Joshua D Welch (Joshua Welch)

ORCID

Publication Activity (10 Years)

Years Active: 2020-2024
Publications (10 Years): 28

Top Venues

bioRxiv : the preprint server for biology

Nature communications

Nature biotechnology

Genome biology

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

Publications

Chao Gao, Joshua D Welch
Integrating single-cell multimodal epigenomic data using 1D-convolutional neural networks. bioRxiv : the preprint server for biology (2024)
Maria C Virgilio, Barkha Ramnani, Thomas Chen, W Miguel Disbennett, Jay Lubow, Joshua D Welch, Kathleen L Collins
HIV-1 Vpr combats the PU.1-driven antiviral response in primary human macrophages. Nature communications 15 (1) (2024)
Maria C Virgilio, Barkha Ramnani, Thomas Chen, W Miguel Disbennett, Jay Lubow, Joshua D Welch, Kathleen L Collins
HIV-1 Vpr combats the PU.1-driven antiviral response in primary human macrophages. Nature communications 15 (1) (2024)
Chao Gao, Joshua D Welch
Integrating single-cell multimodal epigenomic data using 1D-convolutional neural networks. bioRxiv : the preprint server for biology (2024)
Maria C Virgilio, Barkha Ramnani, Thomas Chen, W Miguel Disbennett, Jay Lubow, Joshua D Welch, Kathleen L Collins
HIV-1 Vpr combats the PU.1-driven antiviral response in primary human macrophages. Nature communications 15 (1) (2024)
Maria C Virgilio, Barkha Ramnani, Thomas Chen, W Miguel Disbennett, Jay Lubow, Joshua D Welch, Kathleen L Collins
HIV-1 Vpr combats the PU.1-driven antiviral response in primary human macrophages. Nature communications 15 (1) (2024)
Maria C Virgilio, Barkha Ramnani, Thomas Chen, W Miguel Disbennett, Jay Lubow, Joshua D Welch, Kathleen L Collins
HIV-1 Vpr combats the PU.1-driven antiviral response in primary human macrophages. Nature communications 15 (1) (2024)
Arushi Varshney, Nandini Manickam, Peter Orchard, Adelaide Tovar, Zhenhao Zhang, Fan Feng, Michael R Erdos, Narisu Narisu, Christa Ventresca, Kirsten Nishino, Vivek Rai, Heather M Stringham, Anne U Jackson, Tricia Tamsen, Chao Gao, Mao Yang, Olivia I Koues, Joshua D Welch, Charles F Burant, L Keoki Williams, Chris Jenkinson, Ralph A DeFronzo, Luke Norton, Jouko Saramies, Timo A Lakka, Markku Laakso, Jaakko Tuomilehto, Karen L Mohlke, Jacob O Kitzman, Heikki A Koistinen, Jie Liu, Michael Boehnke, Francis S Collins, Laura J Scott, Stephen C J Parker
Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation. bioRxiv : the preprint server for biology (2023)
Arushi Varshney, Nandini Manickam, Peter Orchard, Adelaide Tovar, Zhenhao Zhang, Fan Feng, Michael R Erdos, Narisu Narisu, Christa Ventresca, Kirsten Nishino, Vivek Rai, Heather M Stringham, Anne U Jackson, Tricia Tamsen, Chao Gao, Mao Yang, Olivia I Koues, Joshua D Welch, Charles F Burant, L Keoki Williams, Chris Jenkinson, Ralph A DeFronzo, Luke Norton, Jouko Saramies, Timo A Lakka, Markku Laakso, Jaakko Tuomilehto, Karen L Mohlke, Jacob O Kitzman, Heikki A Koistinen, Jie Liu, Michael Boehnke, Francis S Collins, Laura J Scott, Stephen C J Parker
Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation. bioRxiv : the preprint server for biology (2023)
Joshua D Welch
Multiplying insights from perturbation experiments: predicting new perturbation combinations. Molecular systems biology (2023)
Arushi Varshney, Nandini Manickam, Peter Orchard, Adelaide Tovar, Zhenhao Zhang, Fan Feng, Michael R Erdos, Narisu Narisu, Christa Ventresca, Kirsten Nishino, Vivek Rai, Heather M Stringham, Anne U Jackson, Tricia Tamsen, Chao Gao, Mao Yang, Olivia I Koues, Joshua D Welch, Charles F Burant, L Keoki Williams, Chris Jenkinson, Ralph A DeFronzo, Luke Norton, Jouko Saramies, Timo A Lakka, Markku Laakso, Jaakko Tuomilehto, Karen L Mohlke, Jacob O Kitzman, Heikki A Koistinen, Jie Liu, Michael Boehnke, Francis S Collins, Laura J Scott, Stephen C J Parker
Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation. bioRxiv : the preprint server for biology (2023)
Arushi Varshney, Nandini Manickam, Peter Orchard, Adelaide Tovar, Zhenhao Zhang, Fan Feng, Michael R Erdos, Narisu Narisu, Christa Ventresca, Kirsten Nishino, Vivek Rai, Heather M Stringham, Anne U Jackson, Tricia Tamsen, Chao Gao, Mao Yang, Olivia I Koues, Joshua D Welch, Charles F Burant, L Keoki Williams, Chris Jenkinson, Ralph A DeFronzo, Luke Norton, Jouko Saramies, Timo A Lakka, Markku Laakso, Jaakko Tuomilehto, Karen L Mohlke, Jacob O Kitzman, Heikki A Koistinen, Jie Liu, Michael Boehnke, Francis S Collins, Laura J Scott, Stephen C J Parker
Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation. bioRxiv : the preprint server for biology (2023)
Yuxuan Song, Chengxin Zhang, Gilbert S Omenn, Matthew J O'Meara, Joshua D Welch
Predicting the Structural Impact of Human Alternative Splicing. bioRxiv : the preprint server for biology (2023)
Yuxuan Song, Chengxin Zhang, Gilbert S Omenn, Matthew J O'Meara, Joshua D Welch
Predicting the Structural Impact of Human Alternative Splicing. bioRxiv : the preprint server for biology (2023)
Arushi Varshney, Nandini Manickam, Peter Orchard, Adelaide Tovar, Zhenhao Zhang, Fan Feng, Michael R Erdos, Narisu Narisu, Christa Ventresca, Kirsten Nishino, Vivek Rai, Heather M Stringham, Anne U Jackson, Tricia Tamsen, Chao Gao, Mao Yang, Olivia I Koues, Joshua D Welch, Charles F Burant, L Keoki Williams, Chris Jenkinson, Ralph A DeFronzo, Luke Norton, Jouko Saramies, Timo A Lakka, Markku Laakso, Jaakko Tuomilehto, Karen L Mohlke, Jacob O Kitzman, Heikki A Koistinen, Jie Liu, Michael Boehnke, Francis S Collins, Laura J Scott, Stephen C J Parker
Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation. bioRxiv : the preprint server for biology (2023)
Arushi Varshney, Nandini Manickam, Peter Orchard, Adelaide Tovar, Zhenhao Zhang, Fan Feng, Michael R Erdos, Narisu Narisu, Christa Ventresca, Kirsten Nishino, Vivek Rai, Heather M Stringham, Anne U Jackson, Tricia Tamsen, Chao Gao, Mao Yang, Olivia I Koues, Joshua D Welch, Charles F Burant, L Keoki Williams, Chris Jenkinson, Ralph A DeFronzo, Luke Norton, Jouko Saramies, Timo A Lakka, Markku Laakso, Jaakko Tuomilehto, Karen L Mohlke, Jacob O Kitzman, Heikki A Koistinen, Jie Liu, Michael Boehnke, Francis S Collins, Laura J Scott, Stephen C J Parker
Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation. bioRxiv : the preprint server for biology (2023)
Yuxuan Song, Chengxin Zhang, Gilbert S Omenn, Matthew J O'Meara, Joshua D Welch
Predicting the Structural Impact of Human Alternative Splicing. bioRxiv : the preprint server for biology (2023)
Maria C Virgilio, W Miguel Disbennett, Thomas Chen, Jay Lubow, Joshua D Welch, Kathleen L Collins
HIV-1 Vpr combats the PU.1-driven antiviral response in primary human macrophages. bioRxiv : the preprint server for biology (2023)
Chen Li, Maria C Virgilio, Kathleen L Collins, Joshua D Welch
Multi-omic single-cell velocity models epigenome-transcriptome interactions and improves cell fate prediction. Nature biotechnology (2022)
Lu Lu, Joshua D Welch
PyLiger: scalable single-cell multi-omic data integration in Python. Bioinformatics (Oxford, England) 38 (10) (2022)
April R Kriebel, Joshua D Welch
