bioRxivThe open-closed mod-minimizer algorithm https://www.biorxiv.org/content/10.1101/2024.11.02.621600v1?med=mas
| GitHub | https://github.com/rob-p |
| website | https://combine-lab.github.io |
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Associate prof. of CS @ University of Maryland. I ♥ science & compiled, statically-typed programming languages! Views are my own.
https://pmc.ncbi.nlm.nih.gov/articles/PMC11523660/
"A recent study reported exaggerated false positives by popular differential expression methods when analyzing large population samples...a caveat...led to incorrect comparisons of benchmark methods."
Normalization & realistic simulation matters critically in evaluation!
Neglecting the impact of normalization in semi-synthetic RNA-seq data simulations generates artificial false positives
A recent study reported exaggerated false positives by popular differential expression methods when analyzing large population samples. We reproduce the differential expression analysis simulation results and identify a caveat in the data generation ...
Process matters! Sometimes, things pan out in a way that you agree with, and sometimes they don’t. But when the process itself is shown to be fundamentally compromised, then this calls all relevant outcomes arrived at by that process into question, be they good or bad.
https://pmc.ncbi.nlm.nih.gov/articles/PMC11523660/
"A recent study reported exaggerated false positives by popular differential expression methods when analyzing large population samples...a caveat...led to incorrect comparisons of benchmark methods."
Normalization & realistic simulation matters critically in evaluation!
Neglecting the impact of normalization in semi-synthetic RNA-seq data simulations generates artificial false positives
A recent study reported exaggerated false positives by popular differential expression methods when analyzing large population samples. We reproduce the differential expression analysis simulation results and identify a caveat in the data generation ...
LaffyI got the hang of it pretty quickly! Why does the program crash on the 47th run when it’s also the week of an autumnal full moon (under g++) or a vernal full moon (under clang)? “Because this is C++!”
The first 5-10 minutes of this talk are, likely unintentionally, a great argument for why C++, at least while the current mindset and philosophy prevail, can never be a language for the future, or even the current. The priorities are askew : https://youtu.be/fcRHiFH04a4?si=0YsUw2km79p4efgh !
This is C++: Uncompromised Performance, Undefined Behavior, & Move Semantics - Jon Kalb C++Now 2024
I'm thrilled to share that our department, UMD CS, is hiring. We are looking for folks broadly across all areas (including bioinformatics / comp bio!) and ranks! Please feel free to reach out if you're interested. Posting below: https://ejobs.umd.edu/postings/124012
Assistant Professor, Associate Professor, Professor
The Department of Computer Science at the University of Maryland, College Park, MD, USA is recruiting to fill multiple tenure-track faculty positions, with starting dates on or after July 1, 2025. The openings are not restricted to any rank and outstanding candidates at all levels are encouraged to apply.The Department seeks exceptional candidates in all areas of computer science, including but not limited to Artificial Intelligence, Computational Biology and Health, Computer Graphics and AR/VR, Computer Systems, Computer Vision, Cybersecurity, Data Sciences, Databases, Human-Computer Interaction, Programming Languages, Quantum Computing, Software Engineering, Theoretical Computer Science, etc. Applicants working at the boundary of computer science and related disciplines, including Computational Linguistics and Natural Language Processing, Reinforcement Learning, Robotics and Scientific Computing are also encouraged to apply, and may be considered for joint positions with other departments or institutes on campus. A candidate should indicate in their cover letter if they might be interested in such a joint appointment.The Department is committed to building a diverse faculty dedicated to its missions of research, teaching and service to the community, and it especially encourages applications from women and members of other underrepresented groups in computing. In addition, candidates who have experience engaging with a diverse range of faculty, staff and students, and contributing to a climate of inclusivity are encouraged to discuss their perspectives on these subjects in their application material.Interested candidates should apply on-line in order to receive consideration. Applicants are strongly encouraged to have complete versions of their materials – including a cover letter, a curriculum vitae, research and teaching statements, and recommendation letters from at least four references – uploaded by 12/15/24. Applications will continue to be accepted and reviewed until all positions are filled. Candidates will be prompted when submitting their application to include information for their references. Questions can be directed to [email protected] Department of Computer Science is top-ranked for research and teaching, with its undergraduate computer science program ranked 9th among public universities by U.S. News & World Report. The undergraduate program currently educates over 3,700 diverse students from around the world. The graduate program is ranked 11th on CS Rankings and 17th in the nation by US News, with over 400 graduate students enrolled. The Department has 62 tenure-track faculty members, many of whom have been recognized with memberships in the National Academy of Engineering, fellowships in professional scientific organizations including ACM and IEEE, NSF Faculty Early Career Development awards and Sloan Fellowships. The Department receives over $30 million annually in external research funding. It is home to the Iribe Initiative for Inclusion and Diversity in Computing (https://inclusion.cs.umd.edu/), whose programs have been funded by more than $4 million in grants and gifts, and it is located in the state-of-the-art Brendan Iribe Center for Computer Science and Engineering (https://iribe.umd.edu/). Additional information about the Department is available at https://www.cs.umd.edu. UMD is committed to fostering a diverse, inclusive, and family-friendly community through programs such as TerrapinSTRONG (https://terrapinstrong.umd.edu/) focusing on building an inclusive community, or the FAMILE diversity initiative (https://faculty.umd.edu/famile-initiative).
It was mentioned in a Slack where I belong that the MiSeq i100 Series comes with builtin DRAGEN software. My thought: what's DRAGEN doing with my data? No idea, b/c it's closed-source!
"DRAGEN: What's in your sequencer? Seriously; we have no idea what this is actually doing!"
The longer I teach CS, the stronger I feel that the move away from C & toward Java (& Python) in intro sequences was a mistake. I don’t think the intro lang has to be C, but I think it should be one that fosters building a useful mental model of the machine & OS.