Human pancreatic progenitor organoids define genetic and epigenetic barriers to early PDAC transformation

Xian Zhang, Wilfred Wong, Hyein S. Cho, Dapeng Yang, Gary Dixon, Renhe Luo, Dingyu Liu, Denis Torre, Shigeaki Umeda, Federico González, Gokce Askan, Aslihan Yavas, Jeyaram Ravichandran Damodaran, Robert W. Rickert, Rajya Kappagantula, Fong Cheng Pan, Victoria G. Aveson, Adrien Grimont, William B. Fall, Xianming Wang, Julian Pulecio, Samuel J. Kaplan, Heng Pan, Xianlu Laura Peng, Jen Jen Yeh, Steven D. Leach, Christine A. Iacobuzio-Donahue, Rohit Chandwani, Christina S. Leslie, Danwei Huangfu

Developmental Cell

Functional chromatin signatures premark future lineage-specific enhancers

Julian Pulecio, Zakieh Tayyebi, Dingyu Liu, Wilfred Wong, Renhe Luo, Jeyaram R. Damodaran, Samuel J. Kaplan, Nan Hu, Hyein S. Cho, Jielin Yan, Dylan Murphy, Robert W. Rickert, Abhijit Shukla, Aaron Zhong, Denis Torre, Qianzi Li, Federico González, Dexin Yang, Wenbo Li, Ting Zhou, Effie Apostolou, Christina S. Leslie, Danwei Huangfu

Cell Genomics

STAR Suite: Transcriptomics processing in a single binary through AI-assisted development

Ling-Hong Hung, Dylan Baker, Bill Flynn, Danwei Huangfu, Renhe Luo, Paul Robson, Ting Zhou, Ka Yee Yeung

openRxiv

FourC: identifying significant and differential contacts in 1D chromatin conformation data

Wilfred Wong, Samuel J Kaplan, Renhe Luo, Julian Pulecio, Jielin Yan, Danwei Huangfu, Christina S. Leslie

openRxiv

Human DICER1 hotspot mutation induces both loss and gain of miRNA function

David Jee, Seungjae Lee, Dapeng Yang, Robert Rickert, Renfu Shang, Danwei Huangfu, Eric C. Lai

Nature Structural & Molecular Biology

Human Dicer1 hotspot mutation induces both loss and gain of miRNA function

David Jee, Seungjae Lee, Dapeng Yang, Robert Rickert, Renfu Shang, Danwei Huangfu, Eric C. Lai

bioRxiv

A chemical epigenetic tool to probe site-specific DNA-binding protein complexes

Jiajun Zhu, Zhucui Li, Dongxiang Xue, Zihe Meng, Sida Shao, Julian Pulecio, Guoan Zhang, Danwei Huangfu, Todd Evans, Shuibing Chen, Peter G. Schultz

Proceedings of the National Academy of Sciences

Perturb-seq reveals distinct responses to pluripotency regulator dosages underlying the control of self-renewal and differentiation

Jielin Yan, Hyein S. Cho, Renhe Luo, Michael A. Beer, Wei Li, Danwei Huangfu

bioRxiv

Discovery of NANOG enhancers and their essential roles in self-renewal and differentiation in human embryonic stem cells

Jielin Yan, Renhe Luo, Bess P. Rosen, Dingyu Liu, Wilfred Wong, Christina S. Leslie, Danwei Huangfu

Stem Cell Reports

Leveraging CRISPR activation for rapid assessment of gene editing products in human pluripotent stem cells

Youjun Wu, Aaron Zhong, Alessandro Evangelisti, Mega Sidharta, Danwei Huangfu, Lorenz Studer, Ting Zhou

Stem Cell Reports

GATA6 regulates WNT and BMP programs to pattern precardiac mesoderm during the earliest stages of human cardiogenesis

Joseph A Bisson, Miriam Gordillo, Ritu Kumar, Neranjan de Silva, Ellen Yang, Kelly M Banks, Zhong-Dong Shi, Kihyun Lee, Dapeng Yang, Wendy K Chung, Danwei Huangfu, Todd Evans

eLife

Decoding heterogeneous single-cell perturbation responses

Bicna Song, Dingyu Liu, Weiwei Dai, Natalie F. McMyn, Qingyang Wang, Dapeng Yang, Adam Krejci, Anatoly Vasilyev, Nicole Untermoser, Anke Loregger, Dongyuan Song, Breanna Williams, Bess Rosen, Xiaolong Cheng, Lumen Chao, Hanuman T. Kale, Hao Zhang, Yarui Diao, Tilmann Bürckstümmer, Janet D. Siliciano, Jingyi Jessica Li, Robert F. Siliciano, Danwei Huangfu, Wei Li

