Publications

Multiomics and deep learning dissect regulatory syntax in human development

Betty B Liu*, Selin Jessa*, Samuel H Kim*, …, Anshul Kundaje^, Kyle K H Farh^, William J Greenleaf^

My main post doc work using deep learning on a new fetal single-cell atlas to learn about the organization of transcription factor binding sites in human development, and where they're perturbed in complex traits. Highlighted in Nature Genetics.

Sensitive, direct detection of non-coding off-target base editor unwinding and editing in primary cells

Tong Wang, Selin Jessa, Georgi K Marinov, Sandy Klemm, Anshul Kundaje, William J Greenleaf

We present a new assay, beCasKAS, to sensitively detect off-target edits from CRISPR base editors, and show how non-coding off-target genome edits can be triaged for epigenetic dysregulation in silico using deep learning.

A unified lexicon of predictive DNA sequence motifs from ENCODE transcription factor binding and chromatin accessibility assays

Salil Deshpande, Chang Min Yun, Vivekanandan Ramalingam, Vivian Hecht, Aman Patel, Anusri Pampari, Selin Jessa, Ryan Zhao, Austin Wang, Anshul Kundaje

Mapping the regulatory effects of common and rare non-coding variants across cellular and developmental contexts in the brain and heart

Andrew R Marderstein, Soumya Kundu, Evin M Padhi, …, Selin Jessa, Anshul Kundaje, Stephen B Montgomery

FOXR2 targets LHX6+/DLX+ neural lineages to drive CNS neuroblastoma

Selin Jessa*, Antonella De Cola*, Bhavyaa Chandarana*, …, Manav Pathania^, Nada Jabado^, Claudia L Kleinman^

We analyzed single-cell profiles of the developing brain together with molecular profiles from patient samples to nominate cell-of-origin, which enabled rationally guided mouse modeling of FOXR2-activated CNS neuroblastoma, a rare pediatric brain tumor subtype. See a commentary on our approach and findings here.

TULIPs decorate the three-dimensional genome of PFA ependymoma

Michael J Johnston, John J Y Lee, Bo Hu, …, Selin Jessa, …, Nada Jabado, Michael D Taylor, Marco Gallo

K27M in canonical and noncanonical H3 variants occurs in distinct oligodendroglial cell lineages in brain midline gliomas

Selin Jessa*, Abdulshakour Mohammadnia*, Ashot S Harutyunyan*, …, Stephen C Mack, Nada Jabado^, Claudia L Kleinman^

Using single-cell and bulk transcriptomics and epigenomics, we provide molecular evidence that deadly childhood gliomas with K27M mutations in different Histone 3 variants arise from distinct anatomical domains in the developing brain. See a News & Views on ours and complementary work here.

Mapping Angiopoietin1 expression in the developing and adult brain

Xin Wei, Selin Jessa, Claudia L Kleinman, Timothy N Phoenix

Epigenetically defined therapeutic targeting in H3.3G34R/V high-grade gliomas

Stefan R Sweha, Chan Chung, Siva Kumar Natarajan, …, Selin Jessa, …, Suzanne J Baker, Arul M Chinnaiyan, Sriram Venneti

ZFTA-RELA Dictates Oncogenic Transcriptional Programs to Drive Aggressive Supratentorial Ependymoma

Amir Arabzade, Yanhua Zhao, Srinidhi Varadharajan, …, Selin Jessa, …, Kelsey C Bertrand, Benjamin Deneen, Stephen C Mack

Histone H3.3G34-Mutant Interneuron Progenitors Co-opt PDGFRA for Gliomagenesis

Carol C L Chen*, Shriya Deshmukh*, Selin Jessa*, …, Paolo Salomoni, Claudia L Kleinman^, Nada Jabado^

We show that despite being histologically considered gliomas, a subtype of Histone 3 mutant childhood brain tumors likely arise in the interneuron lineage in the developing telencephalon; and that these tumors co-opt the PDGFRA oncogene to drive tumorigenesis

Stalled developmental programs at the root of pediatric brain tumors

Selin Jessa, Alexis Blanchet-Cohen, Brian Krug, …, Michael D Taylor^, Nada Jabado^, Claudia L Kleinman^

We generate a single-cell RNAseq atlas of developing brain regions where pediatric brain tumors occur, and use a data-driven approach to systematically nominate cell-of-origin. This work was selected as one of the top 10 discoveries in Quebec for 2020!

Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma

Sarah E Arthur, Aixiang Jiang, Bruno M Grande, …, Selin Jessa, …, Christian Steidl, David W Scott, Ryan D Morin

chromswitch: A flexible method to detect chromatin state switches

Selin Jessa, Claudia L Kleinman

Enhancing knowledge discovery from cancer genomics data with Galaxy

Marco A Albuquerque, Bruno M Grande, Elie J Ritch, Prasath Pararajalingam, Selin Jessa, Martin Krzywinski, Jasleen K Grewal, Sohrab P Shah, Paul C Boutros, Ryan D Morin

Healthcare for All!: Access to healthcare for migrants with precarious status in the Parc-Extension neighbourhood of Montreal, Quebec

Selin Jessa