• Congratulations to MSTP student Han-Seul Ryu for the acceptance of her collaborative paper with the Anguera Lab entitled “B cell stimulation changes the structure and higher-order organization of the inactive X chromosome” in Cell Reports. Amazing job Han-Seul!

  • Congratulations to PhD student Rohan Patel for the acceptance of his paper entitled ” FISHnet: Detecting chromatin domains in single-cell sequential Oligopaints imaging data” in Nature Methods. https://www.biorxiv.org/content/10.1101/2024.06.18.599627v1

  • Congratulations to clinical fellow and postdoc alum  Michael Guo on the publication of his paper entitled ‘Polygenic burden of short tandem repeat expansions promotes risk for Alzheimer’s disease’ in Nature Communications. https://www.nature.com/articles/s41467-025-56400-0

  • Sweety Meel joins us from Dimple Notani’s lab (https://swati.nipgr.ac.in/Scientist/SWEETY%20MEEL) as a new postdoctoral research fellow. Welcome Sweety!

  • Javed Chitman joins us from Florida State as a new postdoctoral research fellow. Welcome Javed!

  • Skenlanda Marseille joins our lab full time for a post-bacc internship to continue her long-time work in our SEEDs program. Welcome, Skenlanda!

  • Congrats to our alum Dr. Jonathan Beagan who has now joined Precede Bio as a computational scientist. He presented his work in a poster and panel at SABCS to ascertain if chromatin signatures can be detected in liquid biopsy and used to diagnose intractable breast cancer. https://www.instagram.com/p/DD4zTogxEqK/

  • Congratulations to our alum Dr. Ji Hun Kim who has started his own laboratory at KAIST and just won his first independent grant.https://www.instagram.com/p/DDkVZRaypWc/

  • Congratulations to PhD candidate Rohan Patel – he is awarded an NIH fellowship for his work to computationally explore chromatin patterns and mechanisms of loop extrusion in sequential oligopaints imaging data.https://www.instagram.com/p/DDPftAlxE86/?img_index=5

  • Katelyn Titus defends their PhD with an unbelievable 11 papers, congratulations, Dr. Titus! We have loved our time working with you and can’t wait to share your achievements with our community.

  • Ali Nikish defends her PhD, congratulations, Dr. Nikish! We are all proud of you!

  • Congratulations to clinical fellow and postdoc alum Michael Guo on starting his independent tenure-track faculty position in the Department of Neurology at Penn.

  • Harshini Chandrashekar is the recipient of the Young TAD 2024 for excellence in research from Genome Organization Australia. Congratulations Harshini!https://x.com/GenomeOrgAus/status/1860926126245216371https://bsky.app/profile/genomeorgaus.bsky.social/post/3lbqxyp6aks2z

  • Dr. Peibo Xu gave his first major postdoc talk at the Penn Epi Institute retreat.https://www.instagram.com/p/DBukz_8x8QU/?img_index=5

  • Jenn gives the NIH Wals lecture to share our labs progress over the last decade and introduce our new focal areas on neuroscience, neurological disorder, and chromatin-synapse communication.https://www.instagram.com/p/DBWw_XKR3zq/?img_index=5The Science of Connections: Bridging chromatin folding, synaptic plasticity, and neurophysiologyhttps://videocast.nih.gov/watch=55006

  • Tim Pollex joins the lab from Edith Heard’s lab in EMBL Heidelberg & The Crick as a research scientist and senior research investigator. Welcome Tim!
https://www.instagram.com/p/DA7Ng9hpMO6/?img_index=5

  • Gui Hu joins the lab as a new research technician. Welcome Gui!



  • Congratulations to our SEEDs 2024 scholars, Skenlanda, Srikar, and Constin, for a successful summer of research.https://www.instagram.com/p/C_TuRZtxlB3/

  • Ravi Boya along with his wife Udaya announce the birth of their son, Adyant Boya. A warm congratulations to the Boya family. Welcome to the world, little one.

  • William Kastor joins the lab as a new research technician. Welcome William!

  • 
Kenneth Pham (MSTP) and Brian Franklin (MTSP) present posters at the Genetics retreat:
and Avi Waldman presents at the NGG event:
https://www.instagram.com/p/C_BwncVRW_c/?img_index=1

  • Harshini Chandrashekar successfully defends her PhD. Congratulations Dr. Chandrashekar!
https://www.instagram.com/p/C-x9_DoR54z/?img_index=1https://www.instagram.com/p/C-x_IOhRy5X/?img_index=1https://www.instagram.com/p/DBKJNW1yL_5/https://www.instagram.com/p/DBKJkr1y6cV/

  • Kate Titus, Harshini Chandrashekar, and Zoltan Simandi published their paper on the link between elongating RNA polymerase II and long-range enhancer-promoter loops during human neural differentiation. Congratulations Kate, Harshini, and Zoltan!https://www.cell.com/cell-genomics/fulltext/S2666-979X(24)00200-3https://www.instagram.com/p/C7Sw3AuRkEr/?img_index=1https://www.instagram.com/p/C9X8PUeRbHB/?img_index=1

  • Sarah Park joins us as our new laboratory manager. Welcome Sarah!

