Back in August, van Rossum published a proposal on the Python mailing list recommending type-checking annotations as a valuable feature for the next version of Python to improve the performance of editors and IDEs, linter capabilities, standard notation, and refactoring. Van Rossum’s latest proposal, posted late last month, outlined plans to publish a Python Enhancement Proposal (PEP) in early January to put the feature now known as type hinting on track for inclusion in Python 3.5, slated for release this September.

Reference

https://quip.com/r69HA9GhGa7J

Address of the bookmark: https://bioinfologics.github.io/post/2018/09/17/k-mer-counting-part-i-introduction/

The role sits at the critical interface between genetics and cancer systems biology, and would suit a candidate who is interested in developing a career at the confluence of Statistics/Data Mining/Machine Learning and Biology. Ideally, you will have experience in development of analytical approaches to high-throughput and multivariate data mining and integration gained through a PhD (or equivalent) in a quantitative subject (eg mathematics, statistics, physics, engineering or computer science).

Experience of statistics and/or machine learning techniques is highly desirable as is evidence of prior experience of developing bioinformatics software and/or analysing complex *omics data sets. You will be able to work as part of a team and independently and deliver results to the required standard and schedule. You should be able to organise and prioritise your own work, as well as have excellent communication skills, both written and oral. The post will involve interactions with collaborators from such diverse fields as applied mathematics, statistics, computer science and medicine.

This is a full-time post, fixed-term until 31 March 2017. For informal enquiries, contact Dr Anastasia Samsonova (bioinformatics@oncology.ox.ac.uk).

All applicants must complete a short application form and upload a CV and supporting statement.

The closing date for applications is 12.00 noon on 26 January 2015.

More at https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.display_form

MitoHiFi was first developed to assemble the mitogenomes for a wide range of species in the Darwin Tree of Life Project (DToL)

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-023-05385-y 

Address of the bookmark: https://github.com/marcelauliano/MitoHiFi

Input

Jabba takes as input a concatenated de Bruijn graph and a set of sequences:

the de Bruijn graph should appear in fasta format with 1 entry per node, the meta information should be in the format:
>NODE
the set of sequences should be in fasta or fastq format. These sequences will be corrected (e.g. PacBio reads). The corrections will be written to a file Jabba fasta.
The output is a file in fasta format with corrections of the long reads, and additionally a file in the input format containing uncorrected reads.

https://github.com/biointec/jabba/wiki

https://almob.biomedcentral.com/articles/10.1186/s13015-016-0075-7

Address of the bookmark: https://github.com/biointec/jabba

Details will be available at: http://www.igib.res.in/sites/default/files/26032015.pdf

No of Post: 01, 01

How To Apply: 1. Please fill up the proforma 2. Candidate cannot apply for more than two posts. Last date of receiving application is 12-03-2015. No application would be entertained with “result awaited” status or after due date. List of shortlisted candidates will be put up on CSIR-IGIB website. No TA/DA will be paid to the candidates to attend the interview. The engagement shall be as per guidelines of CSIR/Funding agency. Candidates will have an option to give reply in Hindi. Note: The shortlisted candidates, have to report at 09:00 AM at Mall Road Campus, Delhi – 110007 on the day of interview along with any Photo ID card, (without photo ID card interview will not be conducted). 3 copies of updated signed C. V. (clearly mentioning Date of Birth and Hightest Qualification with percentage), Dissertation (if any), PhD thesis (if any) and original certificates/Self attested photocopies for verification.

General Instructions: Engagement is for the project and on behalf of the funding agency and the tenure shall be as mentioned above. The duration of the post is initially for One year or till the closing date of the project, whichever is earlier. Tenure may be extendable up to project duration. Contract may be terminated at any time by giving one-month notice by either side. The applicants will have no claim implicit or explicit for consideration against any CSIR/IGIB post. Candidates should note that non-fulfillment of the eligibility criterion will result in cancellation of candidature at any stage.

