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WebAtlas pipeline for integrated single-cell and spatial transcriptomic data Li, Tong; Horsfall, David; Basurto-Lozada, Daniela; Roberts, Kenny; Prete, Martin; Lawrence, John E. G.; He, Peng; Tuck, Elisabeth; Moore, Josh; Yoldas, Aybuke Kupcu; Babalola, Kolawole; Hartley, Matthew; Ghazanfar, Shila; Teichmann, Sarah A.; Haniffa, Muzlifah; Bayraktar, Omer Ali Share Save
Integration mapping of cardiac fibroblast single-cell transcriptomes elucidates cellular principles of fibrosis in diverse pathologies Patrick, Ralph; Janbandhu, Vaibhao; Tallapragada, Vikram; Tan, Shannon S. M.; McKinna, Emily E.; Contreras, Osvaldo; Ghazanfar, Shila; Humphreys, David T.; Murray, Nicholas J.; Tran, Yen T. H.; Hume, Robert D.; Chong, James J. H.; Harvey, Richard P. Share Save
Novel Mouse Model for Selective Tagging, Purification, and Manipulation of Cardiac Myofibroblasts Janbandhu, Vaibhao; Tallapragada, Vikram; Li, Jinyuan Vero; Shewale, Bharti; Ghazanfar, Shila; Patrick, Ralph; Cox, Charles D.; Harvey, Richard P. Share Save
BIDCell: Biologically-informed self-supervised learning for segmentation of subcellular spatial transcriptomics data Fu, Xiaohang; Lin, Yingxin; Lin, David M.; Mechtersheimer, Daniel; Wang, Chuhan; Ameen, Farhan; Ghazanfar, Shila; Patrick, Ellis; Kim, Jinman; Yang, Jean Y. H. Share Save
Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP) Jain, Sanjay; Pei, Liming; Spraggins, Jeffrey M.; Angelo, Michael; Carson, James P.; Gehlenborg, Nils; Ginty, Fiona; Goncalves, Joana P.; Hagood, James S.; Hickey, John W.; Kelleher, Neil L.; Laurent, Louise C.; Lin, Shin; Lin, Yiing; Liu, Huiping; Naba, Alexandra; Nakayasu, Ernesto S.; Qian, Wei-Jun; Radtke, Andrea; Robson, Paul; Stockwell, Brent R.; Van de Plas, Raf; Vlachos, Ioannis S.; Zhou, Mowei; Boerner, Katy; Snyder, Michael P.; Ahn, Kyung Jin; Allen, Jamie; Anderson, David M.; Anderton, Christopher R.; Curcio, Christine; Angelin, Alessia; Arvanitis, Constadina; Atta, Lyla; Awosika-Olumo, Demi; Bahmani, Amir; Bai, Huajun; Balderrama, Karol; Balzano, Leandro; Bandyopadhyay, Gautam; Bandyopadhyay, Shovik; Bar-Joseph, Ziv; Barnhart, Kurt; Barwinska, Daria; Becich, Michael; Becker, Laren; Becker, Winston; Bedi, Kenneth; Bendall, Sean; Benninger, Kathy; Betancur, David; Bettinger, Keith; Billings, Sunteasja; Blood, Philip; Bolin, Daniel; Border, Samuel; Bosse, Marc; Bramer, Lisa; Brewer, Maya; Brusko, Maigan; Bueckle, Andreas; Burke, Karl; Burnum-Johnson, Kristin; Butcher, Eugene; Butterworth, Elizabeth; Cai, Long; Calandrelli, Riccardo; Caldwell, Michael; Campbell-Thompson, Martha; Cao, Dongfeng; Cao-Berg, Ivan; Caprioli, Richard; Caraccio, Chiara; Caron, Anita; Carroll, Megan; Chadwick, Chrystal; Chen, Angela; Chen, Derek; Chen, Fei; Chen, Haoran; Chen, Jing; Chen, Li; Chen, Lu; Chiacchia, Kenneth; Cho, Sanghee; Chou, Peter; Choy, Lisa; Cisar, Cecilia; Clair, Geremy; Clarke, Laura; Clouthier, Kelly