schemes for researchers in bioinformatics.
• Marie Skłodowska-Curie Actions: The MSCA funds fellowships and doctoral programs across Europe, including bioinformatics-related projects.
• Wellcome Trust: Offers research funding and career development opportunities in health-related fields, including bioinformatics.

Europe

• EMBO Fellowships: The European Molecular Biology Organization supports bioinformaticians through fellowships and career grants.
• Max Planck Society: A leading research organization offering bioinformatics positions and fellowships across Europe.
• Helmholtz Association: A major research organization in Germany offering bioinformatics roles in various disciplines.
• Leibniz Association: Offers research opportunities, including bioinformatics, across its numerous institutes.

Australia and New Zealand

• Australian Research Council: Offers funding and research schemes, including in bioinformatics.
• Top Universities: Universities like Sydney, Melbourne, and Queensland have research programs in bioinformatics.

Asia

• Japan Society for the Promotion of Science (JSPS): Offers fellowships for international researchers in bioinformatics.
• Top Institutions: Universities like NUS, CAS, and IISc are leading hubs for bioinformatics research.

Middle East

• Qatar Research, Development, and Innovation (QRDI): Offers research opportunities in bioinformatics.
• KAUST: A leading university in Saudi Arabia offering bioinformatics research positions.

Africa

• African Academy of Sciences: Provides career opportunities and research funding in bioinformatics across Africa.

Conclusion

The field of bioinformatics is full of exciting opportunities for those with the right skills. Whether you are looking for a postdoc position, research funding, or a long-term job in industry, these platforms are an excellent starting point. Explore, apply, and take the next step in your bioinformatics career!

1. Learn and get updated

Some of the bad biological programmers only learn new technical or non-technical things when it’s absolutely necessary. The good biological programmers learn new technical skills proactively. But great biological programmers not only learn new technical skills on their own but also learn non-technical skills, and have an open mind to sources of knowledge that others may shut out.

In other concrete term, the bad biological programmer learn Perl's regular expression when they started a project on comparative genomics; the good biological programmer learned it a year before because it looked interesting; and the great biological programmer also read about the BioPerl packages, genomics, DNA string, genomic theories, or some similar course of study so that they could understand the results and explain it biologically.

2. Not a merely coder!!!

I often encountered with biological programmer who call themself a hard-core computer programmer and avoid biology. I can almost guarantee that if you are one of them then you are not doing research but merely writing "dry" codes.

According to my supervisor most of the computational biologist, don't know what they are doing biologically. Even they struggle to explain their own programs output and results. Therefore, It is highly advisable to learn basic of biology which can assist you to explain the result and understand your discovery. Always remember you are a researcher not a coder.

3. Be Social with biologist

The computational biologist spends most of the time in from of computers, writing codes. They always think their job is to produce working codes, not technical research perfections. But, they are completely wrong. You should not forget that apart from your computational skills you also need some biologist, other than your supervisor, to explain and make you understand the complex biological mechanism.

I highly recommend your to interact with biotech researchers and learn how do they explain their one graph (which they generally produce after one year of work) biologically. Remember, the origin of your research project is complex biological phenomenon, which is more complex than that of your limited programming rules.

4. Do not search, research for answers

Researching for answers means more than typing several keywords into a search engine or posting a question at Stack Overflow or the BioStars forums. I have entered problems into search engines that generate no results, and every question I posted on Stack Overflow or the BioStars forums never got anything resembling an answer, yet I solved the issues and moved on. I’m not a magician — I just know how to find answers or discover root causes.

Many problems are situational, and if you depend on search engines and forums, you can waste a lot of time going down a rabbit hole and possibly never getting a solution. Learn to perform root cause analysis, learn enough about the underlying system to look for other clues and solutions, and learn to take a long distance view of an issue before deep diving into it.

5. Love and defend your research

You cannot rise to the top in this research profession without loving your work. There are some very good “it’s just a job” biological programmers (I’ve been one at times), but if that is your outlook, you won’t be willing to do whatever it takes to succeed. This idea gets a lot of folks in a huff, because they feel it is a personal insult. “I’m a good programmer, but I have other priorities and can’t make work my life.” I understand completely; I have other priorities too. As much as I hate to say it, when I am passionate about my work, I am willing (though not eager) to abandon my other priorities to finish the job. It is not an insult to say that if you aren’t willing to pull out all the stops you can’t be the best, it is a fact.

