Lightnews — Scholar-powered news

Arjun Bhattacharya @arjunbhattac.bsky.social · 6h

Sean and Yung-Han both were awarded travel awards for their presentations, underscoring the importance of their work and the hard work they've put in for these projects. Looking forward to #ashg25.

Arjun Bhattacharya @arjunbhattac.bsky.social · 6h

Star PhD student @ytchang11.bsky.social will present an empirical Bayes method to formally test the replication composite null hypothesis in GWAS, effectively controlling FDR and maintaining strong power. Big downstream implications to check out in her pre-print: www.medrxiv.org/content/10.1....

Formal Statistical Replication Analysis in Lung Cancer Genome-Wide Association Studies

Dozens of genome-wide association studies (GWAS) have identified thousands of single nucleotide polymor-phisms (SNPs) associated with lung cancer risk. However, it remains challenging to translate the...

www.medrxiv.org

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Arjun Bhattacharya @arjunbhattac.bsky.social · 6h

@seantbres.bsky.social will talk about a placental long-read RNA-seq isoform reference + how using it with short reads improves transcript quantification and DTE/U analyses. Cool results in the preprint below. More maternal-fetal health work soon in GxE/POE analyses.

www.biorxiv.org/content/10.1...

Long-read transcriptome assembly reveals vast isoform diversity in the placenta associated with metabolic and endocrine function

The placenta plays a critical role in fetal development and mediates maternal metabolic effects on offspring health outcomes. Despite its importance, the placenta remains understudied in large-scale g...

www.biorxiv.org

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Arjun Bhattacharya @arjunbhattac.bsky.social · 6h

Taylor also was recently nominated internally and submitted an early K99/R00 award to NCI. She did a tremendous amount of work for a really exciting proposal!

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Arjun Bhattacharya @arjunbhattac.bsky.social · 6h

@taylorhead.bsky.social will talk about integrating long-read based transcript assemblies can improve QTL mapping and GWAS integration for breast cancer risk, building off her recent work showing eQTL colocalization and TWAS are HIGHLY sensitive to annotation choice.

www.biorxiv.org/content/10.1...

Quantification method affects replicability of eQTL analysis, colocalization, and TWAS

eQTL mapping and TWAS are widely used to contextualize GWAS, yet the impact of RNA-seq processing choices remains unexplored. We find that RNA-seq quantification method and transcriptomic reference su...

www.biorxiv.org

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Arjun Bhattacharya @arjunbhattac.bsky.social · 6h

A few programming notes for #ashg25 from trainees in my group @mdanderson.bsky.social + a thread of me being a proud PI. Please drop by these sessions and talk to @taylorhead.bsky.social, @seantbres.bsky.social , @ytchang11.bsky.social, and me in Boston @geneticssociety.bsky.social next week!

Presentations for Taylor Head (Room 205ABC Level 2 at 11:15 am on 10/15), Sean Bresnahan (Room 253ABC Level 2 at 8:45 am), and poster for Yung-Han Chang (Board 1108T, 2:30-4:30 pm on 10/16)

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Reposted by Arjun Bhattacharya

Harold Pimentel @hjp.bsky.social · 9d

Super excited to get this out. This collab started a few years ago and is the first paper from it. Here, with experimental and computational approaches we:

1. establish that cell villages can be just as accurate (one might argue more accurate!) than arrayed-based designs

bsky.app/profile/bior...

bioRxiv Genetics @biorxiv-genetic.bsky.social · 9d

Cell villages and Dirichlet modeling map human cell fitness genetics https://www.biorxiv.org/content/10.1101/2025.09.26.678880v1

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Reposted by Arjun Bhattacharya

Wolfgang Huber @wkhuber.bsky.social · Aug 30

When testing a computational data analysis method: simulated data are good for checking whether the method is doing what you think it should be doing, real data for checking whether what you think it should be doing is any good.

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Arjun Bhattacharya @arjunbhattac.bsky.social · Aug 20

On a personal note, I'm honored to be named an Emerging Leader by BJC! We're excited to continue our work in genomic mechanisms for cancer risk and progression to discover novel biomarkers for risk stratification and prognosis.

www.nature.com/collections/...