Nature Cell Biology

MorPhiC Consortium: towards functional characterization of all human genes

Mazhar Adli, Laralynne Przybyla, Tony Burdett, Paul W. Burridge, Pilar Cacheiro, Howard Y. Chang, Jesse M. Engreitz, Luke A. Gilbert, William J. Greenleaf, Li Hsu, Danwei Huangfu, Ling-Hong Hung, Anshul Kundaje, Sheng Li, Helen Parkinson, Xiaojie Qiu, Paul Robson, Stephan C. Schürer, Ali Shojaie, William C. Skarnes, Damian Smedley, Lorenz Studer, Wei Sun, Dušica Vidović, Thomas Vierbuchen, Brian S. White, Ka Yee Yeung, Feng Yue, Ting Zhou, Neda Abbaszadeh, Juliana Alcoforado Diniz, Anahita Amiri, Rohan N. V. S. R. K. Avireddy, Tao Bai, Dylan S. Baker, Jacob J. Baroch, Chia Chan, Sijie Chen, Xintong Chen, Hyein S. Cho, Anshul Choudhary, Caty E. Chung, Thomas J. Dahlstrom, Anthony Doty, Basak Eraslan, Adam L. Felsenfeld, Patrick J. Fleming, Colin F. Fletcher, Jesse Flores, William F. Flynn, Yihao Fu, Bryce Nobutoshi Fukuda, Jessica L. Garofalo, Rachel A. Glenn, Juhee Goyal, Alexandra M. Griffiths, Tingfeng Guo, Revant Gupta, Dipayan Gupta, Nan Hu, Yung-Hsin Huang, Aaron J. Huebner, Carolyn Hutter, Angelina Kendra, Gina Kirsammer, Orges A. Koci, Katerina Kraft, Zhaoheng Li, Shuzhao Li, Si Liu, Zukai Liu, Dingyu Liu, Nianping Liu, Renhe Luo, Davi Lyra Leite, Yuzhen Mao, Gabriel Marengo, Justin A. McDonough, Adrian Melo-Carrillo, Chen Meng, Eyal Metzl-Raz, Joshua M. Mitchell, Varun Mittal, Niharika Nasam, Ozlem Neyisci, Gang Ning, Devon Parker, Marcin Pilarczyk, Ajay Pillai, Olivier B. Poirion, Praeploy Pongpamorn, Arushi Rana, Jamilex Rivera-Diaz, Nicolette C. Ross, Enrique Sapena Ventura, Fidan Seker, Kaustav Sengupta, Anu Shivalikanjli, Wenzhuo Tang, Denis Torre, Ping Wang, Xianming Wang, De Xing, Dapeng Yang, Galabina N. Yordanova, Bo Yu, Tony Zeng, Stephen Zhang, Zhehao Zhang, Nan Zhang, Hengqiang Zhao, Shujian Zheng, Aaron Zhong, Justina Žurauskienė

Nature

Discovery of NANOG enhancers and their essential roles in self-renewal and differentiation in human embryonic stem cells

Jielin Yan, Renhe Luo, Bess P. Rosen, Dingyu Liu, Wilfred Wong, Christina S. Leslie, Danwei Huangfu

bioRxiv

ChromaFold predicts the 3D contact map from single-cell chromatin accessibility

Vianne R. Gao, Rui Yang, Arnav Das, Renhe Luo, Hanzhi Luo, Dylan R. McNally, Ioannis Karagiannidis, Martin A. Rivas, Zhong-Min Wang, Darko Barisic, Alireza Karbalayghareh, Wilfred Wong, Yingqian A. Zhan, Christopher R. Chin, William S. Noble, Jeff A. Bilmes, Effie Apostolou, Michael G. Kharas, Wendy Béguelin, Aaron D. Viny, Danwei Huangfu, Alexander Y. Rudensky, Ari M. Melnick, Christina S. Leslie

Nature Communications

Parallel genome-scale CRISPR-Cas9 screens uncouple human pluripotent stem cell identity versus fitness

Bess P. Rosen, Qing V. Li, Hyein S. Cho, Dingyu Liu, Dapeng Yang, Sarah Graff, Jielin Yan, Renhe Luo, Nipun Verma, Jeyaram R. Damodaran, Hanuman T. Kale, Samuel J. Kaplan, Michael A. Beer, Simone Sidoli, Danwei Huangfu