Last Date: 12-03-2015.
Age Limit: 28 Years

Address of the bookmark: http://www.genome.umd.edu/

Bachelor/ BS Bioinformatics at
1. Al-khair University, Bhimber
2. Government College University, Faisalabad
3. University Of Agriculture, Faisalabad
4. Comsats Institute Of Information Technology [isb], Islamabad
5. International Islamic University, Islamabad
6. Quaid-e-azam University, Islamabad
7. Khushal Khan Khattak University, Karak
8. Virtual University Of Pakistan, Lahore
9. Virtual University Of Pakistan, Lahore
10. Hazara University, Mansehra
11. Shaheed Benazir Bhutto Women University, Peshawar
12. Comsats Institute Of Information Technology, Sahiwal
13. Capital University Of Science And Technology, Islamabad
14. Foundation University, Islamabad
15. Baqai Medical University/hospital, Karachi
16. Institute Of Business And Technology(main Campus), Karachi
17. Sir Syed University Of Engineering & Technology, Karachi
18. Forman Christian College, Lahore
19. Qarshi University (lhr), Lahore
20. The Superior University, Lahore
21. University Of Management And Technology, Lahore
22. Federal Institute Of Health Sciences, Lahore
23. Shaheed Benazir Bhutto Women University Peshawar, Sub Campus, Swabi
24. Government Postgraduate College ( Mandian), Abbottabad
25. Federal Institute Of Health Sciences, Multan
26. Fedral Institute Of Health Sciences, Muzaffarabad
27. The Limit Institution Of Health Sciences, Sahiwal

Master/ MS Bioinformatics cources at
1. Government College University, Faisalabad
2. Comsats Institute Of Information Technology [isb], Islamabad
3. International Islamic University, Islamabad
4. National University Of Science & Technology, Islamabad
5. Quaid-e-azam University, Islamabad
6. University Of Sindh, Jamshoro
7. Virtual University Of Pakistan, Lahore
8. Hazara University, Mansehra
9. Shaheed Benazir Bhutto Women University, Peshawar
10. Capital University Of Science And Technology, Islamabad
11. Cecos University Of Information Tech. & Emerging Sciences, Peshawar

The real bioinformatics scope lies if there are research labs which work in this field. One has to take account of that. If so then try to get information of those labs and visit them to get a hang of the work they pursue.

There is a huge buzz of precision medicine in light of genomics all around the world. One should also try to see how genomics infrastructure is built up or standing in Pakistan. If research labs having collaboration with hospitals employ genomics then one must also visit such labs. This will bring new avenues in healthcare advances. Not only it opens up the wealth of knowledge one can make out of genomics study but will also advance the critical thinking of therapies.

So I would encourage to target research labs working in the fields and also get information of hospitals employing genomics, this will give you an overall understanding of the fields demand in your country.

Before you go down that path, consider this critical biological question:
Are you sequencing human cells—or bacterial contamination?

The Silent Saboteur: Mycoplasma in Cell Cultures

Mycoplasma contamination remains one of the most widespread and underdiagnosed issues in tissue culture work. Studies suggest that 15–35% of cell lines in use may be contaminated, often without visible signs. Unlike other microbial infections, Mycoplasma does not produce cloudiness, odor, or a change in pH. Many researchers won’t detect it unless they specifically test for it.

The consequences, however, are profound. Mycoplasma can significantly alter:

• Host gene expression patterns

• Cell proliferation rates

• Epigenetic profiles and chromatin accessibility

• Cytokine signaling and immune responses

In short, it can skew your results, compromise your biological conclusions, and invalidate weeks or months of research.

A Simple Diagnostic Step: Map Against Mycoplasma Genomes

If you encounter poor alignment rates to the human genome, consider mapping your reads to a Mycoplasma reference genome—or better yet, use a combined human + Mycoplasma reference. There have been cases where over half of all reads, initially assumed to be from human cells, were in fact bacterial in origin. This check is fast, easy, and could save your project.

How Contamination Happens—and Persists

Mycoplasma is small (0.1–0.3 μm), lacks a cell wall, and can pass through standard filters undetected. Common sources include:

• Contaminated reagents (e.g., FBS)

• Infected cell lines obtained from other labs

• Poor aseptic technique or shared equipment

Once present, it spreads quickly between cultures and can persist for months, silently affecting results.

Why Treatment Is Difficult

While antibiotics such as Plasmocin or BM-Cyclin are sometimes used, they often offer only partial resolution and may themselves alter cell behavior. In many cases, the best course of action is to discard the contaminated culture and start with a fresh, verified stock.

Practical Recommendations for Researchers

• Routinely test for Mycoplasma using PCR, qPCR, or fluorescence-based assays

• Incorporate contamination screens into your sequencing QC pipeline

• Use combined reference genomes when mapping ambiguous reads

• Practice strict aseptic technique and monitor all incoming cell lines

• Don’t ignore unexplained data anomalies—they might point to contamination

Closing Thought: Contamination Is a Biological Variable

It’s easy to view poor mapping as a technical issue, but sometimes the problem lies deeper—in the biology itself. Mycoplasma contamination doesn’t just interfere with sequencing; it interferes with science. As a research community, we must treat contamination not as an afterthought, but as a key variable to control.

So next time your reads won’t align, don’t just tune the aligner. Ask if your cells are telling the truth—or if they're hiding something.