Bits of DNA
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Reviews and commentary on computational biology by Lior Pachter.
Bits of DNA
4M ago
by Laura Luebbert and Lior Pachter
Background (by LL)
Four years ago, during the first year of my PhD at Caltech, I participated in a journal club organized by the lab I was rotating in. I was assigned two classic papers on the honeybee waggle dance: “Visually Mediated Odometry in Honeybees” (Srinivasan et al., JEB 1997)1 and “Honeybee Navigation: Nature and Calibration of the ‘Odometer’” (Srinivasan et al., Science 2000)2. Since I was not familiar with honeybee behavior, I decided to expand my literature review to other papers on the topic, including “Honeybee Navigation En Route to the ..read more
Bits of DNA
8M ago
In a Tablet Magazine article titled “How the Gaza Ministry of Health Fakes Casualty Numbers” posted on March 6, 2024, Professor of Statistics and Data Science Abraham Wyner from the Wharton School at the University of Pennsylvania argues that statistical analysis of the casualty numbers reported by the Gaza Ministry of Health is “highly suggestive that a process unconnected or loosely connected to reality was used to report the numbers”.
In the post, he shows the following plot
which he describes as revealing “an extremely regular increase in casualties over the period” and from which he conc ..read more
Bits of DNA
8M ago
The All of Us Research Program, whose mission is to “to accelerate health research and medical breakthroughs, enabling individualized prevention, treatment, and care for all of us”, recently published a flagship paper in Nature on “Genomic Data in the All of Us Research Program“. This is a review of Figure 2 from the paper (referred to below as AoURFig2).
Background
The first U.S. Census that commenced on August 2, 1790 included a record of the race of individuals. It used three categories: “free whites”, “all other free persons”, and “slaves”. Since that time, racial categories as defined for ..read more
Bits of DNA
8M ago
The following describes harassment experienced by a woman who is a professor of mathematics, whose words I’m posting here (anonymously and with names changed) with her permission.
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In November 2023, I visited a Mathematics Department at a respected research university in the USA at the invitation of a professor (I will be calling him Zacharia) who works there. We initially met at a conference where we were both invited as plenary speakers by my former colleague and collaborator Mung. Zacharia appeared to be very interested in my talk and to share my research interests. However, th ..read more
Bits of DNA
1y ago
1. Published 2007 in PNAS. Retracted 2011.
https://portlandpress.com/biochemj/article/434/3/571/80024/Activation-of-hypoxia-inducible-factor-1-in-human
This is a retraction to: Activation of hypoxia-inducible factor 1 in human T-cell leukaemia virus type 1-infected cell lines and primary adult T-cell leukaemia cells.
Following an investigation by the University of the Ryukyus, which revealed that figures that appeared within this paper had also been used in other papers without appropriate attribution or explanation (a pattern repeated over a number of publications in different jour ..read more
Bits of DNA
1y ago
The UC Davis Young Scholars Program is a summer residential program that provides high school students the opportunity to work one-on-one with research faculty in state-of-the-art labs for six weeks. One of the faculty mentors that the program recently showcased on its Facebook page is Chemistry Professor Ting Guo, who has been a faculty mentor in the program for many years.
Professor Guo, who was the chairman of the UC Davis Chemistry Department from 2016-2018, has been mentoring high school students for over a decade. Already in 2010, he was awarded the Chancellor’s Achievement Award for Di ..read more
Bits of DNA
2y ago
A recent opinion piece titled “A decade of molecular cell atlases” by Stephen Quake narrates the incredible single-cell genomics technology advances that have taken place over the last decade, and how they have translated to increasingly resolved cell atlases. While the article tells some fascinating stories (apparently when hearing a report about the CZI mouse cell atlas Priscilla Chan remarked “why don’t we just do human?” and thus the idea for a human cell atlas was born), it contains several errors and omissions. I have summarized some of them below, and have sent a copy to Trends in Genet ..read more
Bits of DNA
3y ago
If you haven’t heard about Clubhouse yet… well, it’s the latest Silicon Valley unicorn, and the popular new chat hole for thought leaders. I heard about it for the first time a few months ago, and was kindly offered an invitation (Club house is invitation only!) so I could explore what it is all about. Clubhouse is an app for audio based social networking, and the content is, as far as I can tell, a mixed bag. I’ve listened to a handful of conversations hosted on the app.. topics include everything from bitcoin to Miami. It was interesting, at times, to hear the thoughts and opinions of some o ..read more
Bits of DNA
4y ago
Steven Miller is a math professor at Williams College who specializes in number theory and theoretical probability theory. A few days ago he published a “declaration” in which he performs an “analysis” of phone bank data of registered Republicans in Pennsylvania. The data was provided to him by Matt Braynyard, who led Trump’s data team during the 2016. Miller frames his “analysis” as an attempt to “estimate the number of fraudulent ballots in Pennsylvania”, and his analysis of the data leads him to conclude that
“almost surely…the number of ballots requested by someone other than the register ..read more
Bits of DNA
4y ago
Lior Pachter
Division of Biology and Biological Engineering &
Department of Computing and Mathematical Sciences California Institute of Technology
Abstract
A recently published pilot study on the efficacy of 25-hydroxyvitamin D3 (calcifediol) in reducing ICU admission of hospitalized COVID-19 patients, concluded that the treatment “seems able to reduce the severity of disease, but larger trials with groups properly matched will be required go show a definitive answer”. In a follow-up paper, Jungreis and Kellis re-examine this so-called “Córdoba study” and argue that the authors of the stud ..read more