Nature Communications

Deciphering the impact of genomic variation on function

Jesse M. Engreitz, Heather A. Lawson, Harinder Singh, Lea M. Starita, Gary C. Hon, Hannah Carter, Nidhi Sahni, Timothy E. Reddy, Xihong Lin, Yun Li, Nikhil V. Munshi, Maria H. Chahrour, Alan P. Boyle, Benjamin C. Hitz, Ali Mortazavi, Mark Craven, Karen L. Mohlke, Luca Pinello, Ting Wang, Anshul Kundaje, Feng Yue, Sarah Cody, Nina P. Farrell, Michael I. Love, Lara A. Muffley, Michael J. Pazin, Fairlie Reese, Eric Van Buren, Kushal K. Dey, Martin Kircher, Jian Ma, Predrag Radivojac, Brunilda Balliu, Brian A. Williams, Danwei Huangfu, Chong Y. Park, Thomas Quertermous, Jishnu Das, Michael A. Calderwood, Douglas M. Fowler, Marc Vidal, Lucas Ferreira, Sean D. Mooney, Vikas Pejaver, Jingjing Zhao, Steven Gazal, Evan Koch, Steven K. Reilly, Shamil Sunyaev, Anne E. Carpenter, Jason D. Buenrostro, Christina S. Leslie, Rachel E. Savage, Stefanija Giric, Chongyuan Luo, Kathrin Plath, Alejandro Barrera, Max Schubach, Andreas R. Gschwind, Jill E. Moore, Nadav Ahituv, S. Stephen Yi, Ingileif Hallgrimsdottir, Kyle J. Gaulton, Saori Sakaue, Sina Booeshaghi, Eugenio Mattei, Surag Nair, Lior Pachter, Austin T. Wang, Jay Shendure, Vikram Agarwal, Andrew Blair, Theofilos Chalkiadakis, Florence M. Chardon, Pyaree M. Dash, Chengyu Deng, Nobuhiko Hamazaki, Pia Keukeleire, Connor Kubo, Jean-Benoît Lalanne, Thorben Maass, Beth Martin, Troy A. McDiarmid, Mai Nobuhara, Nicholas F. Page, Sam Regalado, Jasmine Sims, Aki Ushiki, Sabrina M. Best, Gabe Boyle, Nathan Camp, Silvia Casadei, Estelle Y. Da, Moez Dawood, Samantha C. Dawson, Shawn Fayer, Audrey Hamm, Richard G. James, Gail P. Jarvik, Abbye E. McEwen, Nick Moore, Sriram Pendyala, Nicholas A. Popp, Mason Post, Alan F. Rubin, Nahum T. Smith, Jeremy Stone, Malvika Tejura, Ziyu R. Wang, Melinda K. Wheelock, Ivan Woo, Brendan D. Zapp, Dulguun Amgalan, Aradhana Aradhana, Sophia M. Arana, Michael C. Bassik, Julia R. Bauman, Asmita Bhattacharya, Xiangmeng Shawn Cai, Ziwei Chen, Stephanie Conley, Salil Deshpande, Benjamin R. Doughty, Peter P. Du, James A. Galante, Casey Gifford, William J. Greenleaf, Katherine Guo, Revant Gupta, Sarasa Isobe, Evelyn Jagoda, Nimit Jain, Hank Jones, Helen Y. Kang, Samuel H. Kim, YeEun Kim, Sandy Klemm, Ramen Kundu, Soumya Kundu, Mauro Lago-Docampo, Yannick C. Lee-Yow, Roni Levin-Konigsberg, Daniel Y. Li, Dominik Lindenhofer, X. Rosa Ma, Georgi K. Marinov, Gabriella E. Martyn, Chloe V. McCreery, Eyal Metzl-Raz, Joao P. Monteiro, Michael T. Montgomery, Kristy S. Mualim, Chad Munger, Glen Munson, Tri C. Nguyen, Trieu Nguyen, Brian T. Palmisano, Anusri Pampari, Marlene Rabinovitch, Markus Ramste, Judhajeet Ray, Kevin R. Roy, Oriane M. Rubio, Julia M. Schaepe, Gavin Schnitzler, Jacob Schreiber, Disha Sharma, Maya U. Sheth, Huitong Shi, Vasundhara Singh, Riya Sinha, Lars M. Steinmetz, Jason Tan, Anthony Tan, Josh Tycko, Raeline C. Valbuena, Valeh Valiollah Pour Amiri, Mariëlle J. F. M. van Kooten, Alun Vaughan-Jackson, Anthony Venida, Chad S. Weldy, Matthew D. Worssam, Fan Xia, David Yao, Tony Zeng, Quanyi Zhao, Ronghao Zhou, Zitong Sam Chen, Beth A. Cimini, Georges Coppin, Atina G. Coté, Marzieh Haghighi, Tong Hao, David E. Hill, Jessica Lacoste, Florent Laval, Chloe Reno, Frederick P. Roth, Shantanu Singh, Kerstin Spirohn-Fitzgerald, Mikko Taipale, Tanisha Teelucksingh, Maxime Tixhon, Anupama Yadav, Zhipeng Yang, W. Lee Kraus, Daniel A. Armendariz, Ashley E. Dederich, Ashlesha Gogate, Lauretta El Hayek, Sean C. Goetsch, Kiran Kaur, Hyung Bum Kim, Melissa K. McCoy, Mpathi Z. Nzima, Carlos A. Pinzón-Arteaga, Bruce A. Posner, Daniel A. Schmitz, Sushama Sivakumar, Anjana Sundarrajan, Lei Wang, Yihan Wang, Jun Wu, Lin Xu, Jian Xu, Leqian Yu, Yanfeng Zhang, Huan Zhao, Qinbo Zhou, Hyejung Won, Jessica L. Bell, K. Alaine Broadaway, Katherine N. Degner, Amy S. Etheridge, Beverly H. Koller, Won Mah, Wancen Mu, Kimberly D. Ritola, Jonathan D. Rosen, Sarah A. Schoenrock, Rachel A. Sharp, Daniel Bauer, Guillaume Lettre, Richard Sherwood, Basheer Becerra, Logan J. Blaine, Eric Che, Matthew J. Francoeur, Ellie N. Gibbs, Nahye Kim, Emily M. King, Benjamin P. Kleinstiver, Estelle Lecluze, Zhijian Li, Zain M. Patel, Quang Vinh Phan, Jayoung Ryu, Marlena L. Starr, Ting Wu, Charles A. Gersbach, Gregory E. Crawford, Andrew S. Allen, William H. Majoros, Nahid Iglesias, Ruhi Rai, Revathy Venukuttan, Boxun Li, Taylor Anglen, Lexi R. Bounds, Marisa C. Hamilton, Siyan Liu, Sean R. McCutcheon, Christian D. McRoberts Amador, Samuel J. Reisman, Maria A. ter Weele, Josephine C. Bodle, Helen L. Streff, Keith Siklenka, Kari Strouse, Bradley E. Bernstein, Juliana Babu, Guillermo Barreto Corona, Kevin Dong, Fabiana M. Duarte, Neva C. Durand, Charles B. Epstein, Kaili