You must be passionate about more than programming — you must also be excited about your research, the tools and technology you are using, and so on. I have seen very good and even great biological programmers operating at mediocre levels because something was not a good fit, such as they hated the project or were using a technology they disliked. Therefore, like your research project and get excited about your discoveries. You have not only to discover but also defend your finding with scientific words.

Thanks to all of you for reading.

What Are lncRNAs?

lncRNAs are RNA transcripts longer than 200 nucleotides that do not code for proteins. Despite their non-coding nature, they play diverse roles in gene regulation, including chromatin remodeling, transcriptional control, and post-transcriptional processing. Unlike messenger RNAs (mRNAs), lncRNAs often function as scaffolds, decoys, or guides in cellular machinery, influencing biological processes such as cell differentiation, immune response, and even cancer metastasis.

Challenges in lncRNA Research

Identifying and understanding lncRNAs pose unique challenges:

1. High Sequence Variability: Unlike protein-coding genes, lncRNAs exhibit low sequence conservation across species, making functional predictions difficult.
2. Low Expression Levels: lncRNAs are often expressed at low levels, complicating their detection in transcriptomic data.
3. Diverse Functions: The multifunctional nature of lncRNAs requires advanced computational tools to decipher their roles in complex networks.

Bioinformatics: A Crucial Ally in lncRNA Research

Bioinformatics bridges the gap between raw biological data and meaningful insights, making it indispensable in lncRNA research. Here’s how:

1. Identification and Annotation

High-throughput sequencing technologies like RNA-seq generate vast amounts of data. Bioinformatics tools such as StringTie, Cufflinks, and HISAT2 help assemble and annotate lncRNAs from this data. Additionally, databases like NONCODE, LNCipedia, and Ensembl provide curated repositories of lncRNA sequences and annotations.

2. Functional Prediction

Bioinformatics algorithms predict the potential functions of lncRNAs by analyzing their interactions with DNA, RNA, and proteins. Tools like LncRNA2Function and RIblast utilize sequence motifs and secondary structure predictions to hypothesize about the roles of specific lncRNAs.

3. Network Construction

lncRNAs often act as regulatory hubs. Bioinformatics platforms such as Cytoscape enable the visualization of lncRNA-mediated networks, elucidating their roles in pathways like cell cycle regulation and apoptosis.

4. Epigenetic Studies

lncRNAs are known to interact with chromatin-modifying complexes, influencing gene expression epigenetically. Tools like ChIP-seq and ATAC-seq, combined with computational pipelines, identify these interactions and map them to the genome.

5. Clinical Applications

Bioinformatics aids in the discovery of lncRNA biomarkers for diseases like cancer and neurodegenerative disorders. Machine learning models analyze differential expression profiles, helping prioritize lncRNAs with therapeutic potential.

Case Study: lncRNAs in Cancer Research

lncRNAs such as HOTAIR and MALAT1 have been implicated in cancer progression. Bioinformatics analyses have revealed their roles in promoting metastasis and altering the tumor microenvironment. For example, transcriptome analysis in cancer patients identifies lncRNA expression signatures, enabling precision medicine approaches.

Future Directions

The fusion of bioinformatics with experimental biology is unlocking the secrets of lncRNAs. Advances in artificial intelligence, single-cell sequencing, and structural modeling promise to overcome current limitations. Here are some promising directions:

• Integrative Analysis: Combining multi-omics data to understand the interplay of lncRNAs with other biomolecules.
• CRISPR Screens: Leveraging bioinformatics to design CRISPR-based functional screens for lncRNAs.
• Therapeutic Development: Using bioinformatics to design lncRNA-based therapeutics, including antisense oligonucleotides and RNA interference tools.

Conclusion

lncRNAs are the hidden gems of the genome, and bioinformatics is the key to unearthing their full potential. As research progresses, lncRNAs could pave the way for novel diagnostics, targeted therapies, and personalized medicine, revolutionizing our approach to complex diseases.

The journey into the world of lncRNAs is only beginning, and bioinformatics will continue to play a pivotal role in decoding these molecular mysteries. Whether you’re a researcher, clinician, or bioinformatics enthusiast, the study of lncRNAs offers a fascinating frontier of discovery.

MEME Suite software development; gene expression; mathematical modelling; gene regulation and transcription

Specialization:
Pattern recognition and modelling in computational biology

Link @ http://www.imb.uq.edu.au/tim-bailey