• MSTP student Han-Seul Ryu passes her proposal and becomes a PhD candidate. Congratulations Han-Seul!


  • Huge congratulations to MSTP student Kenneth Pham on receiving his first NIH Notice of Award for his F30 fellowship grant. Great job Kenneth!


  • Edda Schulz writes a commentary on our team’s fragile x paper in Molecular Cell. https://www.sciencedirect.com/science/article/pii/S1097276524000017?dgcid=author


  • NIMH writes a news article on our Fragile X Syndrome work: https://www.nimh.nih.gov/news/science-news/2024/researchers-expand-understanding-of-genetic-mechanisms-underlying-fragile-x-syndrome


  • Kenneth Pham receives a fundable score on his NIH NRSA F30 proposal


  • Warm congratulations to our Ken Chandradoss on his marriage!


  • Thomas, Ravi, Ken, and Linda publish their paper ‘Spatially coordinated heterochromatinization of long synaptic genes in fragile X syndrome’ – warmest congratulations to the lead authors and all members of Team FXS for their extraordinary resilience, rigor, and dedication to seeing this through to the finish line. https://doi.org/10.1016/j.cell.2023.11.019


  • Harshini Chandrashekar, Chuanbin Su, Katelyn Titus, and Rohan Patel present posters on their work at the 4DN annual meeting.


  • Harshini Chandrashekar gives a talk at the 2023 4DN annual meeting.


  • Lab heads to Boston for the 2023 4DN annual meeting. Make way for ducklings!


  • Kate Titus, Harshini Chandrashekar, and Zoltan Simandi post their preprint exploring the role for cell type-specific chromatin loops in RNA Pol2-mediated elongation during human neural differentiation:  https://www.biorxiv.org/content/10.1101/2023.12.04.569731v1


  • Ali Nikish presents her research at the Penn Genetics Research-In-Progress seminar series.


  • Mike Guo posts his preprint finding an increased burden of STR expansions associated with sporadic Alzheimer’s disease:https://medrxiv.org/cgi/content/short/2023.11.16.23298623v1


  • Harshini Chandrashekar gives a talk on her work at Penn’s Genetic retreat in Bear Mountain Creek resort.


  • Thomas, Ken, Ravi, and Linda’s paper on the discovery of BREACHes in fragile X syndrome is accepted. Our warmest congratulations to all authors for their teamwork, resilience, and persistence!


  • Warm congratulations to Daniel Emerson on defending his outstanding thesis. Congratulations Dr. Emerson!


  • Congratulations PhD candidate Thomas Malachowski on passing your thesis proposal!


  • Postdoc alumnus Dr. Mayuri Rege starts a new faculty position as an assistant professor at HBCSE-TIFR in Mumbai, India. Congratulations Mayuri! We are excited to see your adventure unfold.


  • Han-Seul Ryu has been selected by the MSTP Awards Committee as the 2024 recipient of the Michael S. Brown Fellowship, which carries with it two years of support for her graduate studies.


  • Our alumna Jackie Valerie – one of the inaugural members of the SEEDs program – defended her PhD at MIT in Jim Collins lab. Congratulations Dr. Valerie!


  • Jordan’s work in collaboration with the Joyce lab (High-throughput Oligopaint screen identifies druggable regulators of genome folding) is published in Nature https://doi.org/10.1038/s41586-023-06340-w


  • Han-Seul Ryu passes their BE qualifying exam. Congratulations Han-Seul – way to go!


  • Kelly Feng’s work in collaboration with the Sarma lab (G-quadraplexes associated with R-loops promote CTCF binding,) is published in Molecular Cell https://doi.org/10.1016/j.molcel.2023.07.009


  • Thomas Gilgenast’s work in collaboration with the Walsh, Akbarian, and Brennand labs (Schizophrenia-associated somatic copy number variants from 12,834 cases reveal contribution to risk and recurrent, isoform-specific NRXN1 disruptions) is published in Cell Genomics https://doi.org/10.1016/j.xgen.2023.100356


  • The lab contributed to a review on the NIH 4DN common fund initiative (Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project) – and it is published in Molecular Cell https://doi.org/10.1016/j.molcel.2023.06.018


  • We are thrilled to share that Brian Franklin is the recipient of 2023 Blavatnik Family Fellowship. Congratulations Brian!


  • Ali Nikish passes her PhD candidacy exam through BE. Congratulations PhD Candidate Ali Nikish!


