Elizabeth Purdom

Affiliations

Division of Biostatistics, University of California, Berkeley, Berkeley, California.
Department of Statistics, University of California, Berkeley, Berkeley, California.

Publications (22)

MethCP: Differentially Methylated Region Detection with Change Point Models.

Journal of computational biology : a journal of computational molecular cell biology

Improving replicability in single-cell RNA-Seq cell type discovery with Dune.

BMC bioinformatics

Avec: Hector Roux de Bézieux , Kelly Street , Stephan Fischer , Koen Van den Berge , Rebecca Chance , Davide Risso , Jesse Gillis , John Ngai , Elizabeth Purdom , Sandrine Dudoit

Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics.

Nature communications

Avec: Ling Xu , Zhaobin Dong , Dawn Chiniquy , Grady Pierroz , Siwen Deng , Cheng Gao , Spencer Diamond , Tuesday Simmons , Heidi M-L Wipf , Daniel Caddell , Nelle Varoquaux , Mary A Madera , Robert Hutmacher , Adam Deutschbauer , Jeffery A Dahlberg , Mary Lou Guerinot , Elizabeth Purdom , Jillian F Banfield , John W Taylor , Peggy G Lemaux , Devin Coleman-Derr

Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia.

Science advances

Avec: David H Brann , Tatsuya Tsukahara , Caleb Weinreb , Marcela Lipovsek , Koen Van den Berge , Boying Gong , Rebecca Chance , Iain C Macaulay , Hsin-Jung Chou , Russell B Fletcher , Diya Das , Kelly Street , Hector Roux de Bezieux , 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

Successional adaptive strategies revealed by correlating arbuscular mycorrhizal fungal abundance with host plant gene expression.

Molecular ecology

Avec: Cheng Gao , Pierre-Emmanuel Courty , Nelle Varoquaux , Benjamin Cole , Liliam Montoya , Ling Xu , Elizabeth Purdom , John Vogel , Robert B Hutmacher , Jeffery A Dahlberg , Devin Coleman-Derr , Peggy G Lemaux , John W Taylor

Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq.

Cell systems

Avec: Michael B Cole , Davide Risso , Allon Wagner , David DeTomaso , John Ngai , Elizabeth Purdom , Sandrine Dudoit , Nir Yosef

Visualizing scRNA-Seq Data at Population Scale with GloScope.

bioRxiv : the preprint server for biology

Avec: Hao Wang , William Torous , Boying Gong , Elizabeth Purdom

Cobolt: integrative analysis of multimodal single-cell sequencing data.

Genome biology

Avec: Boying Gong , Yun Zhou , Elizabeth Purdom

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex.

Nature

Avec: 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 Bézieux , Tommaso Biancalani , A Sina Booeshaghi , Héctor Corrada Bravo , Tamara Casper , Carlo Colantuoni , Jonathan Crabtree , Heather Creasy , Kirsten Crichton , Megan Crow , Nick Dee , Elizabeth L Dougherty , Wayne I Doyle , Sandrine Dudoit , Rongxin Fang , Victor Felix , Olivia Fong , Michelle Giglio , Jeff Goldy , Mike 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 Mahurkar , Delissa McMillen , Naeem M Nadaf , Joseph R Nery , Thuc Nghi Nguyen , Sheng-Yong Niu , Vasilis Ntranos , Joshua Orvis , Julia K Osteen , Thanh Pham , Antonio Pinto-Duarte , Olivier Poirion , Sebastian Preissl , Elizabeth Purdom , Christine Rimorin , Davide Risso , Angeline C Rivkin , Kimberly Smith , Kelly Street , Josef Sulc , Valentine Svensson , Michael Tieu , Amy Torkelson , Herman Tung , Eeshit Dhaval Vaishnav , Charles R Vanderburg , Cindy 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

Cell Wall Compositions of

Frontiers in plant science

Avec: Tess Scavuzzo-Duggan , Nelle Varoquaux , Mary Madera , John P Vogel , Jeffery Dahlberg , Robert Hutmacher , Michael Belcher , Jasmine Ortega , Devin Coleman-Derr , Peggy Lemaux , Elizabeth Purdom , Henrik V Scheller

mbkmeans: Fast clustering for single cell data using mini-batch k-means.