A.; Colley, Madeline E.; Conlon, Kristin; Conroy, John; Contrepois, Kevin; Corbett, Anthony; Corwin, Alex; Cotter, Daniel; Courtois, Elise; Cruz, Aaron; Csonka, Christopher; Czupil, Kimberley; Daiya, Vicky; Dale, Kali; Davanagere, Shakeel Ahamed; Dayao, Monica; de Caestecker, Mark P.; Decker, Aubrianna; Deems, Stephen; Degnan, David; Desai, Tushar; Deshpande, Vikrant; Deutsch, Gail; Devlin, Michelle; Diep, Dinh; Dodd, Carla; Donahue, Sean; Dong, Weixiu; Peixoto, Rafael dos Santos; Duffy, Michael; Dufresne, Martin; Duong, Thu Elizabeth; Dutra, Jennifer; Eadon, Michael T.; El-Achkar, Tarek M.; Enninful, Archibald; Eraslan, Gokcen; Eshelman, Diane; Espin-Perez, Almudena; Esplin, Edward D.; Esselman, Allison; Falo, Louis D.; Falo, Louis; Fan, Jean; Fan, Rong; Farrow, Melissa A.; Farzad, Negin; Favaro, Patricia; Fermin, Jamie; Filiz, Ferda; Filus, Shane; Fisch, Kathleen; Fisher, Eyal; Fisher, Stephen; Flowers, Katelyn; Flynn, William F.; Fogo, Agnes B.; Fu, Dongtao (Ann); Fulcher, James; Fung, Anthony; Furst, Derek; Gallant, Michael; Gao, Fu; Gao, Yu; Gaulton, Kyle; Gaut, Joseph P.; Gee, James; Ghag, Reetika R.; Ghazanfar, Shila; Ghose, Soumya; Gisch, Debora; Gold, Ilan; Gondalia, Aashay; Gorman, Brittney; Greenleaf, William; Greenwald, Noah; Gregory, Brian; Guo, Rong; Gupta, Rajat; Hakimian, Hunter; Haltom, Jeff; Halushka, Marc; Han, Kyu Sang; Hanson, Casey; Harbury, Pehr; Hardi, Josef; Harlan, Linda; Harris, Raymond C.; Hartman, Austin; Heidari, Elyas; Helfer, Jesse; Helminiak, David; Hemberg, Martin; Henning, Nathaniel; Herr, Bruce W., II; Ho, Jonhan; Holden-Wiltse, Jeanne; Hong, Seung-Hyun; Hong, Young-Kwon; Honick, Brendan; Hood, Greg; Hu, Po; Hu, Qiwen; Huang, Molly; Huyck, Heidie; Imtiaz, Tamjid; Isberg, Olof Gerdur; Itkin, Maxim; Jackson, Dana; Jacobs, Marni; Jain, Yashvardhan; Jewell, David; Jiang, Lihua; Jiang, Zhenghui G.; Johnston, Sarah; Joshi, Pujan; Ju, Yingnan; Judd, Audra; Kagel, Adam; Kahn, Ari; Kalavros, Nikolaos; Kalhor, Kian; Karagkouni, Dimitra; Karathanos, Thomas; Karunamurthy, Arivarasan; Katari, Suhas; Kates, Heather; Kaushal, Madhurima; Keener, Nicholas; Keller, Mark; Kenney, Mariah; Kern, Colin; Kharchenko, Peter; Kim, Junhyong; Kingsford, Carl; Kirwan, Jessica; Kiselev, Vladimir; Kishi, Jocelyn; Kitata, Reta Birhanu; Knoten, Amanda; Kollar, Charles; Krishnamoorthy, Praveen; Kruse, Angela R. S.; Da, Kuang; Kundaje, Anshul; Kutschera, Eric; Kwon, Yumi; Lake, Blue B.; Lancaster, Samuel; Langlieb, Jonah; Lardenoije, Roy; Laronda, Monica; Laskin, Julia; Lau, Ken; Lee, Hayan; Lee, Maria; Lee, Mejeong; Strekalova, Yulia