  • The lab is thrilled to welcome Skenlanda Marseille and Christopher Yi to our group for our summer 2023 SEEDs program. Warm welcome Skenlanda and Chris!


  • Ali Nikish and Harshini Chandrashekar present posters on their work at the Gordon Research conference on genome Architecture in cell fate and disease in Ventura, CA


  • Ravi Boya and Thomas Malachowski speak on their work at the Penn genetics student seminar series


  • Kenneth Pham passes their CAMB qualifying exam. Congratulations Kenneth!


  • Grad student alum Dr. Jonathan Beagan accepts a new job at Dana Farber start-up Precede Biosciences in Boston, MA. Congratulations Jon, we are so proud of you!


  • Spencer Haws presents a short talk and poster at the NYSCF grantee retreat in Montauk New York


  • Dan Emerson speaks on his PhD thesis work linking 3D genome folding to replication origins at the Penn Bioengineering graduate group symposium. Way to go Dan!


  • Harshini Chandrashekar presents a poster at the Penn Bioengineering graduate group symposium.


  • Harshini Chandrashekar passes her PhD candidacy exam through BE. Congratulations PhD Candidate Chandrashekar!


  • Han-Seul Ryu is the recipient of the Gold Humanism Honors Society Award honoring her excellence in compassionate care for her patients. The lab is filled with joy to hear of your award Han-Seul – congratulations! 


  • Thomas Malachowski, Dan Emerson, Ashley Cook, and Ken Chandradoss present posters at the Penn Epigenetics Institute annual retreat at the Phillies ball park


  • The lab takes part in a special service project for our community on Martin Luther King Day at the Marian Anderson Recreation Center


  • Congratulations to Brian Franklin for being appointed to Virginia Lee’s NIH T32 fellowship. Strong work Brian!


  • Dan Emerson passes his PhD candidacy exam through BE. Congratulations PhD Candidate Emerson!


  • Avi’s undergraduate research is published. Congrats Avi! https://pubs.acs.org/doi/abs/10.1021/jacs.2c09346


  • Kenneth Pham joins the lab for their PhD research through Penn’s MSTP program


  • Peibo Xu, PhD joins the lab as a new postdoctoral research fellow


  • Jordan, Ashley, Han-Seul, and Dan’s contributions to a collaboration with the Anguerra lab (Remodeling and compaction of the inactive X is regulated by Xist during female B cell activation) is posted on BioRxiv Preprint: https://doi.org/10.1101/2022.10.19.512821


  • Spencer Haws presents a poster at the NYSCF Regenerative Medicine conference at Rockefeller University


  • Linda and Chunmin’s patent application was granted – congratulations Linda and Chunmin! Epigenomic editing and reactivation of targets for the treatment of Fragile X syndrome, US Patent 17689867, October 13, 2022. https://patents.google.com/patent/US20220323553A1/en


  • Congratulations to Thomas Malachowski for winning an NIH F31 graduate research fellowship. Way to go Thomas!


  • Han-Seul Ryu joins the lab for her PhD research through Penn’s MSTP program


  • Avi Waldman passes his qualifying exam. Congratulations Avi!


  • Spencer, Zoltan, and Jordan’s review (3D genome, on repeat: Higher-order folding principles of the heterochromatinized repetitive genome) is published in Cell 10.1016/j.cell.2022.06.052


  • Rohan Patel passes his qualifying exam. Congratulations Rohan!


  • Ali Nikish is awarded a T32 grant for her PhD research. Congratulations Ali!


  • Zoltan Simandi speaks on his work in a joint talk with Jenn at the Broad Institute chromatin club.


  • Daniel Emerson, Miriam Minsk, Ashley Cook, and Jordan Barnett publish their 3D genome and replication origins paper https://www.nature.com/articles/s41586-022-04803-0


  • Spencer Haws is the recipient of the New York Stem Cell Foundation Druckenmiller Postdoc Fellowship. Congratulations Spencer, and welcome to the NYSCF community!


  • Brian Franklin passes his qualifying exam in the Cell and Molecular Biology graduate group. Congratulations Brian!


  • Katelyn R. Titus defends her PhD proposal and advances as a PhD candidate in Penn’s Bioengineering graduate program. Congratulations Kate!


  • Miriam Minsk will begin the MD/PhD program at UCSF in September 2022. Congratulations Miriam!