PLoS computational biology

Avec: Stephanie C Hicks , Ruoxi Liu , Yuwei Ni , Elizabeth Purdom , Davide Risso

A Latent Activated Olfactory Stem Cell State Revealed by Single Cell Transcriptomic and Epigenomic Profiling.

bioRxiv : the preprint server for biology

Avec: Koen Van den Berge , Hsin-Jung Chou , Divya Kunda , Davide Risso , Kelly Street , Elizabeth Purdom , Sandrine Dudoit , John Ngai , Whitney Heavner

Defining Patient-Level Molecular Heterogeneity in Psoriasis Vulgaris Based on Single-Cell Transcriptomics.

Frontiers in immunology

Avec: Yale Liu , Hao Wang , Christopher Cook , Mark A Taylor , Jeffrey P North , Ashley Hailer , Yanhong Shou , Arsil Sadik , Esther Kim , Elizabeth Purdom , Jeffrey B Cheng , Raymond J Cho

Fungal community assembly in drought-stressed sorghum shows stochasticity, selection, and universal ecological dynamics.

Nature communications

Avec: Cheng Gao , Liliam Montoya , Ling Xu , Mary Madera , Joy Hollingsworth , Elizabeth Purdom , Vasanth Singan , John Vogel , Robert B Hutmacher , Jeffery A Dahlberg , Devin Coleman-Derr , Peggy G Lemaux , John W Taylor

Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses.

Proceedings of the National Academy of Sciences of the United States of America

Avec: Nelle Varoquaux , Benjamin Cole , Cheng Gao , Grady Pierroz , Christopher R Baker , Dhruv Patel , Mary Madera , Tim Jeffers , Joy Hollingsworth , Julie Sievert , Yuko Yoshinaga , Judith A Owiti , Vasanth R Singan , Stephanie DeGraaf , Ling Xu , Matthew J Blow , Maria J Harrison , Axel Visel , Christer Jansson , Krishna K Niyogi , Robert Hutmacher , Devin Coleman-Derr , Ronan C O'Malley , John W Taylor , Jeffery Dahlberg , John P Vogel , Peggy G Lemaux , Elizabeth Purdom

A20 and ABIN1 Suppression of a Keratinocyte Inflammatory Program with a Shared Single-Cell Expression Signature in Diverse Human Rashes.

The Journal of investigative dermatology

Avec: Paymann Harirchian , Jerry Lee , Stephanie Hilz , Andrew J Sedgewick , Bethany E Perez White , Michael J Kesling , Thaddeus Mully , Justin Golovato , Matthew Gray , Theodora M Mauro , Elizabeth Purdom , Esther A Kim , Hani Sbitany , Tina Bhutani , Charles J Vaske , Stephen C Benz , Raymond J Cho , Jeffrey B Cheng

Strong succession in arbuscular mycorrhizal fungal communities.

The ISME journal

Avec: Cheng Gao , Liliam Montoya , Ling Xu , Mary Madera , Joy Hollingsworth , Elizabeth Purdom , Robert B Hutmacher , Jeffery A Dahlberg , Devin Coleman-Derr , Peggy G Lemaux , John W Taylor

Classification of human chronic inflammatory skin disease based on single-cell immune profiling.

Science immunology

Avec: Yale Liu , Hao Wang , Mark Taylor , Christopher Cook , Alejandra Martínez-Berdeja , Jeffrey P North , Paymann Harirchian , Ashley A Hailer , Zijun Zhao , Ruby Ghadially , Roberto R Ricardo-Gonzalez , Roy C Grekin , Theodora M Mauro , Esther Kim , Jaehyuk Choi , Elizabeth Purdom , Raymond J Cho , Jeffrey B Cheng

Co-occurrence networks reveal more complexity than community composition in resistance and resilience of microbial communities.

Nature communications

Avec: Cheng Gao , Ling Xu , Liliam Montoya , Mary Madera , Joy Hollingsworth , Liang Chen , Elizabeth Purdom , Vasanth Singan , John Vogel , Robert B Hutmacher , Jeffery A Dahlberg , Devin Coleman-Derr , Peggy G Lemaux , John W Taylor

A single-cell transcriptional gradient in human cutaneous memory T cells restricts Th17/Tc17 identity.