Emerging Leaders | Emerging Leaders - British Journal of Cancer

BJC’s Emerging Leaders collection recognises stand-out early-to-mid career researchers, clinicians, and educators within the field of oncology.

www.nature.com

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Arjun Bhattacharya @arjunbhattac.bsky.social · Aug 20

Very proud of @ytchang11.bsky.social for her first publication from her doctoral research! She conducted very meticulous genomic analyses that uncovered novel isoform-specific mechanistic hypotheses underlying genetic loci associated with multiple cancers.

www.nature.com/articles/s41...

Isoform-level analyses of 6 cancers uncover extensive genetic risk mechanisms undetected at the gene-level - British Journal of Cancer

British Journal of Cancer - Isoform-level analyses of 6 cancers uncover extensive genetic risk mechanisms undetected at the gene-level

www.nature.com

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Reposted by Arjun Bhattacharya

Michael Love @mikelove.bsky.social · Aug 18

Excited to share this preprint from first author Jon Rosen, a postdoctoral fellow in the @klmohlke.bsky.social lab and my lab. We examine eQTL study sample size and how this affects signal discovery and rates of colocalization with GWAS.

www.biorxiv.org/content/10.1...

Higher eQTL power reveals signals that boost GWAS colocalization

Expression quantitative trait locus (eQTL) studies in human cohorts typically detect at least one regulatory signal per gene, and have been proposed as a way to explain mechanisms of genetic liability...

www.biorxiv.org

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Reposted by Arjun Bhattacharya

hanseulkim.bsky.social @hanseulkim.bsky.social · Jul 3

⚡🦠I'm very excited to share our latest work on the gut microbiome and metabolic dysfunction-associated steatotic liver disease (MASLD) is published in @natmetabolism.nature.com, with @hutlab.bsky.social & @longnguyen.bsky.social!

🔗Check out the paper here:
www.nature.com/articles/s42...

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Reposted by Arjun Bhattacharya

David A Knowles @davidaknowles.bsky.social · Jul 2

New work from the lab trying to wrap our heads around the massive complexity of the human transcriptome revealed by long-read RNA-seq! Fun collab with Gloria Sheynkman. www.biorxiv.org/content/10.1...

Perplexity as a Metric for Isoform Diversity in the Human Transcriptome

Long-read sequencing (LRS) has revealed a far greater diversity of RNA isoforms than earlier technologies, increasing the critical need to determine which, and how many, isoforms per gene are biologic...

www.biorxiv.org

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Arjun Bhattacharya @arjunbhattac.bsky.social · Jul 2

Excited to share new work investigating transcriptional diversity in the placenta from our group led by talented postdoc @seantbres.bsky.social! Thread below describing the salient results. Welcoming any feedback and comments.

Sean Bresnahan @seantbres.bsky.social · Jul 2

🧬🚨PREPRINT🚨- The first placental isoform reference from long-read seq & supporting data! We demonstrate how tissue-specific assembly improves transcript quantification with short-read data from multi-ancestry birth studies & reveals placenta-mediated effects of gestational diabetes on birth weight🫄

Long-read transcriptome assembly reveals vast isoform diversity in the placenta associated with metabolic and endocrine function

The placenta plays a critical role in fetal development and mediates maternal metabolic effects on offspring health outcomes. Despite its importance, the placenta remains understudied in large-scale g...

doi.org

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Reposted by Arjun Bhattacharya

Sean Bresnahan @seantbres.bsky.social · Jun 18

Much more important things going on in the world, but wanted to share this new work on parent-of-origin effects & “non-canonical” genomic imprinting in developmental plasticity of honey bees, out now in Genome Biology 🧪🧬🔄 link.springer.com/article/10.1...

