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Carla Hoge

@choge.bsky.social
2.1K followers 1.4K following 43 posts

Postdoc in the Novembre lab at UChicago. Excited about genomics and cool biology in non-model organisms.

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Reposted by Carla Hoge
Ellie Armstrong @elliecat.bsky.social · 29/09/2026
If you saw me talk at PEQG or PAG and want to try out a new method for assembling sex chromosomes, our paper and pipeline are live! Biggest shoutout to @scarey.bsky.social for pioneering this method and happy to have played a part in its application and deployment!
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Reposted by Carla Hoge
Yun Deng @yundeng.bsky.social · 14/09/2026
I am excited to share that I will be joining the Baker Institute for Animal Health and College of Veterinary Medicine at Cornell University as an Assistant Professor next spring! I am grateful to my mentors and colleagues who have supported me throughout this journey.
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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 26/08/2026
For folks interested I just posted my keynote on ARGs from #PEQG26 on youtube (with permission). Thanks again to @genetics-gsa.bsky.social and organizers for what was a wonderful conference (except for the 24hrs prior to my talk when I was too nervous to sleep or think straight) youtu.be/ntJOdZd0mwc
youtu.be
PEQG Keynote 2026
YouTube video by Jeffrey Ross-Ibarra
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Ben Moran @ben-moran.bsky.social · 25/08/2026
Hybrid zones are increasingly common; to what extent are human impacts on the environment the cause? We used pop gen, water chemistry, GIS, and ecotoxicology to explore the causes of hybridization in swordtails. With @mollyschumer.bsky.social, now out in Current Biology! www.cell.com/current-biol...
cell.com
Increased rates of hybridization in swordtails are associated with water pollution
Anthropogenic disturbance can drive hybridization by altering pre-mating reproductive barriers. Moran et al. pair population genomic surveys with water chemistry and GIS data to show that human develo...
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Julia Kreiner @jmkreiner.bsky.social · 31/07/2026
uchicago.wd5.myworkdayjobs.com/External/job... The Kreiner and Carley Lab groups are hiring a shared Research Analyst to help lead wet lab protocol development and management. We're a fun group and would love to hear from you :) Get in touch with questions!
uchicago.wd5.myworkdayjobs.com
Research, Analyst
Department BSD E&E Carley Lab About the Department The Kreiner Lab (kreinerlab.com) and Carley Lab (carleylab.uchicago.edu) in the Department of Ecology & Evolution at The University of Chicag...
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Michael Clemens @mclem.org · 18/07/2026
Yesterday the US Administration supercharged its explicit effort to bar international students from staying in the US after graduation. All Americans should know: 1/3 of *all* STEM PhDs working in the US are immigrants who graduated from US universities, then stayed. www.piie.com/index%2Ephp/...
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UC Davis Evolution and Ecology Graduate Preview Program @ucdaviseeprogram.bsky.social · 29/06/2026
Interested in applying to a PhD program in ecology or evolution? Don't know where to start, how to apply, and/or how to find your best program or lab fit? Join our free and virtual program August 10th, 13th, 17th, & 20th to get all the help you need! Link in bio! !!!APPLICATIONS OPEN THIS WEEK!!!
Promotional flyer for the 2026 E&E Grad Preview Program aimed at aspiring ecology and evolutionary biology graduate applicants. On a dark brown background, five illustrated panels surround the title: (1) an apple labeled "Professor Q & A Panel," (2) two people at a laptop labeled "One-on-One Mentorship," (3) a feather labeled "Help Writing Applications," (4) a virtual meeting labeled "Learn How to Cold Email Professors," and (5) a microscope labeled "Do Really Cool Science." The center text reads: "WISHLIST (for the budding ecologist or evolutionary biologist applying to graduate school). Sound like you?" Below it: "Apply starting July 1st: https://eegradpreview.weebly.com/" and "2026 E&E Grad Preview Program." Footer text states: "Run by UC Davis graduate students."
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Ran Blekhman @blekhman.bsky.social · 27/06/2026
I wanted to like QED's new 1% preprint ranking. I really did. But the more I looked at the data, the more uncomfortable it made me. Here is my full peer review. open.substack.com/pub/blekhman...
open.substack.com
My Peer Review of The 1%
I wanted to like QED's new 1% ranking. I don't.
