K
Koen Van den Berge
Researcher at University of California, Berkeley
Publications - 33
Citations - 2156
Koen Van den Berge is an academic researcher from University of California, Berkeley. The author has contributed to research in topics: Cell type & Population. The author has an hindex of 13, co-authored 30 publications receiving 1143 citations. Previous affiliations of Koen Van den Berge include Ghent University.
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Journal ArticleDOI
Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia.
David H. Brann,Tatsuya Tsukahara,Caleb Weinreb,Marcela Lipovsek,Koen Van den Berge,Koen Van den Berge,Boying Gong,Rebecca K. Chance,Iain C. Macaulay,Hsin-jung Chou,Russell B. Fletcher,Diya Das,Diya Das,Kelly Street,Hector Roux de Bézieux,Yoon Gi Choi,Davide Risso,Sandrine Dudoit,Elizabeth Purdom,Jonathan Mill,Ralph Abi Hachem,Hiroaki Matsunami,Darren W. Logan,Bradley J. Goldstein,Matthew S. Grubb,John Ngai,Sandeep Robert Datta +26 more
TL;DR: It is suggested that CoV-2 infection of non-neuronal cell types leads to anosmia and related disturbances in odor perception in COVID-19 patients.
Journal ArticleDOI
Trajectory-based differential expression analysis for single-cell sequencing data.
Koen Van den Berge,Koen Van den Berge,Hector Roux de Bézieux,Kelly Street,Wouter Saelens,Robrecht Cannoodt,Robrecht Cannoodt,Yvan Saeys,Sandrine Dudoit,Lieven Clement +9 more
TL;DR: Here, Van den Berge et al. develop tradeSeq, a framework for the inference of within and between-lineage differential expression, based on negative binomial generalized additive models, which yields biological insights through a clear interpretation of the data.
Posted ContentDOI
Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia
David H. Brann,Tatsuya Tsukahara,Caleb Weinreb,Marcela Lipovsek,Koen Van den Berge,Boying Gong,Rebecca K. Chance,Iain C. Macaulay,Hsin-jung Chou,Russell B. Fletcher,Diya Das,Kelly Street,Hector Roux de Bézieux,Yoon Gi Choi,Davide Risso,Sandrine Dudoit,Elizabeth Purdom,Jonathan Mill,Ralph Abi Hachem,Hiroaki Matsunami,Darren W. Logan,Bradley J. Goldstein,Matthew S. Grubb,John Ngai,John Ngai,Sandeep Robert Datta +25 more
TL;DR: Findings suggest that CoV-2 infection of non-neuronal cell types leads to anosmia and related disturbances in odor perception in COVID-19 patients.
Posted ContentDOI
A multimodal cell census and atlas of the mammalian primary motor cortex
Ricky S. Adkins,Andrew Aldridge,Shona Allen,Seth A. Ament,Xu An,Ethan J. Armand,Giorgio A. Ascoli,Trygve E. Bakken,Anita Bandrowski,Samik Banerjee,Nikolaos Barkas,Anna Bartlett,Helen S. Bateup,M. Margarita Behrens,Philipp Berens,Jim Berg,Matteo Bernabucci,Yves Bernaerts,Darren Bertagnolli,Tommaso Biancalani,Lara Boggeman,Sina Booeshaghi,Ian Bowman,Héctor Corrada Bravo,Cathryn R. Cadwell,Edward M. Callaway,Benjamin Carlin,Carolyn O’Connor,Robert A. Carter,Tamara Casper,Rosa Castanon,Jesus Ramon Castro,Rebecca K. Chance,Apaala Chatterjee,Huaming Chen,Jerold Chun,Carlo Colantuoni,Jonathan Crabtree,Heather Huot Creasy,Kirsten Crichton,Megan Crow,Florence D’Orazi,Tanya L. Daigle,Rachel A. Dalley,Nick Dee,Kylee Degatano,Benjamin Dichter,Dinh Diep,Liya Ding,Songlin Ding,Bertha Dominguez,Hong-Wei Dong,Weixiu Dong,Elizabeth L. Dougherty,Sandrine Dudoit,Joseph R. Ecker,Stephen W. Eichhorn,Rongxin Fang,Victor Felix,Guoping Feng,Zhao Feng,Stephan Fischer,Conor Fitzpatrick,Olivia Fong,Nicholas N. Foster,William Galbavy,James C. Gee,Satrajit S. Ghosh,Michelle