Fan, Elizabeth Gaskell, Amelia W. Hall, Alexandra M. Ham, Mei K. Knudson, Noam Shoresh, Siddarth Wekhande, Cassandra M. White, Wang Xi, Ansuman T. Satpathy, M. Ryan Corces, Serena H. Chang, Iris M. Chin, James M. Gardner, Zachary A. Gardell, Jacob C. Gutierrez, Alia W. Johnson, Lucas Kampman, Maya Kasowski, Caleb A. Lareau, Vincent Liu, Leif S. Ludwig, Christopher S. McGinnis, Shreya Menon, Anita Qualls, Katalin Sandor, Adam W. Turner, Chun J. Ye, Yajie Yin, Wenxi Zhang, Barbara J. Wold, Maria Carilli, Dayeon Cheong, Ghassan Filibam, Kim Green, Shimako Kawauchi, Charlene Kim, Heidi Liang, Rebekah Loving, Laura Luebbert, Grant MacGregor, Angel G. Merchan, Elisabeth Rebboah, Narges Rezaie, Jasmine Sakr, Delaney K. Sullivan, Nikki Swarna, Diane Trout, Sean Upchurch, Ryan Weber, Christopher P. Castro, Elysia Chou, Fan Feng, Andre Guerra, Yuanhao Huang, Linghua Jiang, Jie Liu, Ryan E. Mills, Weizhou Qian, Tingting Qin, Maureen A. Sartor, Rintsen N. Sherpa, Jinhao Wang, Yiqun Wang, Joshua D. Welch, Zhenhao Zhang, Nanxiang Zhao, Sayan Mukherjee, C. David Page, Shannon Clarke, Richard W. Doty, Yuncheng Duan, Raluca Gordan, Kuei-Yueh Ko, Shengyu Li, Boyao Li, Alexander Thomson, Soumya Raychaudhuri, Alkes Price, Thahmina A. Ali, Kushal K. Dey, Arun Durvasula, Manolis Kellis, Lilia M. Iakoucheva, Tulika Kakati, Yile Chen, Mariam Benazouz, Shantanu Jain, Daniel Zeiberg, M. Clara De Paolis Kaluza, Michelle Velyunskiy, Audrey Gasch, Kunling Huang, Yiyang Jin, Qiongshi Lu, Jiacheng Miao, Michael Ohtake, Eduardo Scopel, Robert D. Steiner, Yuriy Sverchkov, Zhiping Weng, Manuel Garber, Yu Fu, Natalie Haas, Xihao Li, Nishigandha Phalke, Shuo C. Shan, Nicole Shedd, Tianxiong Yu, Yi Zhang, Hufeng Zhou, Alexis Battle, Livnat Jerby, Eran Kotler, Soumya Kundu, Andrew R. Marderstein, Stephen B. Montgomery, AkshatKumar Nigam, Evin M. Padhi, Aman Patel, Jonathan Pritchard, Ivy Raine, Vivekanandan Ramalingam, Kameron B. Rodrigues, Jacob M. Schreiber, Arpita Singhal, Riya Sinha, Austin T. Wang, Marisa Abundis, Deepa Bisht, Trirupa Chakraborty, Jingyu Fan, David R. Hall, Zarifeh H. Rarani, Abhinav K. Jain, Babita Kaundal, Swapnil Keshari, Daniel McGrail, Nicholas A. Pease, Vivian F. Yi, Hao Wu, Sreeram Kannan, Hongjun Song, Jingli Cai, Ziyue Gao, Ronni Kurzion, Julia I. Leu, Fan Li, Dongming Liang, Guo-li Ming, Kiran Musunuru, Qi Qiu, Junwei Shi, Yijing Su, Sarah Tishkoff, Ning Xie, Qian Yang, Wenli Yang, Hongjie Zhang, Zhijian Zhang, Michael A. Beer, Anna-Katerina Hadjantonakis, Sharon Adeniyi, Hyein Cho, Ronald Cutler, Rachel A. Glenn, David Godovich, Nan Hu, Svetlana Jovanic, Renhe Luo, Jin Woo Oh, Milad Razavi-Mohseni, Dustin Shigaki, Simone Sidoli, Thomas Vierbuchen, Xianming Wang, Breanna Williams, Jielin Yan, Dapeng Yang, Yunxiao Yang, Maike Sander, Kyle J. Gaulton, Bing Ren, Weronika Bartosik, Hannah S. Indralingam, Adam Klie, Hannah Mummey, Mei-Lin Okino, Gaowei Wang, Nathan R. Zemke, Kai Zhang, Han Zhu, Noah Zaitlen, Jason Ernst, Justin Langerman, Terence Li, Yu Sun, Alexander Y. Rudensky, Preethi K. Periyakoil, Vianne R. Gao, Melanie H. Smith, Norman M. Thomas, Laura T. Donlin, Amit Lakhanpal, Kaden M. Southard, Rico C. Ardy, J. Michael Cherry, Mark B. Gerstein, Kalina Andreeva, Pedro R. Assis, Beatrice Borsari, Eric Douglass, Shengcheng Dong, Idan Gabdank, Keenan Graham, Otto Jolanki, Jennifer Jou, Meenakshi S. Kagda, Jin-Wook Lee, Mingjie Li, Khine Lin, Stuart R. Miyasato, Joel Rozowsky, Corinn Small, Emma Spragins, Forrest Y. Tanaka, Ian M. Whaling, Ingrid A. Youngworth, Cricket A. Sloan, Eddie Belter, Xintong Chen, Rex L. Chisholm, Patricia Dickson, Changxu Fan, Lucinda Fulton, Daofeng Li, Tina Lindsay, Yu Luan, Yuan Luo, Huijue Lyu, Xiaowen Ma, Juan Macias-Velasco, Karen H. Miga, Kara Quaid, Nathan Stitziel, Barbara E. Stranger, Chad Tomlinson, Juan Wang, Wenjin Zhang, Bo Zhang, Guoyan Zhao, Xiaoyu Zhuo, Kristen Brennand, Alberto Ciccia, Samuel B. Hayward, Jen-Wei Huang, Giuseppe Leuzzi, Angelo Taglialatela, Tanay Thakar, Alina Vaitsiankova, Kushal K. Dey, Thahmina A. Ali, Artem Kim, H. Leighton Grimes, Nathan Salomonis, Rajat Gupta, Shi Fang, Vivian Lee-Kim, Matthias Heinig, Corinna Losert, Thouis R. Jones, Elisa Donnard, Maddie Murphy, Elizabeth Roberts, Susie Song, Sara Mostafavi, Alexander Sasse, Anna Spiro, Len A. Pennacchio, Momoe Kato, Michael Kosicki, Brandon Mannion, Neil Slaven, Axel Visel, Katherine S. Pollard, Shiron Drusinsky, Sean Whalen, John Ray, Ingrid A. Harten, Ching-Huang Ho, Neville E. Sanjana, Christina Caragine, John A. Morris, Davide Seruggia, Ana Patricia Kutschat, Sandra Wittibschlager, Han Xu, Rongjie Fu, Wei He, Liang Zhang, Daniel Osorio, Zo Bly, Stephanie Calluori, Daniel A. Gilchrist, Carolyn M. Hutter, Stephanie A. Morris, Ella K. Samer