UINMF performs mosaic integration of single-cell multi-omic datasets using nonnegative matrix factorization. Nature communications 13 (1) (2022)
Zizhen Yao, Hanqing Liu, Fangming Xie, Stephan Fischer, Ricky S Adkins, Andrew I Aldridge, Seth A Ament, Anna Bartlett, M Margarita Behrens, Koen Van den Berge, Darren Bertagnolli, Hector Roux de Bezieux, Tommaso Biancalani, Ali Sina Booeshaghi, Héctor Corrada Bravo, Tamara Casper, Carlo Colantuoni, Jonathan Crabtree, Heather H Creasy, Kirsten Crichton, Megan Crow, Nick Dee, Elizabeth L Dougherty, Wayne I Doyle, Sandrine Dudoit, Rongxin Fang, Victor Felix, Olivia Fong, Michelle G Giglio, Jeff Goldy, Michael J Hawrylycz, Brian R Herb, Ronna Hertzano, Xiaomeng Hou, Qiwen Hu, Jayaram Kancherla, Matthew Kroll, Kanan Lathia, Yang Eric Li, Jacinta D Lucero, Chongyuan Luo, Anup A Mahurkar, Delissa McMillen, Naeem M Nadaf, Joseph R Nery, Thuc Nghi Nguyen, Sheng-Yong Niu, Vasilis Ntranos, Joshua Orvis, Julia K Osteen, Trangthanh H Pham, António Pinto-Duarte, Olivier Poirion, Sebastian Preissl, Elizabeth Purdom, Christine Rimorin, Davide Risso, Angeline C Rivkin, Kimberly A Smith, Kelly Street, Josef Sulc, Valentine Svensson, Michael Tieu, Amy Torkelson, Herman Tung, Eeshit Dhaval Vaishnav, Charles R Vanderburg, Cindy T J van Velthoven, Xinxin Wang, Owen R White, Z Josh Huang, Peter V Kharchenko, Lior Pachter, John Ngai, Aviv Regev, Bosiljka Tasic, Joshua D Welch, Jesse Gillis, Evan Z Macosko, Bing Ren, Joseph R Ecker, Hongkui Zeng, Eran A Mukamel
A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. Nature 598 (7879) (2021)
Hong Ma, Ziqing Liu, Yuchen Yang, Dong Feng, Yanhan Dong, Tiffany A Garbutt, Zhiyuan Hu, Li Wang, Changfei Luan, Cynthia D Cooper, Yun Li, Joshua D Welch, Li Qian, Jiandong Liu
Functional coordination of non-myocytes plays a key role in adult zebrafish heart regeneration. EMBO reports 22 (11) (2021)
Yuwei Bao, Jack Wadden, John R Erb-Downward, Piyush Ranjan, Weichen Zhou, Torrin L McDonald, Ryan E Mills, Alan P Boyle, Robert P Dickson, David Blaauw, Joshua D Welch
SquiggleNet: real-time, direct classification of nanopore signals. Genome biology 22 (1) (2021)
Chao Gao, Jialin Liu, April R Kriebel, Sebastian Preissl, Chongyuan Luo, Rosa Castanon, Justin Sandoval, Angeline Rivkin, Joseph R Nery, Margarita M Behrens, Joseph R Ecker, Bing Ren, Joshua D Welch
Iterative single-cell multi-omic integration using online learning. Nature biotechnology 39 (8) (2021)
Hengshi Yu, Joshua D Welch
MichiGAN: sampling from disentangled representations of single-cell data using generative adversarial networks. Genome biology 22 (1) (2021)
Mahmoud S Alghamri, Brandon L McClellan, Ruthvik P Avvari, Rohit Thalla, Stephen V Carney, Margaret S Hartlage, Santiago Haase, Maria Ventosa, Ayman Taher, Neha Kamran, Li Zhang, Syed Mohd Faisal, Felipe J Núñez, María Belén Garcia-Fabiani, Wajd N Al-Holou, Daniel A Orringer, Shawn L Hervey-Jumper, Jason Heth, Parag G Patil, Karen Eddy, Sofia Diana Merajver, Peter J Ulintz, Joshua D Welch, Chao Gao, Jialin Liu, Gabriel Nuñez, Dolores Hambardzumyan, Pedro R Lowenstein, Maria Graciela Castro
G-CSF secreted by mutant IDH1 glioma stem cells abolishes myeloid cell immunosuppression and enhances the efficacy of immunotherapy. Science advances 7 (40) (2021)
Jialin Liu, Chao Gao, Joshua Sodicoff, Velina Kozareva, Evan Z Macosko, Joshua D Welch
Jointly defining cell types from multiple single-cell datasets using LIGER. Nature protocols 15 (11) (2020)

Joshua D Welch.css-eqlu8i{font-size:small;padding-left:4px;} (Joshua Welch)

Publication Activity (10 Years)

Top Topics

Top Venues

Joshua D Welch (Joshua Welch)