Intragenomic conflict associated with extreme phenotypic plasticity in queen-worker caste determination in honey bees (Apis mellifera) - Genome Biology

Background Caste determination of honey bees (Apis mellifera) exemplifies developmental plasticity, where differences in larval diet result in identical genotypes yielding either long-lived, reproduct...

link.springer.com

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Arjun Bhattacharya @arjunbhattac.bsky.social · May 7

Drop by and say hi to @mdanderson.bsky.social Postdoctoral Data Scientist @seantbres.bsky.social if you’re at Biology of Genomes. He’ll be presenting some new work from our group that he’s championed. You’ll have an interesting science and/or science policy discussion!

Sean Bresnahan @seantbres.bsky.social · May 7

In NY for Biology of Genomes @cshlnews.bsky.social this week. During a layover on the way here, I tried to write a bit to communicate some of the work our group is doing, and why federal research funding for basic science matters substack.com/home/post/p-...

From Code to Complexity

How Our Cells Read Between the Lines (and Why Federally-Funded Research Matters)

substack.com

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Reposted by Arjun Bhattacharya

Mark Peifer (He, him) @peiferlabunc.bsky.social · Jan 10

Neglected to share this good news this morning :)

UNC beats Duke in Women's basketball--53-46 in OT

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Reposted by Arjun Bhattacharya

Yoav Gilad @ygilad.bsky.social · Jan 10

Friends and colleagues, I’ve written a book on effective functional genomics study design, which will be available on Amazon in a couple of weeks. Sharing the TOC to spark interest. I hope students and those planning genomics experiments will find it useful! I’ll share updates soon

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Arjun Bhattacharya @arjunbhattac.bsky.social · Dec 26

No espresso martinis for Lola?

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Reposted by Arjun Bhattacharya

Jess Ewald @ewaldlab.org · Dec 13

🎉 I'm starting my own lab at EMBL-EBI (Cambridge, UK; June 2025) 🎉

We will focus on identifying and characterizing chemical hazards to humans and ecosystems using computational biology methods.

I am beginning the search for two postdocs now - stay tuned for more details!

ewaldlab.org

Ewald Lab

@ EMBL-EBI. We identify and characterize chemical hazards to both humans and ecosystems with cell profiling data, machine learning, and integrative data analysis.

ewaldlab.org

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Arjun Bhattacharya @arjunbhattac.bsky.social · Jan 17

DEADLINE EXTENDED to Jan. 21! Open to grads & undergrads, join the world of cancer prevention this summer Jun 3 to Aug 9 at MD Anderson with an NCI funded internship working with too cancer researchers & clinicians! Apply at bit.ly/CPRTP-Summer

CPRTP Summer Research Experience

bit.ly

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Arjun Bhattacharya @arjunbhattac.bsky.social · Dec 2

Thanks, Mike!

Arjun Bhattacharya @arjunbhattac.bsky.social · Nov 30

Our isoTWAS work with the Pasaniuc and Gandal labs is out at Nature Genetics! Great team effort, especially from Daniel Vo and Connor Jops. Appreciate the helpful and thoughtful comments from reviewers that improved our work!

www.nature.com/articles/s41...

Isoform-level transcriptome-wide association uncovers genetic risk mechanisms for neuropsychiatric d...

A multivariate framework for isoform-resolution transcriptome-wide association studies enables modeling of a greater number of genes, with the benefit of identifying isoform-specific associations with...

www.nature.com

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Arjun Bhattacharya @arjunbhattac.bsky.social · Oct 30

If you’re a trainee or know one looking for a postdoctoral position, let’s chat during ASHG this week!

Arjun Bhattacharya @arjunbhattac.bsky.social · Oct 9

Come join me at MD Anderson Cancer Center in Houston and the Texas Medical Center! I'm hiring a Postdoctoral Scholar to lead genetic and molecular epidemiology projects to study breast cancer or pregnancy/childhood outcomes.

More details here: bit.ly/pd_blgc2023

Skyline for MD Anderson Cancer Center and surrounding Texas Medical Center buildings

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Reposted by Arjun Bhattacharya

Michel Nivard @michelnivard.bsky.social · Oct 6

This is a Bluesky feed that tracks #WCPG2023 posts for the world congres of psychiatric genetics 2023, SUBSCRIBE!: bsky.app/profile/did:...

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