Archive for the 'SciLit' Category

Frontiers | InferBERT: A Transformer-Based Causal Inference Framework for Enhancing Pharmacovigilance | Artificial Intelligence

July 31, 2021

Nice talk by W Tong at #ISMBECCB21 (CAMDA session) discussing the FDA perspective on how to do AI for regulatory science. He presents the TRIAL framework: transparency, reliability, interpretability, applicability & liability. #ISMBECCB2021

In relation to interpretability, he discusses InferBert
(https://www.frontiersin.org/articles/10.3389/frai.2021.659622/full) which builds a Bayesian causality framework (using the Do-calculus) for interpreting the BERT transformer based model. #ISMBECCB21 #ISMBECCB2021

Structure-based design of prefusion-stabilized SARS-CoV-2 spikes | Science

July 17, 2021

https://science.sciencemag.org/content/369/6510/1501

BY CHING-LIN HSIEH, JORY A. GOLDSMITH, JEFFREY M. SCHAUB, ANDREA M. DIVENERE, HUNG-CHE KUO, KAMYAB JAVANMARDI, KEVIN C. LE, DANIEL WRAPP, ALISON G. LEE, YUTONG LIU, CHIA-WEI CHOU, PATRICK O. BYRNE, CHRISTY K. HJORTH, NICOLE V. JOHNSON, JOHN LUDES-MEYERS, ANNALEE W. NGUYEN, JUYEON PARK, NIANSHUANG WANG, DZIFA AMENGOR, JASON J. LAVINDER, GREGORY C. IPPOLITO, JENNIFER A. MAYNARD, ILYA J. FINKELSTEIN, JASON S. MCLELLAN

SCIENCE18 SEP 2020 : 1501-1505

The design of stabilizing mutations in the SARS-CoV-2 spike protein allows for high-yield production of a critical vaccine antigen.

In particular,
stabilization is very important for the Moderna vaccine design.

This work builds on :
{{”
Science. 2013 Nov 1;342(6158):592-8. doi: 10.1126/science.1243283.

Structure-based design of a fusion glycoprotein vaccine for
respiratory syncytial virus

Jason S McLellan 1, Man Chen, M Gordon Joyce, Mallika Sastry, Guillaume B E Stewart-Jones, Yongping Yang, Baoshan Zhang, Lei Chen, Sanjay Srivatsan, Anqi Zheng, Tongqing Zhou, Kevin W Graepel, Azad Kumar, Syed Moin, Jeffrey C Boyington, Gwo-Yu Chuang, Cinque Soto, Ulrich Baxa, Arjen Q Bakker, Hergen Spits, Tim Beaumont, Zizheng Zheng, Ningshao Xia, Sung-Youl Ko, John-Paul Todd, Srinivas Rao, Barney S Graham, Peter D Kwong
Affiliations expand

PMID: 24179220 PMCID: PMC4461862 DOI: 10.1126/science.1243283 https://pubmed.ncbi.nlm.nih.gov/24179220/
“}}

Allele-Specific QTL Fine Mapping with PLASMA: The American Journal of Human Genetics

July 17, 2021

https://www.cell.com/ajhg/fulltext/S0002-9297(19)30505-1

metabrain QTL

July 17, 2021

https://www.metabrain.nl/

Brain expression quantitative trait locus and network analysis reveals downstream effects and putative drivers for brain-related diseases by N. de Klein et al., bioRxiv, 2021.

doi:
https://doi.org/10.1101/2021.03.01.433439

Reconciling modern machine-learning practice and the classical bias–variance trade-off

May 31, 2021

QT:{{“U-shaped bias–variance trade-off curve has shaped our view of model selection and directed applications of learning algorithms in practice. “}}
Nice discussion of the limitations of the bias-variance tradeoff for #DeepLearning
https://www.pnas.org/content/116/32/15849

Interpretation of allele-specific chromatin accessibility using cell state-aware deep learning

May 18, 2021

https://genome.cshlp.org/content/early/2021/04/08/gr.260851.120.abstract

Using multiple measurements of tissue to estimate subject- and cell-type-specific gene expression | Bioinformatics | Oxford Academic

May 3, 2021

Nice analysis integrating bulk & single-cell data, to get at inter-individual differences in the expression of genes in specific
cell types https://academic.OUP.com/bioinformaticsformatics/article/36/3/782/5545976

Using multiple measurements of tissue to estimate subject- and cell-type-specific gene expression

https://academic.oup.com/bioinformatics/article/36/3/782/5545976

Prior SARS-CoV-2 infection rescues B and T cell responses to variants after first vaccine dose | Science

May 2, 2021

https://science.sciencemag.org/content/early/2021/04/29/science.abh1282

Pre-symptomatic detection of COVID-19 from smartwatch data | Nature Biomedical Engineering

April 28, 2021

https://www.nature.com/articles/s41551-020-00640-6

Human local adaptation of the TRPM8 cold receptor along a latitudinal cline

April 7, 2021

Stumbled onto this paper. Thought the conclusion that Europeans were more cold-sensitive due to TRPM8 was quite counter-intuitive – but interesting nevertheless
https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007298

cold receptor