Nature

CRISPR screening uncovers a long-range enhancer for ONECUT1 in pancreatic differentiation and links a diabetes risk variant

Samuel Joseph Kaplan, Wilfred Wong, Jielin Yan, Julian Pulecio, Hyein S. Cho, Qianzi Li, Jiahui Zhao, Jayanti Leslie-Iyer, Jonathan Kazakov, Dylan Murphy, Renhe Luo, Kushal K. Dey, Effie Apostolou, Christina S. Leslie, Danwei Huangfu

Cell Reports

Glucose Transporters Are Key Components of the Human Glucostat

Inbal Caspi, Daniel M. Tremmel, Julian Pulecio, Dapeng Yang, Dingyu Liu, Jielin Yan, Jon S. Odorico, Danwei Huangfu

Diabetes

Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project

Job Dekker, Frank Alber, Sarah Aufmkolk, Brian J. Beliveau, Benoit G. Bruneau, Andrew S. Belmont, Lacramioara Bintu, Alistair Boettiger, Riccardo Calandrelli, Christine M. Disteche, David M. Gilbert, Thomas Gregor, Anders S. Hansen, Bo Huang, Danwei Huangfu, Reza Kalhor, Christina S. Leslie, Wenbo Li, Yun Li, Jian Ma, William S. Noble, Peter J. Park, Jennifer E. Phillips-Cremins, Katherine S. Pollard, Susanne M. Rafelski, Bing Ren, Yijun Ruan, Yaron Shav-Tal, Yin Shen, Jay Shendure, Xiaokun Shu, Caterina Strambio-De-Castillia, Anastassiia Vertii, Huaiying Zhang, Sheng Zhong

Molecular Cell

Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions

Renhe Luo, Jielin Yan, Jin Woo Oh, Wang Xi, Dustin Shigaki, Wilfred Wong, Hyein S. Cho, Dylan Murphy, Ronald Cutler, Bess P. Rosen, Julian Pulecio, Dapeng Yang, Rachel A. Glenn, Tingxu Chen, Qing V. Li, Thomas Vierbuchen, Simone Sidoli, Effie Apostolou, Danwei Huangfu, Michael A. Beer

Nature Genetics

MLL3 loss drives metastasis by promoting a hybrid epithelial–mesenchymal transition state

Jihong Cui, Chi Zhang, Ji-Eun Lee, Boris A. Bartholdy, Dapeng Yang, Yu Liu, Piril Erler, Phillip M. Galbo, Dayle Q. Hodge, Danwei Huangfu, Deyou Zheng, Kai Ge, Wenjun Guo

