Publications - New York Genome Center

bioRxiv · March 4, 2025 · Preprint

Targeted BDNF upregulation via upstream open reading frame disruption.

Ning Feng, Thomas Goedert, Nenad Svrzikapa, Dongnan Yan, Britt Hanson, Alicia Ljungdahl, Ruxandra Dafinca, Kevin Talbot, Stephan J Sanders, Dhanu Gupta, Matthew Wood, Thomas C Roberts

Neurodegenerative Disease Polyethnic-1000

bioRxiv · March 3, 2025 · Preprint

Inferring fungal cis-regulatory networks from genome sequences.

Alan M. Moses, Jason E. Stajich, Audrey P Gasch, David A Knowles

Knowles Lab

bioRxiv · March 1, 2025 · Preprint

Multi-sample, multi-platform isoform quantification using empirical Bayes.

Arghamitra Talukder, Shree Thavarekere, Madison Mehlferber, Gloria M Sheynkman, David A Knowles

Knowles Lab

Cell · February 28, 2025

Safeguarding the future of biomedical science in the United States.

Tom Maniatis

Biology, Genomics & Technology

bioRxiv · February 27, 2025 · Preprint

Differential Cellular Mechanisms Underlie Language and Executive Decline in Amyotrophic Lateral Sclerosis.

Joana Petrescu, Claudio Gouveia Roque, Chris Jackson, Aidan Daly, Kristy Kang, Obadele Casel, Mathew Leung, Luke Reilly, Jacqueline Eschbach, Karina McDade, Jenna M Gregory, Colin Smith, Hemali Phatnani

Phatnani Lab

Neurodegenerative Disease

Nature Cell Biology · February 26, 2025

Systematic reconstruction of molecular pathway signatures using scalable single-cell perturbation screens.

Longda Jiang, Carol Dalgarno, Efthymia Papalexi, Isabella Mascio, Hans-Hermann Wessels, Huiyoung Yun, Nika Iremadze, Gila Lithwick-Yanai, Doron Lipson & Rahul Satija

Satija Lab

bioRxiv · February 23, 2025 · Preprint

ScatTR: Estimating the Size of Long Tandem Repeat Expansions from Short-Reads.

Rashid Al-Abri, Gamze Gürsoy

Gürsoy Lab

bioRxiv · February 23, 2025 · Preprint

Lancet2: Improved and accelerated somatic variant calling with joint multi-sample local assembly graph.

Rajeeva Lochan Musunuri, Wayne E. Clarke, Bryan Zhu, William Hooper, Timothy Chu, Jennifer Shelton, André Corvelo, Dickson Chung, Shreya Sundar, Adam M Novak, Benedict Paten, Michael C Zody, Nicolas Robine, Giuseppe Narzisi

Computational Biology Lab

PLOS Biology · February 21, 2025

Caspase 3 and caspase 7 promote cytoprotective autophagy and the DNA damage response during non-lethal stress conditions in human breast cancer cells.

Gayathri Samarasekera, Nancy E. Go, Courtney Choutka, Jing Xu,Yuka Takemon, Jennifer Chan, Michelle Chan, Shivani Perera, Samuel Aparicio, Gregg B. Morin, Marco A. Marra, Suganthi Chittaranjan, Sharon M. Gorski

Cancer

eLife · February 20, 2025

Systems genomics of salinity stress response in rice.

Sonal Gupta, Simon Niels Groen, Maricris L Zaidem, Andres Godwin C Sajise, Irina Calic, Mignon Natividad, Kenneth McNally, Georgina V Vergara, Rahul Satija, Steven J Franks, Rakesh K Singh, Zoé Joly-Lopez, Michael D Purugganan

Satija Lab

bioRxiv · February 20, 2025 · Preprint

Uncovering the Signatures of Cellular Senescence in the Human Dorsolateral Prefrontal Cortex.

Nicholas Sloan, Jason Mares, Aidan C Daly, Lilian Coie, Shaunice Grier, Natalie Barretto, Obadele Casel, Kristy Kang, Chris Jackson, Maria Pedersen, Shruti Khiste, Ben Fullerton, Joana Petrescu, Courteney Mattison, Colin Smith, Yousin Suh, Vilas Menon, Hemali Phatnani.

