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Questions tagged [bioinformatics]

A field spanning biology, mathematics, computer science and statistics, focusing on the acquisition and analysis of biological data. For regular bioinformatics questions, visit our sister site Bioinformatics Stack Exchange.

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2 votes
3 answers
170 views

Can a closed-source research software be published as a journal paper?

I have been developing a piece of software related to my PhD research. My field is bioinformatics and molecular simulation. The reason being that my supervisor's software has been written in a ...
0 votes
2 answers
117 views

Should I stay in my current PIs lab for grad school?

Should I stay in my current PIs lab? I graduated from a Biology program with a 3.49. During that time I didn’t take many quantitative classes. I look calculus 1 and I’m currently competing a data ...
5 votes
4 answers
1k views

How to learn math independently as a biologist/bioinformatician

I am in the same boat as many bioinformaticians, where I got my degrees in biology and taught myself computer science, and that's gotten me pretty far. But unlike those lovely physicists-turned-...
0 votes
1 answer
163 views

Bioinformatics career outlook and education requirement? [closed]

I'm currently applying to a graduate school PhD program and have a question regarding bioinformatics field. Can a person with Biology PhD degree who works in a lab that is heavily informatics, ...
0 votes
1 answer
160 views

Why did the status of my paper change from "with editorial office " to "with editor" in bioinformatics journal?"

I submitted a paper in bioinformatics journal. After a five days, the status of my manuscript changed from "with editorial office " to "with editor." What does this indicate
10 votes
4 answers
685 views

What information to share and what to hide?

Science and research is open knowledge. We should always share our knowledge with each other. However in current competitive world, scooping research is very common (specially in bioinformatics, ...
0 votes
0 answers
44 views

As a MSc. in Civil Engineering what are my chances to find a fully funded Ph.D position in Bioinformatics? [duplicate]

Having graduated with sub 3.0 GPA BSc and MSc with a 3.5 GPA in civil engineering and despite currently working professionally, I am considering a possible career change into bioinformatics. ...
0 votes
1 answer
161 views

No follow-up after pre-employment tasks [duplicate]

I applied for a bioinformatician position at a university lab. Talked to the PI twice and was assigned a total of two tasks, one after each Zoom call. After I turned in the second task the PI replied ...
2 votes
0 answers
282 views

Credit for co-first authorship in Chinese academia

I heard that in Chinese academia, you would not get credit for a co-first-author paper if you are not listed as the first co-first author. Is this true? If so, why non-first co-first authors can't get ...
1 vote
1 answer
98 views

Master thesis biochemistry

I am looking for a topic for my master's thesis in the field of biochemistry, but there is a problem, how can I make sure that the topic I have chosen is not repeated? Because there are many sites, ...
3 votes
2 answers
1k views

"Pausing" my PhD for 3 months to do an internship in industry, pros and cons?

I am a first year PhD student in an interdisciplinary STEM subfield, in a UK-style program (so 3 or 4 years long). I have been offered a 12-week internship in a biotech startup working in a similar ...
-1 votes
1 answer
216 views

Can i publish a book chapter independently?

My question is can I publish a book chapter independently? I have completed my PhD and currently I am not enrolled anywhere, in this case can I publish it without approval of guide or institution?
-2 votes
1 answer
76 views

Can Bioinformatics be used in developing a marketable product? [closed]

As we all know computer science, electrical engineering, etc. knowhows can be used in developing software and electronics/electrical products that can be sold to end-users (B2C). Can bioinformatics be ...
8 votes
2 answers
4k views

How to deal with toxic postdoc and have independent projects?

It has been three months since I joined as a postdoc. This is my first post doc position. I work along with another postdoc to set up pipelines for lab projects. This postdoc that I working along has ...
1 vote
1 answer
109 views

Can I validate the results of my package with that of any tutorial or workshop? [closed]

I have developed a software package for the analysis of genomic data, in which, I have implemented a variety of functions like normalization, clustering etc (from already available tools i.e., clubbed ...
3 votes
3 answers
1k views

Will retracting a paper from biorxiv hurt our future publication chances

I am an undergraduate student. My friends and I found interesting results while applying game theory to biology. However, we have used only one datset and being undergrads can't get access to do ...
1 vote
1 answer
84 views

How can I get involved with applying my expertise in a specific subject?