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Jeff Spence @jeffspence.github.io · 22/06/2026
Excited to see @jonj-udd.bsky.social's fantastic work out @genetics-gsa.bsky.social. Selection in _heterozygotes_ is the primary force shaping allele frequencies of loss-of-function mutations in humans, even in genes only associated with purely recessive diseases. 🧪🧬 doi.org/10.1093/gene...
doi.org
Allele Frequencies at Recessive Disease Genes are Mainly Determined by Pleiotropic Effects in Heterozygotes
Abstract. The classic theory of mutation-selection balance predicts the equilibrium frequency of genetic variation under negative selection. The model pred
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Peter Andolfatto @pandolfatto.bsky.social · 16/06/2026
1/n Check out our new paper, spearheaded by @fborne.bsky.social, just out in PLoS Genetics doi.org/10.1371/jour....
doi.org
Epistasis among clustered lineage-specific amino acid substitutions in the Drosophila Trio protein
Author summary Proteins fold into three-dimensional structures that are essential for their function. Because these structures depend on interactions among amino acids, the fitness effect of a mutatio...
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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 15/06/2026
People. @ksamuk.bsky.social and others have made this argument before. There’s good software to do this right. Here’s the argument again: Invariant sites matter! They’re not in your standard vcf and many programs pretend they are anyway. academic.oup.com/gbe/article/...
academic.oup.com
A Recipe for a Good π. How to Properly Estimate Population Genetics Summary Statistics and Why we Should Systematically Report Them
Abstract. Many long-standing questions in population genomics can now be addressed through comparative analyses and by leveraging the vast amount of genomi
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Ipsita Agarwal @ipsitaagarwal.bsky.social · 20/05/2026
I am delighted to share new work with Simon Myers (www.biorxiv.org/content/10.6...), on how genetic variants that influence binding patterns of PRDM9 and slow down the repair of meiotic double-strand breaks impact mammalian spermatogenesis and fertility. 1/n
biorxiv.org
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Tris Dodge @tododge.bsky.social · 19/05/2026
Thrilled to present my dissertation research at the Hamilton Symposium! We used approaches including GWAS, long-read sequencing, phylogenetic methods, and behavior experiments to uncover the genetic basis and evolutionary history of a shared polymorphism. Can’t wait to share what we’ve learned!
Picture of three diverged Xiphophorus species that display the false gravid spot, a sexual mimicry polymorphism that allows males to mimic females.
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Molly Przeworski @mollyprz.bsky.social · 15/05/2026
Happy to highlight new findings by Vanesa Getseva and Lin Poyraz about the sources of variation in germline mutation rates among humans: www.biorxiv.org/content/10.6... Joint work with Anastasia Stolyarova and @ipsitaagarwal.bsky.social. 1/n
biorxiv.org
A sibling study of variation in parental mutation rates
People are born with variable numbers of de novo germline mutations (DNMs), depending primarily on the ages of their parents. To explore additional causes, we developed an approach to call DNMs from nucleotide differences between siblings in genomic regions inherited identical by descent from both parents. Applying it to whole genome sequences from 28,985 sibling pairs of diverse genetic ancestries present in the UK Biobank and All of Us datasets, as well as 2,330 trios, we identified >800K autosomal DNMs and characterized mutation phenotypes in 27,645 sets of parents. We found subtle shifts in the mutation spectrum but no differences in total DNM rates among genetic ancestry groups, or between smokers and non-smokers. Testing for associations between parental mutation phenotypes and their burden of loss-of-function and deleterious missense variants in a set of 180 DNA repair and maintenance genes, we discovered that disruptions in REV1 and LIG1 increase germline mutation rates, and thus that rare mutator alleles segregate in population cohorts. ### Competing Interest Statement The authors have declared no competing interest. NIH, R35 GM083098
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Chicago Tribune @chicagotribune.com · 14/05/2026
The University of Chicago expanded the range of undergraduate students eligible for free tuition on Wednesday, widening assistance for those from families with incomes below $250,000.
chicagotribune.com
University of Chicago offers free tuition for families earning under $250,000
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Molly Schumer @mollyschumer.bsky.social · 12/05/2026
Excited to share this new pre-print from the fantastic @kelsiehunnicutt.bsky.social! Kelsie put together a thoughtful and thorough review on hybridization in animal evolution: ecoevorxiv.org/repository/v.... She tracks notable shifts in perspectives on the study of hybridization through time.
