Shaun Mahony
@mahonylab
Studying gene regulation and transcription factor binding specificity with machine learning. Assoc Prof @ Penn State. 🇮🇪
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/s4146…
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
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/10.110…
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.
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/early/…
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.molc…
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
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
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-ar…?
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.…
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/
Anyone Looking for a Postdoc? please contact me ASAP especially if you are interested in plant-herbivore interactions in agroecosystems! #ChemEcolPSU
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
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
biorxiv.org/content/10.110… 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!
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
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.
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.
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
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.