Studying gene regulation and transcription factor binding specificity with machine learning. Assoc Prof @ Penn State. 🇮🇪
Penn State University
Joined June 2016
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Shaun Mahony retweeted
Delighted to have worked on this perspective on the cis-regulatory code with @JuliaZeitlinger, @JasonErnstLab, @ferhatay, @AMathelier, @AleMedinaRivera, @mahonylab, @sinhasaur arxiv.org/abs/2411.04363. We provide an overview of current progress and some challenges to think about.
Shaun Mahony retweeted
Excited that we have a paper coming out in @genomeresearch exploring comparisons of epigenetic landscapes between species to find and better understand gene regulatory elements. genome.cshlp.org/content/ear…
Shaun Mahony retweeted
Out now in Molecular Cell! Along with Tan and Mahoney labs, we combine cellular, in vitro, and computational methods to understand how sequence features affect pioneer factor specificity (cofactors play a big role)
doi.org/10.1016/j.molcel.202…
Shaun Mahony retweeted
Penn State Biology is looking for a Tenure Track Evolutionary Genomicist. We are a welcoming and supportive community - come work with us! @PSUScience Read more here: tinyurl.com/599td3nj
#blackinstem #latinxinstem #indigenousinstem #diversityinstem #lgbtSTEM #womeninstem
Shaun Mahony retweeted
My (awesome) department is hiring an evolutionary genomicist. Come be my colleague!
Penn State Biology is looking for a Tenure Track Evolutionary Genomicist. We are a welcoming and supportive community - come work with us! @PSUScience Read more here: tinyurl.com/599td3nj
#blackinstem #latinxinstem #indigenousinstem #diversityinstem #lgbtSTEM #womeninstem
Shaun Mahony retweeted
Very proud of this highly collaborative paper with the @mahonylab @RemoRohs and Gordân labs in which we explore how ApiAP2 transcription factors with similar DNA binding specificities define their target genes, a ubiquitous challenge in all cells! academic.oup.com/nar/advance…?
Shaun Mahony retweeted
Check out our latest paper in @NatureComms where we develop a methylation-based sequencing assay to capture chromosomal interactions with a viewpoint
nature.com/articles/s41467-0…
Shaun Mahony retweeted
Check out our latest work in @eLife! This work, led by graduate student James (graduating Sunday) uses a range of techniques, including a new methylation-based method to dissect gene cluster in haploid yeast.
doi.org/10.7554/eLife.96028
Shaun Mahony retweeted
The foundation has enabled numerous students to attend key conferences in Genomics and Data Science. Help us to continue this mission by donating to the foundation: jxtxfoundation.org/donate/
Shaun Mahony retweeted
Anyone Looking for a Postdoc? please contact me ASAP especially if you are interested in plant-herbivore interactions in agroecosystems! #ChemEcolPSU
Shaun Mahony retweeted
Uh-oh!! We're back!! And this time we're taking no prisoners!! The Penn State Bioinorganic Workshop will be held in person again this summer from May 29-June 4 @PSUScience. Check out the website for further information. Always an awesome time and learning experience!!
The Penn State Bioinorganic Workshop will be offered from May 29 - June 4 - please see updates at sites.psu.edu/bioinorganic/2… with @jmarbol21 @BookerMan_PSU @CotruvoLab @StollPatrol @Prof_SJE @MossbauerLab @ShafaatLab @TamraBlue3 @jwilcoxen and many others
Shaun Mahony retweeted
Thrilled to see my @BMB_PSU colleague Anton Nekrutenko @nekrut and colleagues' @galaxyproject paper in @NatureBiotech. @PSUScience @huckinstitutes
Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy go.nature.com/3HAk6w2
Shaun Mahony retweeted
biorxiv.org/content/10.1101/…
Our manuscript characterizing the shortest k-mer sequences unique in humans. We find that they are enriched in neuronal genes and are hotspots for pathogenic variants!
@i_mouratidis @MaxwellKonnaris @NicoleC42080053 @bigmonty12 and others!
Shaun Mahony retweeted
Yifei HUANG (@huangyifeicmb), our dear colleague, Asst Prof @PennStateBio, passed away from cancer in October at the age of 40. We are collecting donations for his daughter's education. All donations are tax-deductible. @PSUresearch Please RT. gofund.me/ef82effe
ALT Yifei with his family in June 2023
Shaun Mahony retweeted
Working with scATAC-seq data? My student @Yq_Cheng will present a new tool from our lab, EpiPack, designed specifically for the distinct features across scATAC-seq data batches, that performs integration, reference mapping and new cell type identification #rsgdream2023 #RSGDREAM
Shaun Mahony retweeted
Key questions to ask when on the faculty market (which I myself didn't ask): what's the total cost per trainee level, how are trainees recruited, how many trainees does a typical junior lab recruit yearly.
Let's do the same for a PI on a 9-mo salary of $100k, budgeting to cover their summer salary:
Salary: $33.3k
Benefits: $12k
Travel: $6k
F&A: $28k
Total = $82k/y
The point isn't that grad students "cost" a lot, it's that your PI's new 5-year $2M grant isn't stretching very far
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This is a hugely important question for folks negotiating junior faculty positions. It varies widely from place to place. Some places charge tuitions to startup, some use other funds. Some charge F&A to startup, some don't. Some depts cover stipends via TA-ships. Etc.
Shaun Mahony retweeted
Check out this preprint showcasing a collaborative project between three CEGR labs (@BaiLab_PSU, @mahonylab, and Tan lab) studying the sequence features dictating the binding specificity of the FOXA1 pioneer factor in human cancer cells.
Preprint now available: we investigated the binding specificity of pioneer factor FoxA1 by developing a high throughput synthetic approach ChIP-ISO.
biorxiv.org/content/10.1101/…