  • Congratulations to our alum Jon Beagan who received the LSRF postdoctoral fellowship for his work in Daniel Colon Ramos lab at Yale. 


  • Harshini Chandrashekar speaks on her work at Penn’s NeuroEpigenetics interest group.


  • Jon Beagan’s paper on cohesin-independent loops during neural stimulation is accepted at eLIFE!


  • Dan Emerson and Ashley Cook’s paper on cohesin-mediated loops and human replication origins is accepted at Nature!


  • Zoltan Simandi speaks on his work at Penn’s Epigenetics Institute


  • Jordan Barnett’s collaborative work with the Joyce lab is available on BioRxiv: https://doi.org/10.1101/2022.04.08.487672


  • Avi Waldman and Rohan Patel receive Honorable Mentions for the NSF GRFP – congratulations!


  • Thomas Gilgenast work in collaboration with the Akbarian lab (Chromatin domain alterations linked to 3D genome organization in a large cohort of schizophrenia and bipolar disorder brains) is published in Nature Neuroscience. https://doi.org/10.1038/s41593-022-01032-6


  • Linda Zhou matches at her first choice for residency – UPenn Dermatology


  • Alexandria Nikish is the recipient of the UPenn T32 Neurotechnology training grant. Congratulations Ali!


  • Miriam Minsk is accepted into USCF, Johns Hopkins, and Tri-I MD/PhD programs – congratulations Miriam!


  • Ken Chandradoss speaks on his work at Penn’s Epigenetics Institute


  • Congratulations to our postdoc Dr. Ji Hun Kim on receiving a faculty position the Korea Advanced Institute of Science and Technology! Ji Hun will start his lab building upon his light activated dynamic looping tool and understanding the role for loops in gene expression.


  • Cremins lab organizes the 2021 3D genome Keystone conference along with colleagues Stavros Lomvardes and Job Dekker


  • Jenn awarded ISSCR Dr. Susan B. Lim Outstanding New Investigator


  • Lab receives 2021 NIH pioneer award With NIH Pioneer Award, Jennifer E. Phillips-Cremins Will Study Genome Folding’s Role in Long-term Memory


  • Emily Pickup joins the lab – welcome Emily!


  • Harshini Chandrashekar successfully passes her PhD qualifying exam!


  • Thomas Malachowski successfully passes his PhD qualifying exam!


  • Rohan Patel joins the lab – welcome Rohan!


  • Avi Waldman joins the lab – welcome Avi!


  • Brian Franklin passes his Step One exam. Congratulations Brian!


  • Zoltan Simandi attends CZI faculty application training program.


  • Jordan Barnett joins the lab – welcome Jordan!


  • Dan Emerson successfully passes his PhD qualifying exam!


  • Linda Zhou, PhD wins the Saul Winegrad award for 2021 best thesis for Penn GCB.


  • Congratulations to Linda, Ken, Thomas, Chunmin, Ji Hun, Wanfeng, Kate, and Chuanbin for the posting of their new manuscript to BioRxiv.


  • Ali and Kenneth publish their opinion paper on in situ sequencing in Molecular Cell.


  • Spencer Haws joins the lab – welcome Spencer!


  • Michael Guo wins an R25 NIH physician-scientist fellowship. Congratulations Mike!


  • The Lab has officially moved to a new lab space in the Clinical Research Building!


  • Lab receives two U01 grants from the 4D Nucleome Consortium.


  • The lab receives a grant from the Friedreich’s Ataxia Research Alliance.


  • Linda Zhou passes her PhD defense with flying colors. Congratulations Dr. Zhou!


  • Spencer Hawes has decided to join lab!


  • The lab receives funding through the Chan Zuckerberg Initiative for a Neurodegenerative Disease Pairs collaboration with Dr. Kristen Brennand


  • Danying Guan joins the lab for the summer as part of the The American Physician Scientists Association (APSA) Virtual Summer Research Program. Welcome Danying!


  • Congratulations to Ali Nikish for passing her Ph.D. qualifying exam!


  • Noah Barnett, David Barto, Ashley Cook, Nathan Ehrenreich, Thomas Malachowski, and Ken Raanin Chandradoss have officially joined the lab. Welcome!


  • Congratulations to Kate Titus for passing her Ph.D. qualifying exam!


  • Jon Beagan presents at a virtual conference sponsored by Arima alongside Dan Geschwind and Schahram Akbarian