Archive for the 'SciLit' Category

Quantifying SARS-CoV-2 transmission suggests epidemic control with digital contact tracing | Science

April 15, 2020

https://science.sciencemag.org/content/early/2020/03/30/science.abb6936

Great idea for #covid19… However, digital contact tracing has serious #privacy issues that have to be considered and perhaps ameliorated.

Quantifying SARS-CoV-2 transmission suggests epidemic control with digital contact tracing

Luca Ferretti1,*, Chris Wymant1,*, Michelle Kendall1, Lele Zhao1, Anel Nurtay1, Lucie Abeler-Dörner1, Michael Parker2, David Bonsall1,3,†, Christophe Fraser1,4,†,‡

Science 31 Mar 2020: eabb6936
DOI: 10.1126/science.abb6936

Fig 2 shows the breakdown of infections into four types:
pre-symptomatic, symptomatic, environmental, and asymptomatic, and they contribute 0.9, 0.8., 0.2, and 0.1 each to the basic reproduction number of 2. To stop the spread of infections, you need to take measures to get the area under the curve to below 1. The paper then shows that when you do quarantining and contact tracing, you can’t get the reproduction number below 1. However, if you improve the speed of quarantining and contact tracing with a digital app/centralized system, then you can get it below 1.

Somatic evolution and global expansion of an ancient transmissible cancer lineage | Science

April 14, 2020

Adrian Baez-Ortega1, Kevin Gori1,*, Andrea Strakova1,*, Janice L. Allen2, Karen M. Allum3, Leontine Bansse-Issa4, …. Michael R. Stratton62, Ludmil B. Alexandrov63, Iñigo Martincorena62, Elizabeth P. Murchison1,†

Science 02 Aug 2019:
Vol. 365, Issue 6452, eaau9923
DOI: 10.1126/science.aau9923

https://science.sciencemag.org/content/365/6452/eaau9923

Single cell estimation from bulk data

April 12, 2020

Accurate estimation of cell composition in bulk expression through robust integration of single-cell information

Brandon Jew, Marcus Alvarez, Elior Rahmani, Zong Miao, Arthur Ko, Jae Hoon Sul, Kirsi H. Pietiläinen, Päivi Pajukanta, Eran Halperin doi:

https://doi.org/10.1101/669911

Comparing tads across samples

April 6, 2020

newly published tool

TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription

Guangyu Wang, Qingshu Meng, Bo Xia, Shuo Zhang, Jie Lv, Dongyu Zhao, Yanqiang Li, Xin Wang, Lili Zhang, John P. Cooke, Qi Cao & Kaifu Chen

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-01992-7

The effect of travel restrictions on the spread of the 2019 novel coronavirus (COVID-19) outbreak

April 1, 2020

https://science.sciencemag.org/content/early/2020/03/05/science.aba9757

The effect of travel restrictions on the spread of the 2019 novel coronavirus (COVID-19) outbreak

Matteo Chinazzi1, Jessica T. Davis1, Marco Ajelli2, Corrado
Gioannini3, Maria Litvinova3, Stefano Merler2, Ana Pastore y Piontti1, Kunpeng Mu1, Luca Rossi3, Kaiyuan Sun4, Cécile Viboud4, Xinyue Xiong1, Hongjie Yu5, M. Elizabeth Halloran6,7, Ira M. Longini Jr.8,*, Alessandro Vespignani1,3,*

https://www.nytimes.com/2020/03/13/science/coronavirus-social-networks-data.html

Genetic modifiers of risk and age at onset in GBA associated Parkinson’s disease and Lewy body dementia. – PubMed – NCBI

March 8, 2020

https://www.ncbi.nlm.nih.gov/pubmed/31755958

Crack down on genomic surveillance

March 4, 2020

https://www.nature.com/articles/d41586-019-03687-x

Distinct microbial and immune niches of the human colon

February 23, 2020

connects microbiome & immune cells

https://www.nature.com/articles/s41590-020-0602-z.epdf

Kylie R. James, Tomas Gomes, Rasa Elmentaite, …Sarah A. Teichmann

iGenomics: Comprehensive DNA Sequence Analysis on your Smartphone | bioRxiv

February 16, 2020

iGenomics: Comprehensive DNA Sequence Analysis on your Smartphone | bioRxiv https://www.biorxiv.org/content/10.1101/2020.02.11.944132v1

Nongenic cancer-risk SNPs affect oncogenes, tumour-suppressor genes, and immune function

February 8, 2020

https://www.nature.com/articles/s41416-019-0614-3