Kushal K Dey (Kushal Dey)

ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 42

Top Venues

Nature genetics

Nature communications

Nature biotechnology

Genome research

Harvard School of Public Health

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Harvard School of Public Health Sep 01 2018

United States

Postdoctoral Researcher :: Epidemiology

Publications

Sneha Mitra, Rohan Malik, Wilfred Wong, Afsana Rahman, Alexander J Hartemink, Yuri Pritykin, Kushal K Dey, Christina S Leslie
Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis. Nature genetics (2024)
Samuel Sungil Kim, Buu Truong, Karthik Jagadeesh, Kushal K Dey, Amber Z Shen, Soumya Raychaudhuri, Manolis Kellis, Alkes L Price
Leveraging single-cell ATAC-seq and RNA-seq to identify disease-critical fetal and adult brain cell types. Nature communications 15 (1) (2024)
Saori Sakaue, Kathryn Weinand, Shakson Isaac, Kushal K Dey, Karthik A Jagadeesh, Masahiro Kanai, Gerald F M Watts, Zhu Zhu, null null, Michael B Brenner, Andrew McDavid, Laura T Donlin, Kevin Wei, Alkes L Price, Soumya Raychaudhuri
Tissue-specific enhancer-gene maps from multimodal single-cell data identify causal disease alleles. Nature genetics (2024)
Samuel Sungil Kim, Buu Truong, Karthik Jagadeesh, Kushal K Dey, Amber Z Shen, Soumya Raychaudhuri, Manolis Kellis, Alkes L Price
Leveraging single-cell ATAC-seq and RNA-seq to identify disease-critical fetal and adult brain cell types. Nature communications 15 (1) (2024)
Sneha Mitra, Rohan Malik, Wilfred Wong, Afsana Rahman, Alexander J Hartemink, Yuri Pritykin, Kushal K Dey, Christina S Leslie
Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis. Nature genetics 56 (4) (2024)
Saori Sakaue, Kathryn Weinand, Shakson Isaac, Kushal K Dey, Karthik A Jagadeesh, Masahiro Kanai, Gerald F M Watts, Zhu Zhu, null null, Michael B Brenner, Andrew McDavid, Laura T Donlin, Kevin Wei, Alkes L Price, Soumya Raychaudhuri
Tissue-specific enhancer-gene maps from multimodal single-cell data identify causal disease alleles. Nature genetics 56 (4) (2024)
Samuel Sungil Kim, Buu Truong, Karthik Jagadeesh, Kushal K Dey, Amber Z Shen, Soumya Raychaudhuri, Manolis Kellis, Alkes L Price
Leveraging single-cell ATAC-seq and RNA-seq to identify disease-critical fetal and adult brain cell types. Nature communications 15 (1) (2024)
Saori Sakaue, Kathryn Weinand, Shakson Isaac, Kushal K Dey, Karthik A Jagadeesh, Masahiro Kanai, Gerald F M Watts, Zhu Zhu, null null, Michael B Brenner, Andrew McDavid, Laura T Donlin, Kevin Wei, Alkes L Price, Soumya Raychaudhuri
Tissue-specific enhancer-gene maps from multimodal single-cell data identify causal disease alleles. Nature genetics 56 (4) (2024)
Sneha Mitra, Rohan Malik, Wilfred Wong, Afsana Rahman, Alexander J Hartemink, Yuri Pritykin, Kushal K Dey, Christina S Leslie
Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis. Nature genetics 56 (4) (2024)
Sneha Mitra, Rohan Malik, Wilfred Wong, Afsana Rahman, Alexander J Hartemink, Yuri Pritykin, Kushal K Dey, Christina S Leslie
Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis. Nature genetics 56 (4) (2024)
Sneha Mitra, Rohan Malik, Wilfred Wong, Afsana Rahman, Alexander J Hartemink, Yuri Pritykin, Kushal K Dey, Christina S Leslie
Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis. Nature genetics 56 (4) (2024)
Sneha Mitra, Rohan Malik, Wilfred Wong, Afsana Rahman, Alexander J Hartemink, Yuri Pritykin, Kushal K Dey, Christina S Leslie
Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis. Nature genetics 56 (4) (2024)
Sneha Mitra, Rohan Malik, Wilfred Wong, Afsana Rahman, Alexander J Hartemink, Yuri Pritykin, Kushal K Dey, Christina S Leslie
Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis. Nature genetics (2024)
Saori Sakaue, Kathryn Weinand, Shakson Isaac, Kushal K Dey, Karthik A Jagadeesh, Masahiro Kanai, Gerald F M Watts, Zhu Zhu, null null, Michael B Brenner, Andrew McDavid, Laura T Donlin, Kevin Wei, Alkes L Price, Soumya Raychaudhuri
