A new sequence logo plot to highlight enrichment and depletion

por Dey, Kushal K., Xie, Dongyue, Stephens, Matthew
Publicado 2018

Visualizing the structure of RNA-seq expression data using grade of membership models

por Dey, Kushal K., Hsiao, Chiaowen Joyce, Stephens, Matthew
Publicado 2017

Correction: Visualizing the structure of RNA-seq expression data using grade of membership models

por Dey, Kushal K., Hsiao, Chiaowen Joyce, Stephens, Matthew
Publicado 2017

Dispersal syndromes drive the formation of biogeographical regions, illustrated by the case of Wallace’s Line

por White, Alexander E., Dey, Kushal K., Stephens, Matthew, Price, Trevor D.
Publicado 2021

Regional influences on community structure across the tropical-temperate divide

por White, Alexander E., Dey, Kushal K., Mohan, Dhananjai, Stephens, Matthew, Price, Trevor D.
Publicado 2019

Improving the informativeness of Mendelian disease-derived pathogenicity scores for common disease

por Kim, Samuel S., Dey, Kushal K., Weissbrod, Omer, Márquez-Luna, Carla, Gazal, Steven, Price, Alkes L.
Publicado 2020

Evaluating the informativeness of deep learning annotations for human complex diseases

por Dey, Kushal K., van de Geijn, Bryce, Kim, Samuel Sungil, Hormozdiari, Farhad, Kelley, David R., Price, Alkes L.
Publicado 2020

SNP-to-gene linking strategies reveal contributions of enhancer-related and candidate master-regulator genes to autoimmune disease

por Dey, Kushal K., Gazal, Steven, van de Geijn, Bryce, Kim, Samuel Sungil, Nasser, Joseph, Engreitz, Jesse M., Price, Alkes L.
Publicado 2022

Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis

por Hsiao, Chiaowen Joyce, Tung, PoYuan, Blischak, John D., Burnett, Jonathan E., Barr, Kenneth A., Dey, Kushal K., Stephens, Matthew, Gilad, Yoav
Publicado 2020

SAIGE-GENE+ improves the efficiency and accuracy of set-based rare variant association tests

por Zhou, Wei, Bi, Wenjian, Zhao, Zhangchen, Dey, Kushal K., Jagadeesh, Karthik A., Karczewski, Konrad J., Daly, Mark J., Neale, Benjamin M., Lee, Seunggeun
Publicado 2022

Publisher Correction: SAIGE-GENE+ improves the efficiency and accuracy of set-based rare variant association tests

por Zhou, Wei, Bi, Wenjian, Zhao, Zhangchen, Dey, Kushal K., Jagadeesh, Karthik A., Karczewski, Konrad J., Daly, Mark J., Neale, Benjamin M., Lee, Seunggeun
Publicado 2022

Compressed Perturb-seq: highly efficient screens for regulatory circuits using random composite perturbations

por Yao, Douglas, Binan, Loic, Bezney, Jon, Simonton, Brooke, Freedman, Jahanara, Frangieh, Chris J., Dey, Kushal, Geiger-Schuller, Kathryn, Eraslan, Basak, Gusev, Alexander, Regev, Aviv, Cleary, Brian
Publicado 2023

Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution

por Kang, Joyce B., Shen, Amber Z., Sakaue, Saori, Luo, Yang, Gurajala, Saisriram, Nathan, Aparna, Rumker, Laurie, Aguiar, Vitor R. C., Valencia, Cristian, Lagattuta, Kaitlyn, Zhang, Fan, Jonsson, Anna Helena, Yazar, Seyhan, Alquicira-Hernandez, Jose, Khalili, Hamed, Ananthakrishnan, Ashwin N., Jagadeesh, Karthik, Dey, Kushal, Daly, Mark J., Xavier, Ramnik J., Donlin, Laura T., Anolik, Jennifer H., Powell, Joseph E., Rao, Deepak A., Brenner, Michael B., Gutierrez-Arcelus, Maria, Raychaudhuri, Soumya
Publicado 2023

Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia

por Marcus, Joseph H., Posth, Cosimo, Ringbauer, Harald, Lai, Luca, Skeates, Robin, Sidore, Carlo, Beckett, Jessica, Furtwängler, Anja, Olivieri, Anna, Chiang, Charleston W. K., Al-Asadi, Hussein, Dey, Kushal, Joseph, Tyler A., Liu, Chi-Chun, Der Sarkissian, Clio, Radzevičiūtė, Rita, Michel, Megan, Gradoli, Maria Giuseppina, Marongiu, Patrizia, Rubino, Salvatore, Mazzarello, Vittorio, Rovina, Daniela, La Fragola, Alessandra, Serra, Rita Maria, Bandiera, Pasquale, Bianucci, Raffaella, Pompianu, Elisa, Murgia, Clizia, Guirguis, Michele, Orquin, Rosana Pla, Tuross, Noreen, van Dommelen, Peter, Haak, Wolfgang, Reich, David, Schlessinger, David, Cucca, Francesco, Krause, Johannes, Novembre, John
Publicado 2020

A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2

por Delorey, Toni M., Ziegler, Carly G. K., Heimberg, Graham, Normand, Rachelly, Yang, Yiming, Segerstolpe, Asa, Abbondanza, Domenic, Fleming, Stephen J., Subramanian, Ayshwarya, Montoro, Daniel T., Jagadeesh, Karthik A., Dey, Kushal K., Sen, Pritha, Slyper, Michal, Pita-Juárez, Yered H., Phillips, Devan, Bloom-Ackerman, Zohar, Barkas, Nick, Ganna, Andrea, Gomez, James, Normandin, Erica, Naderi, Pourya, Popov, Yury V., Raju, Siddharth S., Niezen, Sebastian, Tsai, Linus T.-Y., Siddle, Katherine J., Sud, Malika, Tran, Victoria M., Vellarikkal, Shamsudheen K., Amir-Zilberstein, Liat, Atri, Deepak S., Beechem, Joseph, Brook, Olga R., Chen, Jonathan, Divakar, Prajan, Dorceus, Phylicia, Engreitz, Jesse M., Essene, Adam, Fitzgerald, Donna M., Fropf, Robin, Gazal, Steven, Gould, Joshua, Grzyb, John, Harvey, Tyler, Hecht, Jonathan, Hether, Tyler, Jane-Valbuena, Judit, Leney-Greene, Michael, Ma, Hui, McCabe, Cristin, McLoughlin, Daniel E., Miller, Eric M., Muus, Christoph, Niemi, Mari, Padera, Robert, Pan, Liuliu, Pant, Deepti, Pe’er, Carmel, Pfiffner-Borges, Jenna, Pinto, Christopher J., Plaisted, Jacob, Reeves, Jason, Ross, Marty, Rudy, Melissa, Rueckert, Erroll H., Siciliano, Michelle, Sturm, Alexander, Todres, Ellen, Waghray, Avinash, Warren, Sarah, Zhang, Shuting, Zollinger, Daniel R., Cosimi, Lisa, Gupta, Rajat M., Hacohen, Nir, Hide, Winston, Price, Alkes L., Rajagopal, Jayaraj, Tata, Purushothama Rao, Riedel, Stefan, Szabo, Gyongyi, Tickle, Timothy L., Hung, Deborah, Sabeti, Pardis C., Novak, Richard, Rogers, Robert, Ingber, Donald E., Jiang, Z. Gordon, Juric, Dejan, Babadi, Mehrtash, Farhi, Samouil L., Stone, James R., Vlachos, Ioannis S., Solomon, Isaac H., Ashenberg, Orr, Porter, Caroline B.M., Li, Bo, Shalek, Alex K., Villani, Alexandra-Chloé, Rozenblatt-Rosen, Orit, Regev, Aviv
Publicado 2021