Di Gioacchino et al. introduce Maximum Entropy Nucleotide Bias models (MENB) to quantify how host identity shapes viral genome composition, predicting viral family and host from sequence motifs.
doi.org/10.1093/molbev/msaf127
#compbio
0 posts0 participants0 posts today
SatuTe by Manuel et al. is a new tool to quantify phylogenetic signal and saturation between subtrees. Applied to the Tree of Life, SatuTe shows that most ribosomal proteins support a eukaryotic clade.
doi.org/10.1093/molbev/msaf090
We need recipes for common bioinformatics tasks 
New post on the blog https://bionics.it/posts/bioinformatics-recipes #bioinformatics #compbio
bionics.itWe need recipes for common bioinformatics tasks | Bionics ITAd-hoc tasks in bioinformatics can contain such an immense number of operations and tasks that need to be performed to achieve a certain goal. Often these are all individually regarded as rather "standard" or "routine". Despite this, it is quite hard to find an authoritative set of "recipes" for how
Today I learned how to store gene expression data in (multiple) parquet files, and query them as a single dataset from R with the {arrow}, {duckdb} or {sparklyr} packages. I am amazed by {duckdb}'s speed 
- even on my laptop! Here's a blog post with what I learned: https://tomsing1.github.io/blog/posts/parquet/ #TIL #RStats #duckdb #parquet #spark #compbio #rnaseq
tomsing1.github.ioThomas Sandmann’s blog - Adventures with parquet: Storing & querying gene expression data
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PS: They're hiring! If you're a #computational #scientist interested in #biology #compbio and #genetics, please take a look at open positions like this one for an Associate Computational Scientist ($96,945 - $162,310 DOE):
They have the coolest data I've ever worked with 
thejacksonlaboratory.wd1.myworkdayjobs.comAssociate Computational ScientistThe Jackson Laboratory (JAX) is seeking an Associate level Computational Scientist, who will work closely with research faculty & genetic resource scientists across all three campuses of JAX on projects of wide-ranging complexity from a diverse array of biomedical disciplines such as cancer biology, aging, neural disorders, muscular disorders, and biostatistics & statistical genetics, under the supervision of the Associate Director, Computational Sciences. In this role the Computational Scientist will participate in the collaborative bioinformatics program that’s aligned with JAX’s institutional strategy and direction and make leading contributions to the cutting-edge projects at The Jackson Laboratory. Successful candidates will have in-depth knowledge and experience in High Throughput Sequence (HTS) data analysis (short-reads and long-reads), spatial biology, data integration, algorithm and workflow development, evaluation of analytical tools and technology, and delivering training to the research community. Candidates with proven track record of “omics” data analysis in the field of cancer, expertise in algorithm development & spatial biology are a plus. We are seeking continuous learners and proactive contributors who exhibit increased ability to work independently, and towards the development of in-depth knowledge in selected biological disciplines to analyze and provide expert reasoning to the relevant projects and make leading contributions to grant applications. They are expected to sustain collaborations with JAX research staff and faculty on both the Farmington, CT and Bar Harbor, ME campuses and to visit the other sites of JAX on a regular basis and as required. Key Responsibilities Under minimal supervision, performs computational analysis of omics data, algorithm development and implementation, as well as bioinformatics programming. Evaluating data for quality assurance and mining bioinformatics databases. Present the results at international conferences and workshops. Contributes to the education and training courses conducted by the Computational Sciences department and JAX for internal and external communities. Demonstrates a strong potential to develop analytical expertise to a few selected biological disciplines, independent collaboration and project leadership. Participates in departmental and project activities such as developing pipelines, participating in conducting courses and workshops at JAX, provide leading contributions to grant applications, helping students and scientists, participating in departmental meetings and presenting results, and processes to the JAX community, at conferences and workshops as assigned. Knowledge, Skills, and Abilities PhD in Bioinformatics, Computer Science, Biostatistics or any relevant area. Candidates who are near the completion of their PhD may also apply. Possesses 2-5 years of experience in Bioinformatics research, excluding time spent to obtain PhD. Excellent verbal and written communication skills. Demonstrated experience managing projects and collaborations is key. Prior successes in and desire to contribute to team projects on an ongoing basis is a must. The salary range is $96,945 - $162,310. Salary will be determined based on qualifications and experience. #LI-MJ1 #LI-Remote About JAX: The Jackson Laboratory is an independent, nonprofit biomedical research institution with a National Cancer Institute-designated Cancer Center and nearly 3,000 employees in locations across the United States (Maine, Connecticut, California), Japan and China. Its mission is to discover precise genomic solutions for disease and empower the global biomedical community in the shared quest to improve human health. Founded in 1929, JAX applies over nine decades of expertise in genetics to increase understanding of human disease, advancing treatments and cures for cancer, neurological and immune disorders, diabetes, aging and heart disease. It models and interprets genomic complexity, integrates basic research with clinical application, educates current and future scientists, and provides critical data, tools and services to the global biomedical community. For more information, please