I have recently obtained my MS in data science, and am interested in applying it in a few specific fields - urogynecology, microbiome research, and others. I'm still connected to my university as a ...
1 vote
3 answers
1k views

Can a Mathematics Undergrad do a Ph.D. in Bioinformatics?

I have a particular background, I studied biology and Chemistry in Highschool, some engineering in college, and I am now majoring in mathematics with a minor in computer science. To some extent I feel ...
2 votes
1 answer
603 views

Transitioning from bioinformatics to wet lab?

I had a very bad PhD experience in developmental biology. My project was supposed to be wet lab and it was, but I didn't learn a lot of techniques. At the end I got into bioinformatics and, because my ...
21 votes
6 answers
11k views

Which is more valued, first authorship articles or the number of articles produced?

What is more important in academia (bioinformatics, computational biology) for a person when he/she has already completed their PhD: Number of first authorship articles he/she has Number of ...
4 votes
2 answers
508 views

My supervisor is putting my name on a paper I disagree with. What will happen if it is found to be wrong?

My supervisor is publishing a paper and naming me as the first author. I did the data analysis for the paper but part of the interpretation in the paper I regard as wrong. I argued with him but he ...
5 votes
5 answers
5k views

How to transition from pure biology PhD to bioinformatics/biostatistics?

I've been working as a PhD student in biology and currently in my last year. However I realised just a year into my PhD that I hated doing experiments, I really hated it. I think one of the reasons ...
5 votes
4 answers
13k views

When can a thesis get rejected or asked for a major revision?

I am planning to submit my thesis next month. I have 4 published SCI-indexed journals (Elsevier, Springer, IEEE transaction, World Scientific) and 2 more journals communicated (all first authors). My ...
0 votes
0 answers
128 views

Does ranking of journals matter in Bioinformatics?

Does the rankings Q1, Q2, Q3, Q4, and Q5 by Scimago Journal & Country Rank matter when looking for post-doc? I am interested to know about Bioinformatics and Computational Biology.
1 vote
2 answers
431 views

How to position myself to transition from doing wet lab research to doing computational work? [closed]

I am in the first quarter of the second year of my PhD. I learned to code as a hobby and have been quite passionate about analytical stuff. I got taken for a PhD basic research project which required ...
17 votes
7 answers
3k views

How to review a manuscript where the software is difficult to install?

I'm reviewing a manuscript that is protocol focussed. This protocol is a bioinformatics workflow that uses the author's own software that has already been published. Part of the peer review ...
1 vote
1 answer
153 views

Bioinformatics pipeline flow chart guidelines? [closed]

I am going to start work on the Materials and Methods for a paper I contributed to a lot in the bioinformatics processing part. I have seen some papers nowadays tend to first present the processing ...
1 vote
1 answer
595 views

Paper Indexed by SCI

One of my papers is online published with volume, issue, and page number. The journal is published by IEEE and SCI-indexed with high impact factor. I need a report from Web-of-Science to obtain the ...
48 votes
10 answers
19k views

Is postdoc experience valued by industry?

I have recently finished my PhD and am currently considering my options. I have come to the conclusion that the teaching or the "publish or perish" nature of academia isn't really appealing for me. ...
1 vote
1 answer
135 views

Editorial perception/bias regarding preprints in bioinformatics

The quality of a journal manuscript submission being equal, does posting a preprint on arXiv or bioRxiv hurt your chances of publication in a journal? I'm asking about bioinformatics, for journals ...
16 votes
2 answers
4k views

Should I decline unrelated work assigned by PhD advisor?

During the past years of my PhD program in biology, my advisor has developed a habit of lending my service to other labs/groups for potential collaborating opportunities. In addition to helping fellow ...
6 votes
2 answers
2k views

Five-year cutoff for postdocs?

I am currently a postdoc in a genomics lab, doing computational work. I will be completing three years in the lab, this fall (this in the US). I graduated with a PhD in theoretical physics in 2012 (US ...
1 vote
1 answer
366 views

Bioinformatics jobs: is experience or education more desirable

I'm a biology postdoc currently working in Data curation for a Bioinformatics institution. I am interested in becoming a Bioinformatician however I have absolutely zero experience both in terms of my ...
7 votes
2 answers
984 views

PhD Bioinformatics academic career outlook

I have a MS in CS with strong interest in statistics. I am very much interested in doing a PhD in bioinformatics as it gives me best of both worlds. After my PhD my goal is to get an academic position ...
6 votes
4 answers
769 views

Is it a good idea to submit to a single-blind journal when I have no affiliation?