Cell reports. Medicine

Avec: Christopher P Cook , Mark Taylor , Yale Liu , Ralf Schmidt , Andrew Sedgewick , Esther Kim , Ashley Hailer , Jeffrey P North , Paymann Harirchian , Hao Wang , Sakeen W Kashem , Yanhong Shou , Timothy C McCalmont , Stephen C Benz , Jaehyuk Choi , Elizabeth Purdom , Alexander Marson , Silvia B V Ramos , Jeffrey B Cheng , Raymond J Cho

A single-cell atlas of IL-23 inhibition in cutaneous psoriasis distinguishes clinical response.

Science immunology

Avec: David Wu , Ashley A Hailer , Sijia Wang , Michelle Yuan , Jamie Chan , Abdullah El Kurdi , David Han , Hira Ali , Blaize D'Angio , Aaron Mayer , Maha Rahim , Ayano Kondo , Daniel Klufas , Esther Kim , A Hunter Shain , Jaehyuk Choi , Tina Bhutani , Gregory Simpson , Roy C Grekin , Roberto Ricardo-Gonzalez , Elizabeth Purdom , Jeffrey P North , Jeffrey B Cheng , Raymond J Cho

Visualizing scRNA-Seq data at population scale with GloScope.

Genome biology

Avec: Hao Wang , William Torous , Boying Gong , Elizabeth Purdom

Réseau de co-auteurs

Devin Coleman-Derr 7 collaborations

Davide Risso 6 collaborations

Ling Xu 6 collaborations

Cheng Gao 6 collaborations

John W Taylor 6 collaborations

Peggy G Lemaux 6 collaborations

Boying Gong 5 collaborations

John Ngai 5 collaborations

Sandrine Dudoit 5 collaborations

Jeffery A Dahlberg 5 collaborations

Hao Wang 5 collaborations

Mary Madera 5 collaborations

Jeffrey B Cheng 5 collaborations

Raymond J Cho 5 collaborations

Kelly Street 4 collaborations

Koen Van den Berge 4 collaborations

Nelle Varoquaux 4 collaborations

Liliam Montoya 4 collaborations

Robert B Hutmacher 4 collaborations

Jeffrey P North 4 collaborations

Esther Kim 4 collaborations

Joy Hollingsworth 4 collaborations

Robert Hutmacher 3 collaborations

John Vogel 3 collaborations

Yale Liu 3 collaborations

Paymann Harirchian 3 collaborations

Jaehyuk Choi 3 collaborations

Hector Roux de Bézieux 2 collaborations

Stephan Fischer 2 collaborations

Rebecca Chance 2 collaborations

Jesse Gillis 2 collaborations

Grady Pierroz 2 collaborations

Hsin-Jung Chou 2 collaborations

Benjamin Cole 2 collaborations

William Torous 2 collaborations

John P Vogel 2 collaborations

Jeffery Dahlberg 2 collaborations

Christopher Cook 2 collaborations

Ashley Hailer 2 collaborations

Yanhong Shou 2 collaborations

Vasanth Singan 2 collaborations

Theodora M Mauro 2 collaborations

Tina Bhutani 2 collaborations

Stephen C Benz 2 collaborations

Mark Taylor 2 collaborations

Ashley A Hailer 2 collaborations

Roy C Grekin 2 collaborations

Zhaobin Dong 1 collaboration

Dawn Chiniquy 1 collaboration

Siwen Deng 1 collaboration

Spencer Diamond 1 collaboration

Tuesday Simmons 1 collaboration

Heidi M-L Wipf 1 collaboration

Daniel Caddell 1 collaboration

Mary A Madera 1 collaboration

Adam Deutschbauer 1 collaboration

Mary Lou Guerinot 1 collaboration

Jillian F Banfield 1 collaboration

David H Brann 1 collaboration

Tatsuya Tsukahara 1 collaboration

Caleb Weinreb 1 collaboration

Marcela Lipovsek 1 collaboration

Iain C Macaulay 1 collaboration

Russell B Fletcher 1 collaboration

Diya Das 1 collaboration

Hector Roux de Bezieux 1 collaboration