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Stephen Turner @stephenturner.us · 03/05/2026
Free and open-source images, icons, and tools for creating scientific illustrations doi.org/10.59350/5zt... 🧪
doi.org
Free and open-source images, icons, and tools for creating scientific illustrations
Phylopic, NIH Bioart, Bioicons, Scidraw, Open Science Art, Health Icons, Servier Medical Art, Biodiversity Heritage Library, the Noun Project, Segment Anything, Excalidraw, draw.io, Biographics
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Simons Foundation @simonsfoundation.org · 01/05/2026
Now accepting applications for our 2027 Simons Graduate Fellowships in Ecology and Evolution! These awards support students entering U.S.-based Ph.D. programs to conduct #ecology and #evolution research. Deadline is June 30, 2026: bit.ly/4umYKZd #science
bit.ly
Applications for 2027 Simons Graduate Fellowships in Ecology and Evolution Now Open
The Simons Foundation’s Life Sciences division is now accepting applications for its 2027 Simons Graduate Fellowships in Ecology and Evolution.
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Holly Moeller @mixotrophe.bsky.social · 01/05/2026
Simons Graduate Fellowship Applications are open! If you're applying to Ph.D. programs in ecology and/or evolution this year, or if you're an incoming Ph.D. student who won't start your degree program until Fall 2026 or later, apply! www.simonsfoundation.org/grant/simons...
simonsfoundation.org
Simons Graduate Fellowships in Ecology and Evolution
The purpose of these awards is to provide support for students entering U.S.-based Ph.D. programs with a plan to perform research in ecology and evolution. While we will consider all projects in ecolo...
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Molly Przeworski @mollyprz.bsky.social · 20/04/2026
For an update on our preprint about the mysterious signature SBS5, see: www.biorxiv.org/content/10.1.... New analyses throughout, but see Figure 5 in particular.
biorxiv.org
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Andres Bendesky @bendeskylab.com · 20/04/2026
Hey @nytimes.com, why⁣ 𝘋𝘳. STEPHEN Kosslyn, 𝘋𝘳. MARTIN Nowak, and 𝘋𝘳. GEORGE Church⁣ but ⁣ 𝘔𝘴. ELISA New and 𝘔𝘴. ANNE Harrington⁣ when these women also have doctorate degrees?⁣ www.nytimes.com/2026/04/20/u...
nytimes.com
Epstein Craved Harvard Connections. Many There Were Eager to Help.
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Jenn Coughlan @jenncoughlan.bsky.social · 10/03/2026
I am SO THRILLED to share our first fully-lab lab paper!!!!!! Led by @hybridzones.bsky.social & @hagarsoliman.bsky.social, w/ a major assist from @pfschwarz.bsky.social!!!!!!!!!!!!! Read more below, if you're curious (you should be- it's AWESOME!!!!!!!) link: www.sciencedirect.com/science/arti...
sciencedirect.com
Introgression and parental conflict shape repeated occurrences of postzygotic isolation in Mimulus
Postzygotic reproductive isolation is often thought to accumulate as a byproduct of neutral divergence. Yet it frequently evolves rapidly, in line wit…
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Molly Przeworski @mollyprz.bsky.social · 12/02/2026
The program for the 2026 New York Population Genetics meeting, hosted by at the @simonsfoundation.org on March 9th 2026, is now up: events.simonsfoundation.org/event/7c91dd....
events.simonsfoundation.org
NY Population Genetics meeting
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Letters of Note @lettersofnote.com · 12/02/2026
Happy birthday to one of my favourite haters, Charles Darwin
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Joyce Wang @joyce-yiyi-wang.bsky.social · 26/01/2026
Our work on the generalizability of polygenic scores (PGS) from the @arbelharpak.bsky.social Lab is now officially out! We examine the accuracy of PGS predictions at the individual level. We make 3 observations that expose gaps in our understanding of PGS “portability.” rdcu.be/e0LAr (1/27)
rdcu.be
Three open questions in polygenic score portability
Nature Communications - Genetic predictors of health outcomes often drop in accuracy when applied to people dissimilar to participants of large genetic studies. Here, the authors investigate the...