Phatnani Lab

Neurodegenerative Disease

Nature Genetics · February 17, 2025

Multiomic single-cell profiling identifies critical regulators of postnatal brain.

Research Sequencing

Nature Communications · February 13, 2025

Comprehensive dissection of cis-regulatory elements in a 2.8 Mb topologically associated domain in six human cancers.

Christina M. Caragine, Victoria T. Le, Meer Mustafa, Bianca Jay Diaz, John A. Morris, Simon Müller, Alejandro Mendez-Mancilla, Evan Geller, Noa Liscovitch-Brauer & Neville E. Sanjana

Sanjana Lab

Cancer

arXiv · February 12, 2025 · Preprint

PLayer-FL: A Principled Approach to Personalized Layer-wise Cross-Silo Federated Learning.

Ahmed Elhussein, Gamze Gürsoy

Gürsoy Lab

Cell Genomics · February 12, 2025

Secure and federated quantitative trait loci mapping with privateQTL.

Yoolim Annie Choi, Yebin Kim, Peihan Miao, Tuuli Lappalainen, Gamze Gürsoy

Gürsoy Lab Lappalainen Lab

Nature Biotechnology · February 11, 2025

Precise RNA targeting with CRISPR–Cas13d.

Sydney K. Hart, Simon Müller, Hans-Hermann Wessels, Alejandro Méndez-Mancilla, Gediminas Drabavicius, Olivia Choi & Neville E. Sanjana

Sanjana Lab

Nature Computational Science · February 7, 2025

A statistical framework for multi-trait rare variant analysis in large-scale whole-genome sequencing studies.

Xihao Li, Han Chen, Margaret Sunitha Selvaraj, Eric Van Buren, Hufeng Zhou, Yuxuan Wang, Ryan Sun, Zachary R. McCaw, Zhi Yu, Min-Zhi Jiang, Daniel DiCorpo, Sheila M. Gaynor, Rounak Dey, Donna K. Arnett, Emelia J. Benjamin, Joshua C. Bis, John Blangero, Eric Boerwinkle, Donald W. Bowden, Jennifer A. Brody, Brian E. Cade, April P. Carson, Jenna C. Carlson, Nathalie Chami, Yii-Der Ida Chen, Joanne E. Curran, Paul S. de Vries, Myriam Fornage, Nora Franceschini, Barry I. Freedman, Charles Gu, Nancy L. Heard-Costa, Jiang He, Lifang Hou, Yi-Jen Hung, Marguerite R. Irvin, Robert C. Kaplan, Sharon L. R. Kardia, Tanika N. Kelly, Iain Konigsberg, Charles Kooperberg, Brian G. Kral, Changwei Li, Yun Li, Honghuang Lin, Ching-Ti Liu, Ruth J. F. Loos, Michael C. Mahaney, Lisa W. Martin, Rasika A. Mathias, Braxton D. Mitchell, May E. Montasser, Alanna C. Morrison, Take Naseri, Kari E. North, Nicholette D. Palmer, Patricia A. Peyser, Bruce M. Psaty, Susan Redline, Alexander P. Reiner, Stephen S. Rich, Colleen M. Sitlani, Jennifer A. Smith, Kent D. Taylor, Hemant K. Tiwari, Ramachandran S. Vasan, Satupa’itea Viali, Zhe Wang, Jennifer Wessel, Lisa R. Yanek, Bing Yu, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Josée Dupuis, James B. Meigs, Paul L. Auer, Laura M. Raffield, Alisa K. Manning, Kenneth M. Rice, Jerome I. Rotter, Gina M. Peloso, Pradeep Natarajan, Zilin Li, Zhonghua Liu & Xihong Lin

Computational Biology Lab

Research Sequencing

Scientific Reports · February 5, 2025

Whole genome sequencing in early onset advanced heart failure.