Tissue-specific enhancer-gene maps from multimodal single-cell data identify causal disease alleles. Nature genetics 56 (4) (2024)
Saori Sakaue, Kathryn Weinand, Shakson Isaac, Kushal K Dey, Karthik A Jagadeesh, Masahiro Kanai, Gerald F M Watts, Zhu Zhu, null null, Michael B Brenner, Andrew McDavid, Laura T Donlin, Kevin Wei, Alkes L Price, Soumya Raychaudhuri
Tissue-specific enhancer-gene maps from multimodal single-cell data identify causal disease alleles. Nature genetics 56 (4) (2024)
Samuel Sungil Kim, Buu Truong, Karthik Jagadeesh, Kushal K Dey, Amber Z Shen, Soumya Raychaudhuri, Manolis Kellis, Alkes L Price
Leveraging single-cell ATAC-seq and RNA-seq to identify disease-critical fetal and adult brain cell types. Nature communications 15 (1) (2024)
Sneha Mitra, Rohan Malik, Wilfred Wong, Afsana Rahman, Alexander J Hartemink, Yuri Pritykin, Kushal K Dey, Christina S Leslie
Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis. Nature genetics 56 (4) (2024)
Sneha Mitra, Rohan Malik, Wilfred Wong, Afsana Rahman, Alexander J Hartemink, Yuri Pritykin, Kushal K Dey, Christina S Leslie
Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis. Nature genetics 56 (4) (2024)
Sneha Mitra, Rohan Malik, Wilfred Wong, Afsana Rahman, Alexander J Hartemink, Yuri Pritykin, Kushal K Dey, Christina S Leslie
Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis. Nature genetics 56 (4) (2024)
Saori Sakaue, Kathryn Weinand, Shakson Isaac, Kushal K Dey, Karthik A Jagadeesh, Masahiro Kanai, Gerald F M Watts, Zhu Zhu, null null, Michael B Brenner, Andrew McDavid, Laura T Donlin, Kevin Wei, Alkes L Price, Soumya Raychaudhuri
Tissue-specific enhancer-gene maps from multimodal single-cell data identify causal disease alleles. Nature genetics 56 (4) (2024)
Sneha Mitra, Rohan Malik, Wilfred Wong, Afsana Rahman, Alexander J Hartemink, Yuri Pritykin, Kushal K Dey, Christina S Leslie
Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis. Nature genetics (2024)
Samuel Sungil Kim, Buu Truong, Karthik Jagadeesh, Kushal K Dey, Amber Z Shen, Soumya Raychaudhuri, Manolis Kellis, Alkes L Price
Leveraging single-cell ATAC-seq and RNA-seq to identify disease-critical fetal and adult brain cell types. Nature communications 15 (1) (2024)
Sneha Mitra, Rohan Malik, Wilfred Wong, Afsana Rahman, Alexander J Hartemink, Yuri Pritykin, Kushal K Dey, Christina S Leslie
Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis. Nature genetics 56 (4) (2024)
Samuel Sungil Kim, Buu Truong, Karthik Jagadeesh, Kushal K Dey, Amber Z Shen, Soumya Raychaudhuri, Manolis Kellis, Alkes L Price
Leveraging single-cell ATAC-seq and RNA-seq to identify disease-critical fetal and adult brain cell types. Nature communications 15 (1) (2024)
Sneha Mitra, Rohan Malik, Wilfred Wong, Afsana Rahman, Alexander J Hartemink, Yuri Pritykin, Kushal K Dey, Christina S Leslie
Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis. Nature genetics 56 (4) (2024)
Sneha Mitra, Rohan Malik, Wilfred Wong, Afsana Rahman, Alexander J Hartemink, Yuri Pritykin, Kushal K Dey, Christina S Leslie
Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis. Nature genetics 56 (4) (2024)
Sneha Mitra, Rohan Malik, Wilfred Wong, Afsana Rahman, Alexander J Hartemink, Yuri Pritykin, Kushal K Dey, Christina S Leslie
Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis. Nature genetics 56 (4) (2024)
Saori Sakaue, Kathryn Weinand, Shakson Isaac, Kushal K Dey, Karthik A Jagadeesh, Masahiro Kanai, Gerald F M Watts, Zhu Zhu, null null, Michael B Brenner, Andrew McDavid, Laura T Donlin, Kevin Wei, Alkes L Price, Soumya Raychaudhuri
Tissue-specific enhancer-gene maps from multimodal single-cell data identify causal disease alleles. Nature genetics 56 (4) (2024)
Sneha Mitra, Rohan Malik, Wilfred Wong, Afsana Rahman, Alexander J Hartemink, Yuri Pritykin, Kushal K Dey, Christina S Leslie