Nature Cell Biology

Genetic Engineering of Immune Evasive Stem Cell-Derived Islets

Sara D. Sackett, Samuel J. Kaplan, Samantha A. Mitchell, Matthew E. Brown, Adam L. Burrack, Shane Grey, Danwei Huangfu, Jon Odorico

Transplant International

A hypomorphic mutation in Pold1 disrupts the coordination of embryo size expansion and morphogenesis during gastrulation

Tingxu Chen, Heather Alcorn, Sujan Devbhandari, Dirk Remus, Elizabeth Lacy, Danwei Huangfu, Kathryn V. Anderson

Biology Open

CRISPR screening uncovers a central requirement for HHEX in pancreatic lineage commitment and plasticity restriction

Dapeng Yang, Hyunwoo Cho, Zakieh Tayyebi, Abhijit Shukla, Renhe Luo, Gary Dixon, Valeria Ursu, Stephanie Stransky, Daniel M. Tremmel, Sara D. Sackett, Richard Koche, Samuel J. Kaplan, Qing V. Li, Jiwoon Park, Zengrong Zhu, Bess P. Rosen, Julian Pulecio, Zhong-Dong Shi, Yaron Bram, Robert E. Schwartz, Jon S. Odorico, Simone Sidoli, Christopher V. Wright, Christina S. Leslie, Danwei Huangfu

Nature Cell Biology

A hypomorphic mutation in Pold1 disrupts the coordination of embryo size expansion and morphogenesis during gastrulation

Tingxu Chen, Heather Alcorn, Sujan Devbhandari, Dirk Remus, Elizabeth Lacy, Danwei Huangfu, Kathryn V. Anderson

bioRxiv

Epigenome rewiring in human pluripotent stem cells

Jielin Yan, Danwei Huangfu

Trends in Cell Biology

Abnormal exocrine–endocrine cell cross-talk promotes β-cell dysfunction and loss in MODY8

Sevim Kahraman, Ercument Dirice, Giorgio Basile, Danielle Diegisser, Jahedul Alam, Bente B. Johansson, Manoj K. Gupta, Jiang Hu, Ling Huang, Chew-Li Soh, Danwei Huangfu, Senthil K. Muthuswamy, Helge Raeder, Anders Molven, Rohit N. Kulkarni

Nature Metabolism

Stage-specific regulation of DNA methylation by TET enzymes during human cardiac differentiation

Yahui Lan, Kelly M. Banks, Heng Pan, Nipun Verma, Gary R. Dixon, Ting Zhou, Bo Ding, Olivier Elemento, Shuibing Chen, Danwei Huangfu, Todd Evans

Cell Reports

209.7: An Inducible Genome Engineering Approach for Preventing Immune Rejection of hESC-derived Beta Cells

Sara D. Sackett, Samantha A. Mitchell, Nicholas Quirini, Chew-Li Soh, Inbal Caspi, Anna Mikat, Danwei Huangfu, Jon Odorico

Transplantation

Generation of human embryonic stem cell models to exploit the EWSR1-CREB fusion promiscuity as a common pathway of transformation in human tumors

Fabio Vanoli, Brigita Meskauskaite, Laurie Herviou, William Mallen, Yun-Shao Sung, Yumi Fujisawa, Lei Zhang, Steven Simon, Danwei Huangfu, Maria Jasin, Cristina R. Antonescu

Oncogene

QSER1 protects DNA methylation valleys from de novo methylation

Gary Dixon, Heng Pan, Dapeng Yang, Bess P. Rosen, Therande Jashari, Nipun Verma, Julian Pulecio, Inbal Caspi, Kihyun Lee, Stephanie Stransky, Abigail Glezer, Chang Liu, Marco Rivas, Ritu Kumar, Yahui Lan, Ingrid Torregroza, Chuan He, Simone Sidoli, Todd Evans, Olivier Elemento, Danwei Huangfu

Science

Kathryn Anderson (1952–2020)

Zhirong Bao, Mary K. Baylies, Anna-Katerina Hadjantonakis, Danwei Huangfu, Maria Jasin, Alexandra L. Joyner, Elizabeth Lacy, Eric C. Lai, Lorenz Studer, Thomas Vierbuchen, Jennifer A. Zallen

Cell

Kathryn Anderson (1952–2020)

Danwei Huangfu, María J. García-García, Jonathan Eggenschwiler

Developmental Cell

Enhancer Predictions and Genome-Wide Regulatory Circuits

Michael A. Beer, Dustin Shigaki, Danwei Huangfu

Annual Review of Genomics and Human Genetics

Decoding pluripotency: Genetic screens to interrogate the acquisition, maintenance, and exit of pluripotency

Qing V. Li, Bess P. Rosen, Danwei Huangfu

WIREs Systems Biology and Medicine

Glutamine independence is a selectable feature of pluripotent stem cells

Santosha A. Vardhana, Paige K. Arnold, Bess P. Rosen, Yanyang Chen, Bryce W. Carey, Danwei Huangfu, Carlos Carmona-Fontaine, Craig B. Thompson, Lydia W. S. Finley