G. Giglio,Thomas R. Gillespie,Jesse Gillis,Melissa Goldman,Jeff Goldy,Hui Gong,Lin Gou,Michael Grauer,Yaroslav O. Halchenko,Julie M. Harris,Leonard Hartmanis,Joshua T. Hatfield,Michael Hawrylycz,Brian Helba,Brian R. Herb,Ronna Hertzano,Houri Hintiryan,Karla E. Hirokawa,Dirk Hockemeyer,Rebecca D. Hodge,Greg Hood,Gregory D. Horwitz,Xiaomeng Hou,Lijuan Hu,Qiwen Hu,Josh Huang,Bing-Xing Huo,Tony Ito-Cole,Matthew W. Jacobs,Xueyan Jia,Shengdian Jiang,Tao Jiang,Xiaolong Jiang,Xin Jin,Nikolas L. Jorstad,Brian E. Kalmbach,Jayaram Kancherla,C. Dirk Keene,Kathleen Kelly,Farzaneh Khajouei,Peter V. Kharchenko,Gukhan Kim,Andrew L. Ko,Dmitry Kobak,Kishori Konwar,Daniel J. Kramer,Fenna M. Krienen,Matthew Kroll,Xiuli Kuang,Hsien-Chi Kuo,Rachael Larsen,Kanan Lathia,Sophie Laturnus,Angus Y. Lee,Cheng-Ta Lee,Kuo-Fen Lee,Ed S. Lein,Phil Lesnar,Anan Li,Xiangning Li,Xu Li,Yang Eric Li,Yaoyao Li,Yuanyuan Li,Byung Kook Lim,Sten Linnarsson,Christine S. Liu,Hanqing Liu,Lijuan Liu,Jacinta Lucero,Chongyuan Luo,Qingming Luo,Evan Z. Macosko,Anup Mahurkar,Maryann E. Martone,Katherine Matho,Steven A. McCarroll,Carrie McCracken,Delissa McMillen,Elanine Miranda,Partha P. Mitra,Paula Assakura Miyazaki,Judith Mizrachi,Stephanie Mok,Eran A. Mukamel,Shalaka Mulherkar,Naeem Nadaf,Maitham Naeemi,Arun Narasimhan,Joseph R. Nery,Lydia Ng,John Ngai,Thuc Nghi Nguyen,Lance Nickel,Philip R. Nicovich,Sheng-Yong Niu,Vasilis Ntranos,Michael Nunn,Dustin Olley,Joshua Orvis,Julia K. Osteen,Pavel Osten,Scott F. Owen,Lior Pachter,Ramesh Palaniswamy,C. Palmer,Yan Pang,Hanchuan Peng,Thanh Pham,Antonio Pinto-Duarte,Nongluk Plongthongkum,Olivier Poirion,Sebastian Preissl,Elizabeth Purdom,Lei Qu,Mohammad S. Rashid,Nora Reed,Aviv Regev,Bing Ren,Miao Ren,Christine Rimorin,Davide Risso,Angeline Rivkin,Rodrigo Muñoz-Castañeda,William J. Romanow,Alexander J. Ropelewski,Hector Roux de Bézieux,Zongcai Ruan,Rickard Sandberg,Steven Savoia,Federico Scala,Michael Schor,Elise Shen,Kimberly Siletti,Jared B. Smith,Kimberly A. Smith,Saroja Somasundaram,Yuanyuan Song,Staci A. Sorensen,David A. Stafford,Kelly Street,Josef Sulc,Susan M. Sunkin,Valentine Svensson,Pengcheng Tan,Zheng Huan Tan,Bosiljka Tasic,Carol L. Thompson,Wei Tian,Timothy L. Tickle,Michael Tieu,Jonathan T. Ting,Andreas S. Tolias,Amy Torkelson,Herman Tung,Eeshit Dhaval Vaishnav,Koen Van den Berge,Cindy T. J. van Velthoven,Charles R. Vanderburg,Matthew B. Veldman,Minh Vu,Wayne Wakeman,Peng Wang,Quanxin Wang,Xinxin Wang,Yimin Wang,Yun Wang,Joshua D. Welch,Owen White,Elora W Williams,Fangming Xie,Peng Xie,Feng Xiong,William Yang,Anna Marie Yanny,Zizhen Yao,Lulu Yin,Yang Yu,Jing Yuan,Hongkui Z +247 more
TL;DR: This study reveals a unified molecular genetic landscape of cortical cell types that congruently integrates their transcriptome, open chromatin and DNA methylation maps, and establishes a unified and mechanistic framework of neuronal cell type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.
Journal ArticleDOI
Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications.
Koen Van den Berge,Fanny Perraudeau,Charlotte Soneson,Charlotte Soneson,Michael I. Love,Davide Risso,Jean-Philippe Vert,Mark D. Robinson,Mark D. Robinson,Sandrine Dudoit,Lieven Clement +10 more
TL;DR: A weighting strategy is introduced, based on a zero-inflated negative binomial model, that identifies excess zero counts and generates gene- and cell-specific weights to unlock bulk RNA-seq DE pipelines for zero- inflated data, boosting performance for scRNA-seq.