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Rajiv McCoy @rajivmccoy.bsky.social · 21/01/2026
Pregnancy loss is common in humans, and chromosomal abnormalities are the leading cause. Using genetic data from ~140,000 IVF embryos, we show that maternal variation in meiosis genes influences recombination and aneuploidy risk. First authors: @saracarioscia.bsky.social & @aabiddanda.github.io
nature.com
Common variation in meiosis genes shapes human recombination and aneuploidy - Nature
Analysis of data from pre-implantation genetic testing sheds light on the genetic basis of meiotic-origin aneuploidy, the leading cause of human pregnancy loss, identifying common genetic variants ass...
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NPR @npr.org · 14/01/2026
Just in: The Trump administration sent hundreds of letters Tuesday terminating federal grants supporting mental health and drug addiction services.
n.pr
Trump administration sends letter wiping out addiction, mental health grants
The Trump administration sent hundreds of letters Tuesday terminating federal grants supporting mental health and drug addiction services.
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Dr. Jessica L Ware @jessicalwarelab.bsky.social · 18/12/2025
Come learn with us! #REU!
AMNH REU
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Javier Apfeld @javierapfeld.bsky.social · 06/01/2026
🚨My department is hiring a full-time Assistant Teaching Professor to teach undergrad Genetics & Genomics, upper-level Genomics, and an inquiry-based Computational Genomics course where students can do authentic research. 🧬💻 I’m on the search committee. DM me if you’re interested. Please share! 🙏
northeastern.wd1.myworkdayjobs.com
Assistant Teaching Professor, Biology
About the Opportunity About the Opportunity: We invite applications from qualified candidates for a full-time Non-Tenure-Track (NTT) Assistant Teaching Professor faculty position within the Department...
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Molly Przeworski @mollyprz.bsky.social · 22/12/2025
Happy to highlight an essay I wrote together with @marcdemanuel.bsky.social, @natanaels.bsky.social and Anastasia Stolyarova, trying to think through what sets the mutation rate of a cell type in an animal species: www.biorxiv.org/content/10.6... 1/n
biorxiv.org
What sets the mutation rate of a cell type in an animal species?
Germline mutation rates per generation are strikingly similar across animals, despite vast differences in life histories. Analogously, in at least one somatic cell type, mutation rates at the end of l...
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Mia Levine @levine-lab.bsky.social · 28/11/2025
How to keep in step when your (protein) partner speeds up… Here we investigated the adaptive remodeling of a protein-protein interaction surface essential for telomere protection. Congrats to whole team! www.science.org/doi/10.1126/...
science.org
Rapid compensatory evolution within a multiprotein complex preserves telomere integrity
Intragenomic conflict with selfish genetic elements spurs adaptive changes in subunits of essential multiprotein complexes. Whether and how these adaptive changes disrupt interactions within such comp...
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Lino Ferreira @linoafferreira.bsky.social · 24/11/2025
Excited to share a preprint of my PhD project looking at interactions between SNPs and polygenic scores in the UK Biobank! A thread... 🧵 www.medrxiv.org/content/10.1...
medrxiv.org
Interactions with polygenic background impact quantitative traits in the UK Biobank
Association studies have linked many genetic variants to a variety of phenotypes but under-standing the biological mechanisms underlying these signals remains a major challenge. Since genes operate wi...
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Molly Przeworski @mollyprz.bsky.social · 14/11/2025
SAVE THE DATE: the yearly NY Population Genetics meeting will be back on March 9 2026, generously hosted by the @simonsfoundation.org. Details to follow. Please RT.
