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Rupert Overall

The latest update from the COVID-19 Disease Map consortium is now available as a preprint.

In this work, we show how the map can be used for of disease mechanisms and . With new winter waves beginning, there is still much to be done in this field.

biorxiv.org/content/10.1101/20

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Rupert Overall boosted
FRO VO

ME: is this a date? it feels like a date

MICROSOFT EXCEL: i have no idea

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Rupert Overall boosted
Saez-Rodriguez Group

Metabolic footprints are defined as sets of metabolites that can be directly or indirectly influenced by enzyme activity changes. This helps to identify metabolic enzyme deregulations that have systematic impact on metabolic abundances. Tutorial: github.com/saezlab/ocean/blob/

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Rupert Overall

@nakdim Yes, I use daily for collecting papers (one-click plugin in Firefox), for reading (sync to the excellent iPad app), citing (in Word and RStudio mostly) and working with shared libraries (project-specific literature collections together with my students and international collaborations).

Dimitris Nakos, MSc  
Do you people use #zotero? If yes how often, how much and how easier has it made your life?
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Rupert Overall

The latest update from the COVID-19 Disease Map consortium is now available as a preprint.

In this work, we show how the map can be used for of disease mechanisms and . With new winter waves beginning, there is still much to be done in this field.

biorxiv.org/content/10.1101/20

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Rupert Overall boosted
bioRxiv

A versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms biorxiv.org/content/10.1101/20

A versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms

The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing. Community-driven and highly interdisciplinary, the project is collaborative and supports community standards, open access, and the FAIR data principles. The coordination of community work allowed for an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework links key molecules highlighted from broad omics data analysis and computational modeling to dysregulated pathways in a cell-, tissue- or patient-specific manner. We also employ text mining and AI-assisted analysis to identify potential drugs and drug targets and use topological analysis to reveal interesting structural features of the map. The proposed framework is versatile and expandable, offering a significant upgrade in the arsenal used to understand virus-host interactions and other complex pathologies. ### Competing Interest Statement A. Niarakis collaborates with SANOFI-AVENTIS R&D via a public private partnership grant (CIFRE contract, no 2020/0766). D. Maier and A. Bauch are employed at Biomax Informatics AG and will be affected by any effect of this publication on the commercial version of the AILANI software. J.A. Bachman and B. Gyori received consulting fees from Two Six Labs, LLC. T. Helikar has served as a shareholder and has consulted for Discovery Collective, Inc. R. Balling and R. Schneider are founders and shareholders of MEGENO S.A. and ITTM S.A. J. Saez-Rodriguez receives funding from GSK and Sanofi and consultant fees from Travere Therapeutics. Janet Pinero and Laura I. Furlong are employees and shareholders of MedBioinformatics Solutions SL. The remaining authors have declared that they have no Conflict of interest.

www.biorxiv.org
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Rupert Overall

Skis out in today for a truly gorgeous wintry 4th Advent!

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Rupert Overall

That's like the 'Turkey test' - to see if someone can spell it correctly without the 'r'...

Simon E. Fisher  
“Bonferonni correction”, an invaluable method in #statistics, refers to the act of repeatedly correcting misspellings of the word Bonferroni at mul...
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Rupert Overall

RT @hillermich@twitter.com
We have a postdoc opening to integrate TOGA (biorxiv.org/content/10.1101/20) with transcriptomics data to generate high-quality gene annotations for bats, cetaceans, snakes & fish genomes sequenced by us and others. Pls apply and RT. tbg.senckenberg.de/hillerlab/j @LOEWE_TBG@twitter.com @Senckenberg@twitter.com

TOGA integrates gene annotation with orthology inference at scale

Annotating coding genes and inferring orthologs are two classical challenges in genomics and evolutionary biology that have traditionally been approached separately, which limits scalability. We present TOGA, the first method that integrates gene annotation and orthology inference. TOGA implements a novel paradigm to infer orthologous genes, improves ortholog detection and annotation completeness compared to state-of-the-art methods, and handles even highly-fragmented assemblies. TOGA scales to hundreds of genomes, which we demonstrate by applying it to 488 placental mammal and 308 bird assemblies, creating the largest comparative gene resources so far. Additionally, TOGA detects gene losses, enables selection screens, and automatically provides a superior measure of mammalian genome quality. Together, TOGA is a powerful and scalable method to annotate and compare genes in the genomic era. 1 sentence Summary A scalable gene annotation approach using a novel paradigm to detect orthologous loci provides comparative data for hundreds of mammals and birds. ### Competing Interest Statement The authors have declared no competing interest.