Nature Metabolism

FOXA2 Is Required for Enhancer Priming during Pancreatic Differentiation

Kihyun Lee, Hyunwoo Cho, Robert W. Rickert, Qing V. Li, Julian Pulecio, Christina S. Leslie, Danwei Huangfu

Cell Reports

Genome-scale screens identify JNK–JUN signaling as a barrier for pluripotency exit and endoderm differentiation

Qing V. Li, Gary Dixon, Nipun Verma, Bess P. Rosen, Miriam Gordillo, Renhe Luo, Chunlong Xu, Qiong Wang, Chew-Li Soh, Dapeng Yang, Miguel Crespo, Abhijit Shukla, Qing Xiang, Friederike Dündar, Paul Zumbo, Matthew Witkin, Richard Koche, Doron Betel, Shuibing Chen, Joan Massagué, Ralph Garippa, Todd Evans, Michael A. Beer, Danwei Huangfu

Nature Genetics

Decoding the noncoding genome via large-scale CRISPR screens

Abhijit Shukla, Danwei Huangfu

Current Opinion in Genetics & Development

DICER1 Is Essential for Self-Renewal of Human Embryonic Stem Cells

Virginia Teijeiro, Dapeng Yang, Sonali Majumdar, Federico González, Robert W. Rickert, Chunlong Xu, Richard Koche, Nipun Verma, Eric C. Lai, Danwei Huangfu

Stem Cell Reports

Report of the Key Opinion Leaders Meeting on Stem Cell-derived Beta Cells

Jon Odorico, James Markmann, Douglas Melton, Julia Greenstein, Albert Hwa, Cristina Nostro, Alireza Rezania, Jose Oberholzer, Daniel Pipeleers, Luhan Yang, Chad Cowan, Danwei Huangfu, Dieter Egli, Uri Ben-David, Ludovic Vallier, Shane T. Grey, Qizhi Tang, Bart Roep, Camilo Ricordi, Ali Naji, Giuseppe Orlando, Daniel G. Anderson, Mark Poznansky, Barbara Ludwig, Alice Tomei, Dale L. Greiner, Melanie Graham, Melissa Carpenter, Giovanni Migliaccio, Kevin D’Amour, Bernhard Hering, Lorenzo Piemonti, Thierry Berney, Mike Rickels, Thomas Kay, Ann Adams

Transplantation

Discovery of a drug candidate for GLIS3-associated diabetes

Sadaf Amin, Brandoch Cook, Ting Zhou, Zaniar Ghazizadeh, Raphael Lis, Tuo Zhang, Mona Khalaj, Miguel Crespo, Manuradhi Perera, Jenny Zhaoying Xiang, Zengrong Zhu, Mark Tomishima, Chengyang Liu, Ali Naji, Todd Evans, Danwei Huangfu, Shuibing Chen

Nature Communications

Genome-Wide Identification of HES1 Target Genes Uncover Novel Roles for HES1 in Pancreatic Development

Kristian Honnens de Lichtenberg, Nina Funa, Nikolina Nakic, Jorge Ferrer, Zengrong Zhu, Danwei Huangfu, Palle Serup

bioRxiv

TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells

Nipun Verma, Heng Pan, Louis C. Doré, Abhijit Shukla, Qing V. Li, Bobbie Pelham-Webb, Virginia Teijeiro, Federico González, Andrei Krivtsov, Chan-Jung Chang, Eirini P. Papapetrou, Chuan He, Olivier Elemento, Danwei Huangfu

Nature Genetics

CRISPR/Cas9-Based Engineering of the Epigenome

Julian Pulecio, Nipun Verma, Eva Mejía-Ramírez, Danwei Huangfu, Angel Raya

Cell Stem Cell

Genome Editing in hPSCs Reveals GATA6 Haploinsufficiency and a Genetic Interaction with GATA4 in Human Pancreatic Development

Zhong-Dong Shi, Kihyun Lee, Dapeng Yang, Sadaf Amin, Nipun Verma, Qing V. Li, Zengrong Zhu, Chew-Li Soh, Ritu Kumar, Todd Evans, Shuibing Chen, Danwei Huangfu

Cell Stem Cell

Genome Editing and Directed Differentiation of hPSCs for Interrogating Lineage Determinants in Human Pancreatic Development

Zhong-Dong Shi, Chew-Li Soh, Zengrong Zhu, Danwei Huangfu

Journal of Visualized Experiments

The p53 Family Coordinates Wnt and Nodal Inputs in Mesendodermal Differentiation of Embryonic Stem Cells

Qiong Wang, Yilong Zou, Sonja Nowotschin, Sang Yong Kim, Qing V. Li, Chew-Li Soh, Jie Su, Chao Zhang, Weiping Shu, Qiaoran Xi, Danwei Huangfu, Anna-Katerina Hadjantonakis, Joan Massagué

Cell Stem Cell

CRISPR/Cas-Mediated Knockin in Human Pluripotent Stem Cells

Nipun Verma, Zengrong Zhu, Danwei Huangfu

Methods in Molecular Biology

CRISPR/Cas9-Mediated Mutagenesis of Human Pluripotent Stem Cells in Defined Xeno-Free E8 Medium