visit www.jax.org. EEO Statement: The Jackson Laboratory provides equal employment opportunities to all employees and applicants for employment in all job classifications without regard to race, color, religion, age, mental disability, physical disability, medical condition, gender, sexual orientation, genetic information, ancestry, marital status, national origin, veteran status, and other classifications protected by applicable state and local non-discrimination laws. Bar Harbor: The Jackson Laboratory's 43-acre scenic Bar Harbor campus is nestled between the Gulf of Maine and the mountains of Acadia National Park. Some of the best hiking and biking in the world (over 50 square miles of mountains, lakes, views, and dramatic coastline) is accessible from our campus. We are one mile from downtown Bar Harbor, which offers a vibrant downtown district with a plethora of restaurants, shops, museums, and galleries. Ellsworth: The Charles E. Hewett Center in Ellsworth, Maine, is a state-of-the-art facility that serves researchers world wide. The facility represents the culmination of nine decades of unmatched experience and leadership in breeding and caring for laboratory mice. Ellsworth, Maine, is one of Maine’s fastest growing cities. With a growth rate of nearly 20%, Ellsworth is a bustling year-round community and acts as a hub for surrounding towns. It is located nearby Acadia National Park and hosts numerous special events, concerts and festivals each year. Residents have access to fabulous shopping, recreation, museums, galleries, and dining at a variety of independent restaurants. Farmington: JAX Genomic Medicine is transforming medicine by improving patient care, lowering costs, and increasing life span and health span. JAX Genomic Medicine’s research focuses on the complex genetic causes of disease and on the development of genomic solutions tailored to each person's unique genetic makeup. JAX Genomic Medicine sits on a 17-acre site on the campus of the University of Connecticut Health Center. The 183,500-square-foot facility opened in the fall of 2014. Now, it houses over 300 biomedical researchers, technicians, and support staff in state-of-the-art computing facilities and laboratories. In Connecticut, JAX resides in the scenic town of Farmington, in the state’s capitol region. The Hartford region, which offers some of the best public schools in the country, is made up of both bigger cities and smaller, charming historic New England towns. JAX Genomic Medicine is also geographically located within 2 hours of Boston and New York and is close to multiple transportation systems, including bus lines, highways, railroads and international airports. Sacramento: The JAX® Mice, Clinical and Research Services facility is located in Sacramento, the state capital of California. Sacramento is less than a two-hour drive from San Francisco, Napa Valley, and scenic Lake Tahoe, and a short flight to both Los Angeles and Orange County. Sacramento is the birthplace of the nation’s Farm to Fork movement, and offers excellent restaurants, gastro-pubs, wineries, theaters, and museums. Outdoor activities are plentiful: Boating, white water rafting, and riding the scenic bicycle trails are popular. Housing and other costs of living are more affordable in Sacramento and its surrounding suburbs than in most other neighboring areas in the North Bay, making Sacramento one of the hottest housing markets in the country year after year. Augusta: JAX’s Maine Cancer Genomics Initiative (MCGI) is located in Augusta, Maine, in the Harold Alfond Center for Cancer Care (HACCC), at Maine General Hospital. It began operations in 2016 with three overarching goals: to provide cancer genomic testing for Maine cancer patients; to develop and deliver physician education about clinical genomic cancer diagnostics; and to build a network in Maine of oncology practices conducting studies in genomic medicine.
Very cool preprint by Adam P Cribbs's group: "Correcting PCR amplification errors in unique molecular identifiers to generate absolute numbers of sequencing molecules." https://www.biorxiv.org/content/10.1101/2023.04.06.535911v1 with lots of innovative ideas to a) measure and b) correct PCR induced errors in RNA-seq experiments. #rnaseq #ngs #singlecells #compbio #illumina #nanopore
bioRxivCorrecting PCR amplification errors in unique molecular identifiers to generate absolute numbers of sequencing molecules.Unique Molecular Identifiers (UMIs) are random oligonucleotide sequences that remove PCR amplification biases. However, the impact that PCR associated sequencing errors have on the accuracy of generating absolute counts of RNA molecules is underappreciated. We show that PCR errors are the main source of inaccuracy in both bulk and single-cell sequencing data, and synthesizing UMIs using homotrimeric nucleotide blocks provides an error correcting solution, that allows absolute counting of sequenced molecules.
### Competing Interest Statement
A.P.C, U.O and M.P are co-founders of Caeruleus Genomics Ltd and are inventors on several patents related to sequencing technologies filed by Oxford University Innovations. T.B. Jr. is a director and shareholder of ATDBio. T.B. Sr. is a director of ATDBio. The other authors declare no competing interests.
Hi all! I'm Joseph Szymborski, a #PhD student at McGill university studying #deeplearning models as applied to molecular biology.
Specifically, I'm working on predicting the interaction of proteins based solely on their amino acid sequence.
Follow for upcoming blog posts on topics related to #bioinformatics , molecular biology, and other generally nerdy things.
Eager to meet and share ideas with #compbio #netbio and #deeplearning people here!
Since it’s the new year, I figure an #introduction is in order. My name is Taylor, and I’m entering my final year as a #CompBio PhD candidate at Cornell.
My research is primarily focused on using #ML to understand #regulation of gene expression in grasses. I am particularly interested in #representation and #mechanistic modeling.