www.biorxiv.org
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Ewan Birney

As we don’t have elegance or design principles to inform the models having a “throw all the data at it, give something like the right form / constraints and then fit a bonkers big model” is … well… honest to the biology

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Rupert Overall

If we forget about politics for a minute and think about the _practical_ side of scientific publishing, we might find that the two are linked.

Imagine how much easier it would be to verify scientific claims if those claims were made in terms of structured statements (which could also be parsed by machine learning algorithms).

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Rupert Overall

My weekend task: extracting sensible machine-readable text from a scientific journal article. Of course, articles are published using PDF - so any text flow has been completely garbled. Why do we do this in 2022?

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Maggie Appleton

Want to help redesign one of the most popular and widely-used tools for researchers?

Zotero is hiring a designer: zotero.org/jobs/ui_designer

Would do it if I could. Ideal for someone else who has great UX / product design chops.

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Filip W

Very interesting #science news - the first SI prefixes since 1991 were announced today at the General Conference on Weights and Measures.
➡️ quetta = \( 10^{30}\), Q
➡️ ronna = \( 10^{27}\), R
➡️ ronto = \( 10^{-27}\), r
➡️ quecto = \( 10^{-30}\), q

For example the mass of an electron is just under one quectogram (1qg).

🔗 The resolution (in French) is available here bipm.org/documents/20126/64811

#math #physics

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Rupert Overall

We have written a piece describing how our new home-cage tracking paradigm can be applied to questions of behavioural individuality.

The manuscript is now online (): doi.org/10.1016/j.nbd.2022.105

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Aging Highlights

RNAseq analysis of brain #aging in wild specimens of short-lived Turquoise #Killifish: commonalities and differences with aging under laboratory conditions

academic.oup.com/mbe/article/3

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Miguel Hernan

Upgrade your #causalinference arsenal.

A revision of our book "Causal Inference: What If" is now available

👇
hsph.harvard.edu/miguel-hernan

Thanks to everyone who suggested improvements, reported typos, and proposed new citations and material.

Enjoy the #WhatIfBook.

Also, it's free.

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Julien Colomb

Never thought Elon Musk would do so much for the adoption of a decentralised infrastructure…

Please Elon, can you buy Elsevier ?

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Marc J. Lajeunesse

There is tremendous risk in repeatedly analyzing data as it comes in…

For example, in the absence of any effect, the p-values of repeated t-tests on a growing dataset will randomly walk between 1 and 0!

Thanks to @lakens for inspiring this simulation!

#RStats #dataviz #statistics

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Tan

As someone maintaining one of said affected CRAN packages - immensely grateful for everything Hadley & the tidyverse team do for the #rstats community

Making PRs to fix breaking changes in all of your reverse dependencies is a high, high bar to follow...

twitter.com/hadleywickham/stat

A tweet from Hadley Wickham: purrr 1.0.0 contains a few breaking changes, so as is our new policy, I made PRs to all affected CRAN packages. You can see all my PRs at https://github.com/tidyverse/purrr https://twitter.com/hadleywickham/status/1590455226569408512
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Aki Vehtari

All three books I've co-authored are freely available online for non-commercial use:

#Bayesian Data Analysis, 3rd ed (aka BDA3) at stat.columbia.edu/~gelman/book and lectures plus #rstats, #Python and #Stan code at avehtari.github.io/BDA_course_

#Regression and Other Stories at avehtari.github.io/ROS-Example including #rstats and #Stan code

Active Statistics at avehtari.github.io/ActiveStati

The websites also have links to the publishers' web stores if you prefer hard copies of these

Cover of the book Bayesian Data Analysis, 3rd ed
The cover of the book Regression and Other Stories
Cover of the book Active Statistics: Stories, Games, Problems, and Hands-on Demonstrations for Applied Regression and Causal Inference by Andrew Gelman and Aki Vehtari
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