Here are some slides I show sometimes with data (from biorxiv.org/content/10.110…) on skewed journal citation distributions. JIF is a preposterous and inappropriate measure of individual article quality. Don’t get beclowned by the JIF

If you publish papers your data (and code) has to be fully open for anyone to do as they please #OpenData #GreaterGood (If you want to hide your data don't publish things 😉)

Loved it. It matters who does science science.org/content/blog-p…

HCLDR Moderator ~Implement universal healthcare ~Untether health insurance from employment ~Invest in public health at point of need (meet people where they are) ~Adopt systems approach to elevate health literacy across all communities (Sad typing this. Been saying same words for 10yrs.) #hcldr

The Monarch Initiative Biolink Model Brings Data Together! Find out more about our top 3 most downloaded papers in 2022 from the journal ASCPT here: ascpt.org/Journals/CTS/T… #BiolinkModel #TeamScience #Collaboration #RareDisease #DrugRepurposing #TranslationalScience LinkML - Linked (Open) Data Modeling Language

Imagine writing this paragraph about our dysfunctional system of publishing and career advancement and thinking “how do I get everyone to sacrifice their freedom and sanity to propagate it?” instead of “how can I use my position and platform to get us out of this hellscape?”

Why not just publish the data and skip the paper?

We are deeply saddened by the loss of Michael Ashburner, a pioneering co-founder and former Head of Research at EMBL-EBI. His contributions to bioinformatics have been immeasurable. Our thoughts are with his family, colleagues and all those whose lives were enriched by his work.

An Atlas of Variant Effects to understand the genome at nucleotide resolution | Genome Biology genomebiology.biomedcentral.com/articles/10.11… #genomics

The Impact of Genomic Variation on Function Consortium (IGVF) has published a "marker" preprint on the arXiv.org: arxiv.org/abs/2307.13708

This paper is very worth reading for anyone interested in science, or who’s ever told something by a doctor. Inference uncertainty is very easy to confuse with outcome variability, and it’s easy to mislead readers and practitioners (h/t Carl T. Bergstrom) pnas.org/doi/full/10.10…

New preprint: "Integrative chromatin state annotation of 234 human ENCODE4 cell types using Segway reveals disease drivers" Marjan Farahbod Mehdi Foroozandeh Habib Daneshpajouh Ben Hitz J. Michael Cherry Max Libbrecht biorxiv.org/content/10.110…

Excited to share our latest work on bioRxiv! biorxiv.org/content/10.110… A highly collaborative effort with Kristy S. Mualim Alireza Karbalayghareh, maya sheth, Kushal K Dey, Evelyn Jagoda, PhD👩🏻‍🔬,Wang Xi, Lars Steinmetz, Anshul Kundaje (anshulkundaje@bluesky), Jesse Engreitz and many others from ENCODE Project! Thread👇

Excited to share this ENCODE collaboration on the latest enhancer-gene regulatory maps to link GWAS variants to target genes and infer likely causal cell types.

ENCODE-rE2G: An encyclopedia of enhancer-gene regulatory interactions in the human genome biorxiv.org/content/10.110…

I think the sad actual answer to "What is the biggest open challenge in biology?" is: 1. Getting people to share data. 2. Structuring, organizing, and annotating data with metadata so it's useful. 3. Building higher-level abstractions so people can efficiently work with big data.

Our paper "A machine readable specification for genomics assays" is now published in Bioinformatics, @OUPBioinfo. In short, we present a lightweight file format and command-line tool to document the structure of sequencing reads. Coauthored with Xi Chen and Lior Pachter. Paper:

Dear big consortia, It is never too late to be brave and use all that visibility you have to make a strong statement that academia will not be held hostage by glam journals & their shiny JIFs 1/

One funny story about this: I spent hours creating a figure in my book explaining 0 versus 1-based indexing and closed versus right-open intervals. The illustrator thought I made a careless error in starting one from 0 and the other from 1, and changed them to match 😱

1/ One of the most common mistakes in bioinformatics is the one-off error. If you are not careful, you will make mistakes. Even experienced bioinformaticians are not aware of it and the mistake prevails in many bioinformatics tools. A thread 🧵