My other interests include science in the media, supporting Black scientists, and trivia podcasts.
I hope to have some great discussions on here! 
Today I learned how to create an interactive HTML report for gene-set enrichment analysis in R. It allows readers to examine set-level results & drill down into the underlying gene-level statistics interactively.
https://tomsing1.github.io/blog/posts/interactive-gene-set-results/
It's a static HTML page, e.g. no server (#shiny, #dash, etc) needed. Thanks a lot to the authors of the #plotly #reactable #crosstalk and #htmlwidget tools for making this so easy #til #rstats #bioconductor #gsea #compbio #visualization @lianos
New blog post:
Using the terminal at Warp speed
AI suggested terminal commands. #compbio #bioinformatics #genomics #coding
https://www.badgrammargoodsyntax.com/compbio/2022/12/12/compbio-026-using-the-terminal-at-warp-speed
Bad Grammar, Good SyntaxCompbio 026: Using the terminal at Warp speed — Bad Grammar, Good SyntaxI have always just used a regular terminal, such as the MacOS Terminal app, or PuTTY on Windows when accessing a server. They have served me well. But apparently there is a world of more advanced terminals out there. I have stayed away from them, preferring something very simple, but a frien
Biomedical #Informatics, #AIInMedicine, #DigitalHealth folks:
You are invited to add yourself to the Biomedical & #HealthInformatics Social Media Directory maintained by me:
https://sites.google.com/view/informaticsdirectory
Hopefully this will help us stay connected no matter what platform!
Please Boost!
#TwitterMigration #MastadonMigration #AMIAInformatics #BiomedicalInformatics #DataScience #AI
@healthinformatics
@informatics
#EHR #bioinformatics #compbio #clinicalinformatics #informatician #informaticist
sites.google.comHome
Biomedical & Health Informatics Social Media Directory
Job alert: TT Assistant Professor of Biological Sciences (MolBio, EcoEvo, CompBio)
Hi all. First post on here. In case you don’t know me, I’ve been in #machinelearning for a while (trained my first #neural networks in 1999, but they were rubbish!) now focused on #compBio applications (mainly #proteinengineering ), but also interests in #bayesian statistics, #PrivacyEnhancingTechnologies and #continuallearning . Currently leading a fantastic team of scientists and engineers at Amazon. Slightly sad at the demise of Twitter, hoping #mastodon can fill the hole it left!
#Introduction after moving from mastodon.social
I'm a Computational Biologist at Denali Therapeutics in California's Bay Area.
My journey includes a Masters in Biochemistry, a PhD in Developmental Biology and high-throughput experiments exploring genetic interactions.
You can usually find me either collaboratively designing experiments or analyzing genomics data.
Next, I would love to learn about image analysis.
#single-cell #biotech #neurodegeneration #compbio #r #python #nextflow
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As for what I'll use this platform for: I'm still exploring, but hope to expand the conversation on creating #inclusive and #sustainable frameworks that empower Black women to equitably engage in #CompBio across the diaspora. This includes sharing information and creating safe, #community-driven spaces for learning and storytelling.
I'm excited to continue interacting with the #CompBio and #DataScience scholarship and #network with other scientists.
#followfriday #introduction #ff
/fin
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In January 2022, I created an online #networking platform for Black Women in #CompBio to connect, build social capital, and collaborate.
Since then, we've grown to over 200 members from 4+ continents, 300+ supporters throughout the CompBio field, and are run by an amazing team of 8 scientists across professional stages.
We host the#BlackInCompBio series, which gives folx a platform to share their science & journeys through #seminars or #podcast interviews.
www.blackwomencompbio.org
2/n
#Introduction Part 1:
Hi! I'm a mid-career scientist at the Broad Institute in Cambridge Massachusetts USA and I tend to follow conversations about the career side of science and how to make it a more humane and equitable path. I've been told I have an "overdeveloped" sense of justice/conscientiousness. I have 5 kids; between science and family I've no other hobbies :D
#BroadInstitute #CompBio #ComputationalBiology #STEM #DEI #academia
My first real day on #mastadon has been interesting. I forgot how much time I put into finding the diversity that I had on the bird site. I'm still trying to find more folks in #compbio - specifically those who use #rstats or #networks in disease, those studying #cancer via #systemsbiology approaches, and anyone looking at #neurofibromatosis.
Ok, after a couple of days getting used to this, here is my #introduction
I'm a computational biologist and group leader in Newcastle University (UK) working on the genetics of human age related diseases and the regulation of molecular phenotypes with ageing.
Some Keywords for searches: #genetics #QTLs #eQTLs #multiomics #omics #science #transcriptomics #proteomics #metabolomics #genomics #compbio #diabetes #NAFLD
By way of #introduction for the great migration: I am a builder of models: computational (#ml, #machinelearning), mathematical, and scale models (#hoscale #scalemodel). Working as a computational biologist / bioinformaticist for ExosomeDx. (#multiomics #scRNA-seq #dimensionality #bioinformatics #computationalbiology #compbio) Follower of and/or interested in #osint, science history, nuclear power, #trains, pretty birds, canyon hikes, and scientific ethics.