Preprint Archives - Page 8 of 24 - New York Genome Center

bioRxiv · October 13, 2025 · Preprint

Large-scale single-cell phylogenetic mapping of clonal evolution in the human aging esophagus.

Tamara Prieto, Dennis J Yuan, John Zinno, Clayton Hughes, Nicholas Midler, Sheng Kao, Jani Huuhtanen, Ramya Raviram, Fenia Fotopoulou, Neil Ruthen, Srinivas Rajagopalan, Joshua S Schiffman, Andrew R D Avino, Sang-Ho Yoon, Jesus Sotelo, Nathaniel D Omans, Noelle Wheeler, Alejandro Garces, Barun Pradhan, Alexandre Pellan Cheng, Nicolas Robine, Catherine Potenski, Katharine Godfrey, Nobuyuki Kakiuchi, Akira Yokoyama, Seishi Ogawa, Julian Abrams, Ivan Raimondi, Dan A Landau.

Landau Lab

bioRxiv · October 10, 2025 · Preprint

A Physically-Realistic Simulator and Cosine-Based Decoder for MERFISH Spatial Transcriptomics.

Jenkin Tsui, Naila Adam, Woongcheol Choi, Luna Liu, Cristina Flores, Shadi Ansari, Esther Kong, Yukta Thapliyal, Hakwoo Lee, Shahid Haider, Isaac Von Riedemann, Ciara O’Flanagan, IMAXT Cancer Grand Challenges Consortium, Samuel Aparicio, Andrew Roth.

Aparicio Lab

bioRxiv · October 8, 2025 · Preprint

African Green Monkeys Respond to Synthetic AB Oligomers with Persistent Alzheimers-like Activation.

Bianca Brown, Xiaoting Li, Monica R Grasty, Isabela Lopez, Sara Dzigurski, Maya Geradi, Matthew Lawrence, John Elsworth, Matthew Lawrence, Micahel Weed, Gamze Gursoy, Andrew David Miranker.

Neurodegenerative Disease

medRxiv · September 30, 2025 · Preprint

Meta-analysis of genetic regulation of RNA editing in the human brain identifies new genes underlying neurological disease.

Winston H Dredge, Kailash BP, Aline Réal, Benjamin Z Muller, Beomjin Jang, Ting Fu, Hyomin Seo, Hong-Hee Won, Michael S Breen, Xinshu Xiao, David A Knowles, Jack Humphrey, Towfique Raj.

Knowles Lab

Neuropsychiatric Disease

bioRxiv · October 3, 2025 · Preprint

A conserved logic for the development of cortical layering in tetrapods.

Astrid Deryckere, Saket Choudhary, Connor Lynch, Lian Kirit V. P. Limperis, Pauline Affatato, Jamie Woych, Elias Gumnit, Alonso Ortega Gurrola, Rahul Satija, Christian Mayer, Maria Antonietta Tosches.

Satija Lab Research Sequencing

bioRxiv · September 29, 2025 · Preprint

Brain Region-Specific Epigenomic Reorganization and Altered Cell States in Alzheimer’s Disease.

Wenliang Wang, Peter Berube, Bing Yang, Rosa Castanon, Anna Bartlett, Kaushik Komandur, Joseph R. Nery, Cesar Barragan, Mia Kenworthy, Cynthia Valadon, Jordan Altshul, Alaina Petrella, Derek Chan, Chumo Chen, Andrea Saldana Acerbo, Jammy Luo, Manya Jain, Eshaan Soma, Huaming Chen, Michelle Liem, Mikayla Marrin, Caz O’Connor, Nathan Zemke, Derek H. Oakley, Bing Ren, Bradley T. Hyman, Joseph R. Ecker.

Ren Lab

Neurodegenerative Disease

medRxiv · September 26, 2025 · Preprint

Mapping genetic effects on splicing in ten thousand post-mortem brain samples reveals novel mediators of neurological disease risk.

Aline Réal, B P Kailash, Winston H Cuddleston, Benjamin Z Muller, Beomjin Jang, Alex Tokolyi, Hong-Hee Won, Jack Humphrey, Towfique Raj, David A Knowles.

Knowles Lab

bioRxiv · September 20, 2025 · Preprint

Mapping transcriptional responses to cellular perturbation dictionaries with RNA fingerprinting.

Isabella N Grabski, Junsuk Lee, John Blair, Carol Dalgarno, Isabella Mascio, Alexandra Bradu, David A Knowles, Rahul Satija.

Satija Lab Knowles Lab

bioRxiv · September 2, 2025 · Preprint

Multiscale Integration of Genetic, Transcriptomic, and Structural Data Identifies Calcium Homeostasis as a Core Mechanism Underlying Neuropsychiatric Disorders.

Sherif Gerges, Nikolaj Catois Straarup, Mohamed A El-Brolosy, F. Kyle Satterstrom, Nolan Kamitaki, Jiayi Yuan, Emi Ling, Raozhou Lin, Melissa Goldman, Tarjinder Singh, Jonathan S. Weissman, Sabina Berretta, Jen Qian Pan, Hilary Finucane, Charlott Stock, Poul Nissen, Steven A. McCarroll, Mark J. Daly.