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Molly Przeworski @mollyprz.bsky.social · 11/11/2025
An empirical approach to evaluating the prevalence of long-lived balancing selection in humans--and important limitations. Work by @hannahmm.bsky.social
hannahmm.bsky.social
Hannah Munby (@hannahmm.bsky.social)
PhD candidate @ Biological Sciences, Columbia
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Sally Aitken 🇨🇦 @sallyaitken.bsky.social · 25/09/2025
We are searching for a Forest Ecophysiologist (tenure track Assistant or Associate Professor) to join the Department of Forest and Conservation Sciences, University of British Columbia Faculty of Forestry. Please share! Details are here: ubc.wd10.myworkdayjobs.com/ubcfacultyjobs
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Graham Coop @gcbias.bsky.social · 15/10/2025
We're excited to be recruiting an NIH funded postdoc to work in the Coop lab at UC Davis. We're specifically interested in candidates who are want to work at the intersection of human genetics, GWAS, and population genetics modeling. Please RT
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Rachel Moran @rachelmoran.bsky.social · 10/10/2025
When sex chromosomes turnover, they can reset the rules of genomic conflict. New preprint exploring how turnover reshapes barriers to gene flow through an “escape-hatch” model for mitonuclear conflict. Any feedback would be welcome! ecoevorxiv.org/repository/v...
ecoevorxiv.org
Resetting the rules: Sex chromosome turnover as an escape hatch for mitonuclear conflict
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Jeremy Yoder says no war @jbyoder.org · 29/09/2025
New today: We're petitioning NSF to revert GRFP eligibility criteria to last year's terms, to avoid pulling the rug out from under the earliest of early-career scientists who had every reason to think they'd be able to apply this year. Sign and spread the word! laurenkuehne.github.io/grfpChanges/
laurenkuehne.github.io
Petition to NSF to Restore Eligibility for the 2026 Graduate Research Fellowship Program Competition
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Daniel Bolnick @danielbolnick.bsky.social · 26/09/2025
The GRFP announcement from NSF cuts out an entire cohort of 2nd year students from consideration, without warning. This is so deeply unfair that it warrants a formal protest from the scientific community. If someone wants to work with me to craft an open letter and solicit signatures, LMK.
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Dan Garisto @dangaristo.bsky.social · 26/09/2025
As others have pointed out, the fellowship is now available only to 1st year grad students. (Left is last year, right is this year)
Be a U.S. citizen, national, or permanent resident
Intend to enroll or be enrolled full-time in a research-based Master's or doctoral degree program in an eligible Field of Study in STEM or STEM education (See Appendix and Section IV.3 for eligible Fields of Study
Never previously accepted a Graduate Research Fellowship
Declined any previously offered Graduate Research Fellowship by the acceptance deadline
Never previously applied to GRFP while enrolled in a graduate degree program
Never earned a doctoral or terminal degree in any field
Have completed no more than one academic year (according to institution's academic calendar) while enrolled in a graduate degree program (non-degree coursework must be clearly identified in the transcript and does not count toward this limit)
Individuals holding joint Bachelor's-Master's degrees who did not apply while enrolled in the joint program, may apply as second-year graduate applicants if enrolled in an eligible doctoral program the beginning of the academic year immediately following the academic award year of the joint degree
Individuals with prior graduate enrollment who have: (i) completed more than one academic year in any graduate degree-granting program, (ii) earned a previous master's degree of any kind (see guidance for joint Bachelor's-Master's degree-holders above), or (iii) earned a professional degree must meet the following requirements:
not enrolled in a graduate degree program at application deadline
two or more consecutive years past graduate degree enrollment or completion at the application deadline
Not be a current NSF employee.Must, at the time of submission, be a U.S. citizen, national, or a permanent resident (“green-card” holder)
Must intend to enroll or be enrolled in an eligible research-based master's or doctoral degree program in an eligible field of study in STEM, including STEM education (See Appendix and Section IV.3 for eligible Fields of Study);
Never have previously accepted a Graduate Research Fellowship;
Have declined any previously offered Graduate Research Fellowship by the declination deadline (if applicable);
Have completed less than one academic year in a graduate degree program (according to the institution’s academic calendar; non-degree coursework must be clearly identified in the transcript and does not count toward this limit). 