Levites; Li, Dongshunyi; Li, Jennifer; Li, Jilong; Li, Xiangtang; Li, Zhi; Liao, Yen-Chen; Liaw, Tiffany; Lin, Pei; Lin, Yulieh; Lindsay, Scott; Liu, Chunjie; Liu, Yang; Liu, Yuan; Lott, Marie; Lotz, Martin; Lowery, Lisa; Lu, Peiran; Lu, Xinyue; Lucarelli, Nicholas; Lun, Xiaokang; Luo, Zhifei; Ma, Jian; Macosko, Evan; Mahajan, Mayank; Maier, Libby; Makowski, Danika; Malek, Morad; Manthey, David; Manz, Trevor; Margulies, Kenneth; Marioni, John; Martindale, Matthew; Mason, Cayla; Mathews, Clayton; Maye, Peter; McCallum, Chuck; McDonough, Elizabeth; McDonough, Liz; Mcdowell, Hannah; Meads, Morgan; Medina-Serpas, Miguel; Ferreira, Ricardo Melo; Messinger, Jeffrey; Metis, Kay; Migas, Lukasz G.; Miller, Brendan; Mimar, Sayat; Minor, Brittany; Misra, Ravi; Missarova, Alsu; Mistretta, Christopher; Moens, Roger; Moerth, Eric; Moffitt, Jeffrey; Molla, Gesmira; Monroe, Matthew; Monte, Emma; Morgan, Mike; Muraro, Daniele; Murphy, Bob (Robert); Murray, Evan; Musen, Mark A.; Naglah, Ahmed; Nasamran, Chanond; Neelakantan, Taruna; Nevins, Stephanie; Hieu Nguyen; Nam Nguyen; Tram Nguyen; Tri Nguyen; Nigra, Deb; Nofal, Michel; Nolan, Garry; Nwanne, Gerald; O'Connor, Martin; Okuda, Kenichi; Olmer, Merissa; O'Neill, Kathleen; Otaluka, Nancy; Pang, Minxing; Parast, Mana; Pasa-Tolic, Ljiljana; Paten, Benedict; Patterson, Nathan Heath; Peng, Ting; Phillips, Gesina; Pichavant, Mina; Piehowski, Paul; Pilner, Hannah; Pingry, Ellie; Pita-Juarez, Yered; Plevritis, Sylvia; Ploumakis, Athanasios; Pouch, Alison; Pryhuber, Gloria; Puerto, Juan; Qaurooni, Danial; Qin, Ling; Quardokus, Ellen M.; Rajbhandari, Presha; Rakow-Penner, Rebecca; Ramasamy, Ramalakshmi; Read, David; Record, Elizabeth G.; Reeves, David; Ricarte, Allyson; Rodriguez-Soto, Ana; Ropelewski, Alexander; Rosario, Jean; Roselkis, Morla-Adames; Rowe, David; Roy, Tarun Kanti; Ruffalo, Matt; Ruschman, Nancy; Sabo, Angela; Sachdev, Nina; Saka, Sinem; Salamon, Diane; Sarder, Pinaki; Sasaki, Hiroshi; Satija, Rahul; Saunders, Diane; Sawka, Riley; Schey, Kevin; Schlehlein, Heidi; Scholten, David; Schultz, Sarah; Schwartz, Lauren; Schwenk, Melissa; Scibek, Robin; Segre, Ayellet; Serrata, Matthew; Shands, Walter; Shen, Xiaotao; Shendure, Jay; Shephard, Holly; Shi, Lingyan; Shi, Tujin; Shin, Dong-Guk; Shirey, Bill; Sibilla, Max; Silber, Michal; Silverstein, Jonathan; Simmel, Derek; Simmons, Alan; Singhal, Dhruv; Sivajothi, Santhosh; Smits, Thomas; Soncin, Francesca; Song, Qi; Stanley, Valentina; Stuart, Tim; Su, Hanquan; Su, Pei; Sun, Xin; Surrette, Christine; Swahn, Hannah; Tan, Kai; Teichmann, Sarah; Tejomay, Abhiroop; Tellides, George; Thomas, Kathleen; Thomas, Tracey; Thompson, Marissa; Tian, Hua; Tideman, Leonoor; Trapnell, Cole; Tsai, Albert G.; Tsai, Chia-Feng; Tsai, Leo; Tsui, Elizabeth; Tsui, Tina; Tung, Jason; Turner, Morgan; Uranic, Jackie; Vaishnav, Eeshit