Bohan Ni (@bohan_ni) profile picture

Bohan Ni

@bohan_ni

PhD student in JHU Computer science compbio.

Joined February 2020
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I very excited to be DEFENDING MY THESIS on February 28, 2025. The seminar will recap empirical tests of large-scale gene regulatory network models and other models that predict transcription. Email or DM for details!
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Today, I'm excited to present the second big chunk of my Ph.D. work. We are building a thorough assessment of the burgeoning field of gene expression forecasting. Something is deeply wrong.🧵 - Preprint: biorxiv.org/content/10.1101/… - Code: github.com/ekernf01/perturba…
A systematic comparison of computational methods for expression forecasting

A systematic comparison of computational methods for expression forecasting

Expression forecasting methods use machine learning models to predict how a cell will alter its transcriptome upon perturbation. Such methods are enticing because they promise to answer pressing...

biorxiv.org
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Very excited that my meta-analysis of telomere length GWAS and experimental validation showing that POP5 and KBTBD6 are human telomere length regulation genes is out in @NatureComms! Shout out to my mentors @alexisjbattle and @RasikaMathias nature.com/articles/s41467-0…
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Bohan Ni retweeted
Mathieu (@miniapeur) profile picture
Mathieu
@miniapeur12 May 2024
Image from Mathieu (@miniapeur)
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We look at QTLs in dozens of differentiating cell types and dynamic trajectories simultaneously in vitro - check out our new preprint and @popp_josh 's thread! biorxiv.org/content/10.1101/…
Cell-type and dynamic state govern genetic regulation of gene expression in heterogeneous differe...

Cell-type and dynamic state govern genetic regulation of gene expression in heterogeneous differe...

Identifying the molecular effects of human genetic variation across cellular contexts is crucial for understanding the mechanisms underlying disease-associated loci, yet many cell-types and develop...

biorxiv.org
Josh Popp (@popp_josh) profile pictureJosh Popp@popp_josh4 May 2024
SO excited to share our recent work! To better understand the molecular impacts of human genetic variation, we need models that offer access to MANY more cell types and cell states. Here, we’re using a system called heterogeneous differentiating cultures (HDCs) to do this (1/n)
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Happy to share our preprint for ModDotPlot - Rapid and Interactive Visualization of Complex Repeats biorxiv.org/content/10.1101/…
ModDotPlot—Rapid and interactive visualization of complex repeats

ModDotPlot—Rapid and interactive visualization of complex repeats

Motivation A common method for analyzing genomic repeats is to produce a sequence similarity matrix visualized via a dot plot. Innovative approaches such as StainedGlass have improved upon this...

biorxiv.org
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Excited to share our preprint: Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease. medrxiv.org/content/10.1101/….
Integration of transcriptomics and long-read genomics prioritizes structural variants in rare...

Integration of transcriptomics and long-read genomics prioritizes structural variants in rare...

Rare structural variants (SVs) — insertions, deletions, and complex rearrangements — can cause Mendelian disease, yet they remain difficult to accurately detect and interpret. We sequenced and...

medrxiv.org
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Special thanks to @BennyStrobes, @taibo_li for many discussions of Watershed, and @J__Stock, @RebeccaKeener9 for the numerous advice and editing of this manuscript.
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And thank you to all co-authors on the paper for their contributions!
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My lab is looking for postdocs! Contact me directly if interested and also consider applying for the Malone Postdoc Fellows Program. Please retweet!
Alexis Battle (@alexisjbattle) profile pictureAlexis Battle@alexisjbattle8 Dec 2023
Looking for a postdoc opportunity in computational and engineering applications in medicine and healthcare? Apply to @JHUMCEH and work with mentors in * genomics, AI/data science, robotics, HCI, AR/VR, and more: Deadline coming up: Jan 31, 2024 malonecenter.jhu.edu/malone-…
Malone Fellows Program

Malone Fellows Program

malonecenter.jhu.edu
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Looking for a postdoc opportunity in computational and engineering applications in medicine and healthcare? Apply to @JHUMCEH and work with mentors in * genomics, AI/data science, robotics, HCI, AR/VR, and more: Deadline coming up: Jan 31, 2024 malonecenter.jhu.edu/malone-…
Malone Fellows Program

Malone Fellows Program

malonecenter.jhu.edu
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