This means individuals in the following statuses at the time of application are eligible:

Undergraduate in the final (senior) year of a bachelor’s degree program
Bachelor’s degree-holder with NO enrollment in a graduate degree program (non-degree graduate coursework allowed)
Individual enrolled in a joint bachelor’s-master’s degree program with at least three undergraduate years completed  
First-year graduate student in their first graduate degree program with less than one academic year completed in the degree program (according to institution’s academic calendar)
Individuals enrolled in joint bachelor’s-master’s degree programs are considered graduate students. For GRFP, joint bachelor’s-master’s degrees are defined as degrees concurrently pursued and awarded.
Not be a current NSF employee.
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Dan Garisto @dangaristo.bsky.social · 26/09/2025
New: After a long wait, the GRFP solicitation is live! Deadlines have been extended to early November, so applicants have a bit over a month to submit. www.nsf.gov/funding/oppo...
nsf.gov
NSF Graduate Research Fellowship Program (GRFP)
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Lino Ferreira @linoafferreira.bsky.social · 10/09/2025
Delighted to see this paper with @anaignatieva.bsky.social now published in Genetics! academic.oup.com/genetics/adv... We tackle a thorny issue arising in statistical tests for genetic interactions (epistasis) using ancestral recombination graphs (ARGs)... 🧵
academic.oup.com
Phantom epistasis through the lens of genealogies
Abstract. Phantom epistasis arises when, in the course of testing for gene-by-gene interactions, the omission of a causal variant with a purely additive ef
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Rachel Moran @rachelmoran.bsky.social · 04/09/2025
First pop gen paper from our lab! We find repeated evolutionary turn over of sex chromosomes in darters contributes to reproductive isolation. Turnover may be an escape hatch to resolve mitonuclear conflict & neo sex chromosomes evolved via a rare recessive mutation. www.biorxiv.org/content/10.1...
Top left: Results of genome-wide association study (GWAS) for sex in E. caeruleum, E. radiosum, and E. spectabile showing sex chromosome turnover has occurred repeatedly. Top right: Phylogeny showing sex chromosome turnover in darters and non-darter percids. Chromosome 9 is the putative ancestral sex chromosome, shared by Perca flavescens and multiple members of the orangethroat darter complex (e.g., E. spectabile, E. pulchellum). Bottom: Schematic depicting repeated turnover of sex chromosomes as a mechanism to resolve mitonuclear conflict and promote speciation.
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Natanael Spisak @natanaels.bsky.social · 03/09/2025
Very happy to share our work on signature SBS5. See Molly's thread for a short summary
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Molly Przeworski @mollyprz.bsky.social · 02/09/2025
In these dark times, it comes as a rare pleasure to highlight @natanaels.bsky.social ‬ & @marcdemanuel.bsky.social's work on germline and somatic mutations in humans. 1/n www.biorxiv.org/cgi/content/...
biorxiv.org
Collateral mutagenesis funnels multiple sources of DNA damage into a ubiquitous mutational signature
Mutations reflect the net effects of myriad types of damage, replication errors, and repair mechanisms, and thus are expected to differ across cell types with distinct exposures to mutagens, division ...
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Catherine Rampell @crampell.bsky.social · 29/08/2025
Trump admin planning to change student visas from lasting for duration of academic program to fixed 4-yr term, and then much harder to renew Could destroy US ability to attract global talent, particularly those seeking advanced degrees in STEM. The median time to complete a PhD is 5.7 yrs per NSF.
forbes.com
Trump Deals A New Immigration Blow To International Students
Trump officials have proposed a new rule limiting international students to fixed periods of entry, making a U.S. education more precarious.
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Carla Hoge @choge.bsky.social · 24/08/2025
This seems like a wildly useful resource for students applying to college and trying to compare costs - collegetables.info The cost after need-based financial aid varies widely, and often not in ways one might expect
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Laura K Hayward @lkhayward.bsky.social · 24/08/2025
Why do males and females often differ in traits? The expected answer: selection. But our new paper in GENETICS shows that genetic drift alone can generate sexual dimorphism — even when male & female optima are the same
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