Dhaval; Varra, Sricharan Reddy; Vaskivskyi, Vasyl; Velickovic, Dusan; Velickovic, Marija; Verheyden, Jamie; Waldrip, Jessica; Wallace, Douglas; Wan, Xueyi; Wang, Allen; Wang, Fusheng; Wang, Meng; Wang, Shuoshuo; Wang, Xuefei; Wasserfall, Clive; Wayne, Leonard; Webber, James; Weber, Griffin M.; Wei, Bei; Wei, Jian-Jun; Weimer, Annika; Welling, Joel; Wen, Xingzhao; Wen, Zishen; Williams, MacKenzie; Winfree, Seth; Winograd, Nicholas; Woodard, Abashai; Wright, Devin; Wu, Fan; Wu, Pei-Hsun; Wu, Qiuyang; Wu, Xiaodong; Xing, Yi; Xu, Tiangyang; Yang, Manxi; Yang, Mingyu; Yap, Joseph; Ye, Dong Hye; Yin, Peng; Yuan, Zhou; Yun, Chi (Jina); Zahraei, Ali; Zemaitis, Kevin; Zhang, Bo; Zhang, Caibin; Zhang, Chenyu; Zhang, Chi; Zhang, Kun; Zhang, Shiping; Zhang, Ted; Zhang, Yida; Zhao, Bingqing; Zhao, Wenxin; Zheng, Jia Wen; Zhong, Sheng; Zhu, Bokai; Zhu, Chenchen; Zhu, Diming; Zhu, Quan; Zhu, Ying Share Save
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The 2022 generation Barry-Hundeyin, Mautin; Carrot-Zhang, Jian; Dayton, Talya; Ghazanfar, Shila; Guenther, Lillian M.; Nguyen, Diu T. T.; Pitarresi, Jason R.; Rajput, Sheerien; Santana-Codina, Naiara; Shree, Tanaya; Zeng, Zexian; Zhang, Ying Share Save
Mesp1 controls the chromatin and enhancer landscapes essential for spatiotemporal patterning of early cardiovascular progenitors Lie, Xionghui; Swedlund, Benjamin; Ton, Mai-Linh N.; Ghazanfar, Shila; Guibentif, Carolina; Paulissen, Catherine; Baudelet, Elodie; Plaindoux, Elise; Achouri, Younes; Calonne, Emilie; Dubois, Christine; Mansfield, William; Zaffran, Stephane; Marioni, John C.; Fuks, Francois; Goettgens, Berthold; Lescroart, Fabienne; Blanpain, Cedric Share Save
Genetic variation of macronutrient tolerance in Drosophila melanogaster Havula, E.; Ghazanfar, S.; Lamichane, N.; Francis, D.; Hasygar, K.; Liu, Y.; Alton, L. A.; Johnstone, J.; Needham, E. J.; Pulpitel, T.; Clark, T.; Niranjan, H. N.; Shang, V; Tong, V; Jiwnani, N.; Audia, G.; Alves, A. N.; Sylow, L.; Mirth, C.; Neely, G. G.; Yang, J.; Hietakangas, V; Simpson, S. J.; Senior, A. M. Share Save
geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq Missarova, Alsu; Jain, Jaison; Butler, Andrew; Ghazanfar, Shila; Stuart, Tim; Brusko, Maigan; Wasserfall, Clive; Nick, Harry; Brusko, Todd; Atkinson, Mark; Satija, Rahul; Marioni, John C. Share Save
Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis Lohoff, T.; Ghazanfar, S.; Missarova, A.; Koulena, N.; Pierson, N.; Griffiths, J. A.; Bardot, E. S.; Eng, C. -H. L.; Tyser, R. C. V.; Argelaguet, R.; Guibentif, C.; Srinivas, S.; Briscoe, J.; Simons, B. D.; Hadjantonakis, A. -K.; Gottgens, B.; Reik, W.; Nichols, J.; Cai, L.; Marioni, J. C. Share Save
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