  • Ken Chandradoss presents a talk on his work at the Chromatin and Epigenetics Gordon Research conference in Newport, Rhode Island.

  • Jenn loved visiting Puerto Rico this summer to celebrate 25 years of science and mentorship for her PhD advisor Dr. Andres Garcia. So much gratitude to Andres for his long-time role in Jenn’s life.

  • Our Ninth annual SEEDs program took place in Summer 2024. We welcomed Skenlanda Marseille (UBinghamton) and Srikar Muppidi (UPenn) for summer research while preparing their medical school applications. We also welcomed Constin Liu (WUSTL) to the program!https://www.instagram.com/p/C8nDLzwxFab/?img_index=1

  • Rohan Patel and Kenneth Pham submit their new manuscript on FISHnet – a tool for identifying chromatin domains in single-cell sequential Oligopaints imaging data. Congrats Rohan and Kenneth! https://www.biorxiv.org/content/10.1101/2024.06.18.599627v1

  • Rahul Sureka joins the lab from EMBL Rome as a research scientist and senior research investigator. Welcome Rahul!

  • We are thrilled to share the news that our post-bacc alum James Sun will defend his PhD from NYU Grossman School of Medicine. James, we are filled with pride and joy to see all you have gone on to accomplish. Cannot wait to see what you achieve as you finish up your medical school training…

  • Delighted to share the news of renewal of a grant through the National Institute of Mental Health on 3D genome misfolding in human models of fragile X syndrome. Kenneth Pham, Thomas Malachowski, Chuanbin Su, Rohan Patel, Ravi Boya, and Ken Chandradoss will be working in part on projects related to this topic.

  • The Cremins lab is honored to announce a new partnership with the Cure Huntington’s Disease Initiative (CHDI). Han-Seul Ryu will be leading the initiative to study chromatin-mediated regulation of genome instability in single cells.

  • Sarah Park joins the lab as our new lab manager. Welcome Sarah, we are all so happy to work with you!

  • Strikar Muppidi, a current SEEDs scholar, has received his first acceptances into medical school. Congrats Srikar!

  • Harshini Chandrashekar presents her work at the 4DN consortium webinar series.

  • Congratulations to PhD candidate Avi Waldman for successfully proposing his thesis plans today. Many thanks to a great committee Dan Huh, Colin Conine, Jian Ma, and Yangxing Deng for a fun discussion.|https://www.instagram.com/p/C6_t5QruRHN/

  • Kenneth Pham had a great committee meeting today. Good stuff Kenneth, and thank you to great colleagues Rahul Kohli, Elizabeth Bhoj, Ken Zaret, and Mo Kahlil. https://www.instagram.com/p/C7AgPZXJ3oE/

  • Dr. Chuanbin Su posts a first-author preprint on the development of his new technology: MASTR-seq for Multiplexed Analysis of Short Tandem Repeats with Sequencing. Congratulations Chuanbin!https://www.biorxiv.org/content/10.1101/2024.04.29.591790v1

  • Congratulations to our Chuanbin Su for posting his new preprint on his technology MASTR-seq for high throughput multimodal measurement of dna methylation and STR tract length at single molecule resolution. Strong work Chuanbin! https://www.biorxiv.org/content/10.1101/2024.04.29.591790v1https://www.instagram.com/p/C6pURqGp-Uu/

  • Su Gu joins the lab as a new research technician. Su is a virus packaging and table tennis wiz, and we are excited to have his skills in the lab.

  • PhD student Harshini Chandrashekar wins first prize for her research presentation at the bioengineering graduate group annual symposium. Congratulations Harshini!https://www.instagram.com/p/C6MF2LBrWZN/

  • Our alum, Dr. Ji Hun Kim, wins his first research grant as an assistant professor at KAIST. Dr. Kim is using the LADL (Light-activated Dynamic Looping) technology he built to study the role for loops in gene expression regulation in cancer. Congratulations Ji Hun!

  • Our alum, Dr. Thomas Gilgenast, visits KAIST to visit Ji Hun and give a seminar on his collaborative work with Scharam Akbarian. Congratulations Thomas!

  • Congratulations to Harshini Chandrashekar for winning first prize for her oral presentation in the Bioengineering PhD program symposium.

  • Warm congratulations to Harshini, Zoltan, Heesun, Avi, Ali, and Han-Seul for posting their new BioRxiv preprint uncovering a role for dynamic multi-loops in gene expression dysregulation in post-mitotic human neurons homozygously-engineered with familial Alzheimer’s disease mutations. https://www.biorxiv.org/content/10.1101/2024.02.27.582395v1

  • Congratulations to Dr. Peibo Xu – one of his first-author PhD papers entitled ‘High-throughput mapping of single-neuron projection and molecular features by retrograde barcoded labeling‘ is now published in eLife. Congratulations Peibo!https://pubmed.ncbi.nlm.nih.gov/38390967/

  • 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!

  • Congratulations to MSTP student Kenneth Pham – he is awarded an NIH NRSA F30 fellowship for his work to understand chromatin in repeat expansion disorders in single cells.

  • 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!