Erik Linnér, Tomasz Czuba, Olof Gidlöf, Jakob Lundgren, Entela Bollano, Maria Hellberg, Selvi Celik, Neha Pimpalwar, Philipp Rentzsch, Molly Martorella, Anders Gummesson, Olle Melander, Sebastian Albinsson, Göran Dellgren, Jan Borén, Anders Jeppsson, R. Thomas Lumbers, Sonia Shah, Johan Nilsson, Pradeep Natarajan, Tuuli Lappalainen, Malin Levin, Hans Ehrencrona & J. Gustav Smith

Lappalainen Lab

Biology, Genomics & Technology

Nature Communications · February 4, 2025

Phospho-seq: integrated, multi-modal profiling of intracellular protein dynamics in single cells.

John D. Blair, Austin Hartman, Fides Zenk, Philipp Wahle, Giovanna Brancati, Carol Dalgarno, Barbara Treutlein & Rahul Satija

Satija Lab

Cancer Research · February 1, 2025

Kinome-Focused CRISPR-Cas9 Screens in African Ancestry Patient-Derived Breast Cancer Organoids Identify Essential Kinases and Synergy of EGFR and FGFR1 Inhibition.

Madorsky Rowdo FP, Martini R, Ackermann SE, Tang CP, Tranquille M, Irizarry A, Us I, Alawa O, Moyer JE, Sigouros M, Nguyen J, Al Assaad M, Cheng E, Ginter PS, Manohar J, Stonaker B, Boateng R, Oppong JK, Adjei EK, Awuah B, Kyei I, Aitpillah FS, Adinku MO, Ankomah K, Osei-Bonsu EB, Gyan KK, Hoda S, Newman L, Mosquera JM, Sboner A, Elemento O, Dow LE, Davis MB, Martin ML.

M. Davis Lab

Cancer

Thyroid · January 27, 2025

Strength of Genetic Associations with Thyrotropin Values Differs Between Populations with Similarity to African and European Reference Populations.

Alisha N. Wade, Lindsay Guare, Mahtaab Hayat, Peter Straub, Ziyue Gao, Marco Medici, Alexander Teumer, Lea K. Davis, Michèle Ramsay, Marylyn D.

L. Davis Lab

Our Scientific Publications

Targeted BDNF upregulation via upstream open reading frame disruption.

Inferring fungal cis-regulatory networks from genome sequences.

Multi-sample, multi-platform isoform quantification using empirical Bayes.

Safeguarding the future of biomedical science in the United States.

Differential Cellular Mechanisms Underlie Language and Executive Decline in Amyotrophic Lateral Sclerosis.

Systematic reconstruction of molecular pathway signatures using scalable single-cell perturbation screens.

ScatTR: Estimating the Size of Long Tandem Repeat Expansions from Short-Reads.

Lancet2: Improved and accelerated somatic variant calling with joint multi-sample local assembly graph.

Caspase 3 and caspase 7 promote cytoprotective autophagy and the DNA damage response during non-lethal stress conditions in human breast cancer cells.

Systems genomics of salinity stress response in rice.

Uncovering the Signatures of Cellular Senescence in the Human Dorsolateral Prefrontal Cortex.

Multiomic single-cell profiling identifies critical regulators of postnatal brain.

Comprehensive dissection of cis-regulatory elements in a 2.8 Mb topologically associated domain in six human cancers.

PLayer-FL: A Principled Approach to Personalized Layer-wise Cross-Silo Federated Learning.

Secure and federated quantitative trait loci mapping with privateQTL.

Precise RNA targeting with CRISPR–Cas13d.

A statistical framework for multi-trait rare variant analysis in large-scale whole-genome sequencing studies.

Whole genome sequencing in early onset advanced heart failure.

Phospho-seq: integrated, multi-modal profiling of intracellular protein dynamics in single cells.

Kinome-Focused CRISPR-Cas9 Screens in African Ancestry Patient-Derived Breast Cancer Organoids Identify Essential Kinases and Synergy of EGFR and FGFR1 Inhibition.

Strength of Genetic Associations with Thyrotropin Values Differs Between Populations with Similarity to African and European Reference Populations.