Author Correction: Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis. Nature genetics (2024)
Elizabeth Dorans, Karthik A Jagadeesh, Kushal K Dey, Alkes L Price
Linking regulatory variants to target genes by integrating single-cell multiome methods and genomic distance. medRxiv : the preprint server for health sciences (2024)
Sneha Mitra, Rohan Malik, Wilfred Wong, Afsana Rahman, Alexander J Hartemink, Yuri Pritykin, Kushal K Dey, Christina S Leslie
Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis. Nature genetics 56 (4) (2024)
Joyce B Kang, Amber Z Shen, Saisriram Gurajala, Aparna Nathan, Laurie Rumker, Vitor R C Aguiar, Cristian Valencia, Kaitlyn A Lagattuta, Fan Zhang, Anna Helena Jonsson, Seyhan Yazar, Jose Alquicira-Hernandez, Hamed Khalili, Ashwin N Ananthakrishnan, Karthik A Jagadeesh, Kushal K Dey, null null, Mark J Daly, Ramnik J Xavier, Laura T Donlin, Jennifer H Anolik, Joseph E Powell, Deepak A Rao, Michael B Brenner, Maria Gutierrez-Arcelus, Yang Luo, Saori Sakaue, Soumya Raychaudhuri
Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution. Nature genetics (2023)
Douglas W Yao, Loic Binan, Jon Bezney, Brooke Simonton, Jahanara Freedman, Chris J Frangieh, Kushal K Dey, Kathryn Geiger-Schuller, Basak Eraslan, Alexander Gusev, Aviv Regev, Brian Cleary
Scalable genetic screening for regulatory circuits using compressed Perturb-seq. Nature biotechnology (2023)
Martin Jinye Zhang, Kangcheng Hou, Kushal K Dey, Saori Sakaue, Karthik A Jagadeesh, Kathryn Weinand, Aris Taychameekiatchai, Poorvi Rao, Angela Oliveira Pisco, James Zou, Bruce Wang, Michael J Gandal, Soumya Raychaudhuri, Bogdan Pasaniuc, Alkes L Price
Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data. Nature genetics 54 (10) (2022)
Steven Gazal, Omer Weissbrod, Farhad Hormozdiari, Kushal K Dey, Joseph Nasser, Karthik A Jagadeesh, Daniel J Weiner, Huwenbo Shi, Charles P Fulco, Luke O' Connor, Bogdan Pasaniuc, Jesse M Engreitz, Alkes L Price
Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity. Nature genetics 54 (6) (2022)
Wei Zhou, Wenjian Bi, Zhangchen Zhao, Kushal K Dey, Karthik A Jagadeesh, Konrad J Karczewski, Mark J Daly, Benjamin M Neale, Seunggeun Lee
SAIGE-GENE+ improves the efficiency and accuracy of set-based rare variant association tests. Nature genetics 54 (10) (2022)
Karthik A Jagadeesh, Kushal K Dey, Daniel T Montoro, Rahul Mohan, Steven Gazal, Jesse M Engreitz, Ramnik J Xavier, Alkes L Price, Aviv Regev
Identifying disease-critical cell types and cellular processes by integrating single-cell RNA-sequencing and human genetics. Nature genetics 54 (10) (2022)
Tiffany Amariuta, Kazuyoshi Ishigaki, Hiroki Sugishita, Tazro Ohta, Masaru Koido, Kushal K Dey, Koichi Matsuda, Yoshinori Murakami, Alkes L Price, Eiryo Kawakami, Chikashi C Terao, Soumya Raychaudhuri
Improving the trans-ancestry portability of polygenic risk scores by prioritizing variants in predicted cell-type-specific regulatory elements. Nature genetics 52 (12) (2020)
Chiaowen Joyce Hsiao, PoYuan Tung, John D Blischak, Jonathan E Burnett, Kenneth A Barr, Kushal K Dey, Matthew Stephens, Yoav Gilad
Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis. Genome research 30 (4) (2020)
Samuel Sungil Kim, Kushal K Dey, Omer Weissbrod, Carla Márquez-Luna, Steven Gazal, Alkes L Price
Improving the informativeness of Mendelian disease-derived pathogenicity scores for common disease. Nature communications 11 (1) (2020)
Kushal K Dey, Bryce van de Geijn, Samuel Sungil Kim, Farhad Hormozdiari, David R Kelley, Alkes L Price
Evaluating the informativeness of deep learning annotations for human complex diseases. Nature communications 11 (1) (2020)
Kushal K Dey, Chiaowen Joyce Hsiao, Matthew Stephens
Visualizing the structure of RNA-seq expression data using grade of membership models. PLoS genetics 13 (3) (2017)

Kushal K Dey.css-eqlu8i{font-size:small;padding-left:4px;} (Kushal Dey)

Publication Activity (10 Years)

Top Topics

Top Venues

Kushal K Dey (Kushal Dey)