Chew-Li Soh, Danwei Huangfu

Methods in Molecular Biology

Genome Editing of Lineage Determinants in Human Pluripotent Stem Cells Reveals Mechanisms of Pancreatic Development and Diabetes

Zengrong Zhu, Qing V. Li, Kihyun Lee, Bess P. Rosen, Federico González, Chew-Li Soh, Danwei Huangfu

Cell Stem Cell

Mechanisms underlying the formation of induced pluripotent stem cells

Federico González, Danwei Huangfu

WIREs Developmental Biology

A CRISPR/Cas-Mediated Selection-free Knockin Strategy in Human Embryonic Stem Cells

Zengrong Zhu, Nipun Verma, Federico González, Zhong-Dong Shi, Danwei Huangfu

Stem Cell Reports

Functional analysis of a chromosomal deletion associated with myelodysplastic syndromes using isogenic human induced pluripotent stem cells

Andriana G Kotini, Chan-Jung Chang, Ibrahim Boussaad, Jeffrey J Delrow, Emily K Dolezal, Abhinav B Nagulapally, Fabiana Perna, Gregory A Fishbein, Virginia M Klimek, R David Hawkins, Danwei Huangfu, Charles E Murry, Timothy Graubert, Stephen D Nimer, Eirini P Papapetrou

Nature Biotechnology

An iCRISPR Platform for Rapid, Multiplexable, and Inducible Genome Editing in Human Pluripotent Stem Cells

Federico González, Zengrong Zhu, Zhong-Dong Shi, Katherine Lelli, Nipun Verma, Qing V. Li, Danwei Huangfu

Cell Stem Cell

Chemicals Facilitating Reprogramming

Zhong‐Dong Shi, Federico González, Danwei Huangfu

Chemical Biology in Regenerative Medicine

Stem Cell Epigenetics: Looking Forward

Cell Stem Cell

The iCRISPR Platform for Rapid Genome Editing in Human Pluripotent Stem Cells

Zengrong Zhu, Federico González, Danwei Huangfu

Methods in Enzymology

Homologous Recombination DNA Repair Genes Play a Critical Role in Reprogramming to a Pluripotent State

Federico González, Daniela Georgieva, Fabio Vanoli, Zhong-Dong Shi, Matthias Stadtfeld, Thomas Ludwig, Maria Jasin, Danwei Huangfu

Cell Reports

Human pluripotent stem cells: an emerging model in developmental biology

Zengrong Zhu, Danwei Huangfu

Development

Glucose and aging control the quiescence period that follows pancreatic beta cell replication

Seth J. Salpeter, Allon M. Klein, Danwei Huangfu, Joseph Grimsby, Yuval Dor

Development

A Small-Molecule Inhibitor of Tgf-β Signaling Replaces Sox2 in Reprogramming by Inducing Nanog

Justin K. Ichida, Joel Blanchard, Kelvin Lam, Esther Y. Son, Julia E. Chung, Dieter Egli, Kyle M. Loh, Ava C. Carter, Francesco P. Di Giorgio, Kathryn Koszka, Danwei Huangfu, Hidenori Akutsu, David R. Liu, Lee L. Rubin, Kevin Eggan

Cell Stem Cell

Induction of pluripotent stem cells from primary human fibroblasts with only Oct4 and Sox2

Danwei Huangfu, Kenji Osafune, René Maehr, Wenjun Guo, Astrid Eijkelenboom, Shuibing Chen, Whitney Muhlestein, Douglas A Melton

Nature Biotechnology

Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds

Danwei Huangfu, René Maehr, Wenjun Guo, Astrid Eijkelenboom, Melinda Snitow, Alice E Chen, Douglas A Melton

Nature Biotechnology

All β Cells Contribute Equally to Islet Growth and Maintenance

Kristen Brennand, Danwei Huangfu, Doug Melton

PLoS Biology

Signaling from Smo to Ci/Gli: conservation and divergence of Hedgehog pathways fromDrosophilato vertebrates

Danwei Huangfu, Kathryn V. Anderson

Development

Cilia and Hedgehog responsiveness in the mouse

Danwei Huangfu, Kathryn V. Anderson

Proceedings of the National Academy of Sciences

Analysis of mouse embryonic patterning and morphogenesis by forward genetics

María J. García-García, Jonathan T. Eggenschwiler, Tamara Caspary, Heather L. Alcorn, Michael R. Wyler, Danwei Huangfu, Andrew S. Rakeman, Jeffrey D. Lee, Evan H. Feinberg, John R. Timmer, Kathryn V. Anderson

Proceedings of the National Academy of Sciences

Hedgehog signalling in the mouse requires intraflagellar transport proteins

Danwei Huangfu, Aimin Liu, Andrew S. Rakeman, Noel S. Murcia, Lee Niswander, Kathryn V. Anderson

Nature

Mouse Dispatched homolog1 Is Required for Long-Range, but Not Juxtacrine, Hh Signaling

Tamara Caspary, Marı́a Jesús Garcı́a-Garcı́a, Danwei Huangfu, Jonathan T. Eggenschwiler, Michael R. Wyler, Andrew S. Rakeman, Heather L. Alcorn, Kathryn V. Anderson

Current Biology