I am looking to publish a paper in computational biology. However, I have no affiliation (I have been affiliated with some institutions in the past, but am not currently affiliated with anyone now). I ...
12 votes
2 answers
3k views

Rules for notifying co-authors about re-presenting a project at a conference

I am a PhD student in molecular biology & bioinformatics in Australia. I have previously presented one of my projects as a poster at a conference. This was sent for review to all co-authors, ...
5 votes
2 answers
1k views

How hard is it to get admitted to a PhD programm in UK/Ireland having specialist's degree from a mediocre Russian university?

I am going to study "Bioengineering and bioinformatics" for the next 5 years and plan to pursue a scientific career afterwards. My family does not have much money to support me studying in cities like ...
3 votes
1 answer
90 views

Are there any pre-print services that accept manuscripts already accepted by a journal?

My publication was accepted by a journal, however I want to post it online prior to publication. BioRxiv was the original repository of choice, however they do not accept articles accepted by other ...
3 votes
1 answer
148 views

Finding specific types of manuscripts of a journal

I am considering writing an article to a journal. This journal (Bioinformatics) accepts different manuscripts: Original Papers Discovery Notes Application Notes Reviews Letters to the Editor ...
26 votes
3 answers
4k views

How to deal with scooping when doing open-source tools development?

I am developing a tool for bioinformatics ... it is an application that will be open source when finished. It is something that has use outside of bioinformatics as well. I am also using some open ...
2 votes
0 answers
207 views

Is it disadvantageous to my research career in bioinformatics if my PhD work is mainly software development? [closed]

I am in the fourth year of my Ph.D. studies in bioinformatics. I have published two articles, one in my second year on the comparative genomics of a group of bacteria as a co-first author. Since ...
1 vote
1 answer
127 views

Research on Biological Networks [closed]

I have a background in Physics and am currently pursuing a research career in experimental Biophysics. I've spent over a year on my project and am struggling terribly. I'm considering switching to ...
2 votes
3 answers
3k views

How to make my master thesis defending smooth with good english speech?

My master thesis dissertation is approaching, but I have a few concerns. First of all, I am not native English speaker. When I practiced my presentation on my own (I recorded my speech), it was not ...
3 votes
0 answers
384 views

Avoiding scientific salami slicing [closed]

As part of my master thesis in bioinformatics I built a tool A, which is similar to tool B which uses other data. Tool's B original paper is a description of the software and methods implemented, ...
0 votes
1 answer
169 views

Transitioning from MS to PhD - International Student

I will be enrolling in a Master's program for Biomedical Informatics next fall. I already know the faculty member that I would like to be mentored by (working as a student intern with one of his ...
1 vote
1 answer
194 views

In case I have to take a gap year before MS, what can I do in terms of reading and independent study to prepare for graduate school? [closed]

I will be graduating with a BS in Computer Science in 2017 and have applied to a couple of graduate school to pursue MS in Biomedical Informatics/Bioinformatics. I'm interested in translational ...
9 votes
3 answers
429 views

What differentiates Bioinformatics from Computational Biology? [closed]

I am a university level student of Computer Science. I like to know what really differentiates Bioinformatics from Computational Biology in terms of the core area of study and the nature of subjects ...
3 votes
1 answer
937 views

Submit my R-package to CRAN or Bioconductor?

I have a new academics R-package for bioinformatics and I would like to submit my package online. Where I should submit? If I submit to Bioconductor, they have a 6 months release cycle. What about ...
2 votes
4 answers
621 views

Is a PhD useful if you are interested in a career as a staff researcher, not leader of your own research lab?

How useful is a PhD if my final career goals don't involve leading my own research lab? In a perfect world I would like to end up as a bioinformatics programmer/analyst in a lab or a core facility to ...
1 vote
0 answers
188 views

What are the differences between PhD programs in the US and UK? (biology/bioinformatics)

A significant part of the PhD process in the US involves deciding on and doing the background research for your project. Is it true that in the UK you basically get a predetermined project handed to ...