Yoon-Gi Choi 1 collaboration

Jonathan Mill 1 collaboration

Ralph Abi Hachem 1 collaboration

Hiroaki Matsunami 1 collaboration

Darren W Logan 1 collaboration

Bradley J Goldstein 1 collaboration

Matthew S Grubb 1 collaboration

Sandeep Robert Datta 1 collaboration

Pierre-Emmanuel Courty 1 collaboration

Michael B Cole 1 collaboration

Allon Wagner 1 collaboration

David DeTomaso 1 collaboration

Nir Yosef 1 collaboration

Yun Zhou 1 collaboration

Zizhen Yao 1 collaboration

Hanqing Liu 1 collaboration

Fangming Xie 1 collaboration

Ricky S Adkins 1 collaboration

Andrew I Aldridge 1 collaboration

Seth A Ament 1 collaboration

Anna Bartlett 1 collaboration

M Margarita Behrens 1 collaboration

Darren Bertagnolli 1 collaboration

Tommaso Biancalani 1 collaboration

A Sina Booeshaghi 1 collaboration

Héctor Corrada Bravo 1 collaboration

Tamara Casper 1 collaboration

Carlo Colantuoni 1 collaboration

Jonathan Crabtree 1 collaboration

Heather Creasy 1 collaboration

Kirsten Crichton 1 collaboration

Megan Crow 1 collaboration

Nick Dee 1 collaboration

Elizabeth L Dougherty 1 collaboration

Wayne I Doyle 1 collaboration

Rongxin Fang 1 collaboration

Victor Felix 1 collaboration

Olivia Fong 1 collaboration

Michelle Giglio 1 collaboration

Jeff Goldy 1 collaboration

Mike Hawrylycz 1 collaboration

Brian R Herb 1 collaboration

Ronna Hertzano 1 collaboration

Xiaomeng Hou 1 collaboration

Qiwen Hu 1 collaboration

Jayaram Kancherla 1 collaboration

Matthew Kroll 1 collaboration

Kanan Lathia 1 collaboration

Yang Eric Li 1 collaboration

Jacinta D Lucero 1 collaboration

Chongyuan Luo 1 collaboration

Anup Mahurkar 1 collaboration

Delissa McMillen 1 collaboration

Naeem M Nadaf 1 collaboration

Joseph R Nery 1 collaboration

Thuc Nghi Nguyen 1 collaboration

Sheng-Yong Niu 1 collaboration

Vasilis Ntranos 1 collaboration

Joshua Orvis 1 collaboration

Julia K Osteen 1 collaboration

Thanh Pham 1 collaboration

Antonio Pinto-Duarte 1 collaboration

Olivier Poirion 1 collaboration

Sebastian Preissl 1 collaboration

Christine Rimorin 1 collaboration

Angeline C Rivkin 1 collaboration

Kimberly Smith 1 collaboration

Josef Sulc 1 collaboration

Valentine Svensson 1 collaboration

Michael Tieu 1 collaboration

Amy Torkelson 1 collaboration

Herman Tung 1 collaboration

Eeshit Dhaval Vaishnav 1 collaboration

Charles R Vanderburg 1 collaboration

Cindy van Velthoven 1 collaboration

Xinxin Wang 1 collaboration

Owen R White 1 collaboration

Z Josh Huang 1 collaboration

Peter V Kharchenko 1 collaboration

Lior Pachter 1 collaboration

Aviv Regev 1 collaboration

Bosiljka Tasic 1 collaboration

Joshua D Welch 1 collaboration

Evan Z Macosko 1 collaboration

Bing Ren 1 collaboration

Joseph R Ecker 1 collaboration

Hongkui Zeng 1 collaboration

Eran A Mukamel 1 collaboration

Tess Scavuzzo-Duggan 1 collaboration

Michael Belcher 1 collaboration

Jasmine Ortega 1 collaboration

Peggy Lemaux 1 collaboration

Henrik V Scheller 1 collaboration

Stephanie C Hicks 1 collaboration

Ruoxi Liu 1 collaboration

Yuwei Ni 1 collaboration

Divya Kunda 1 collaboration

Whitney Heavner 1 collaboration

Mark A Taylor 1 collaboration

Arsil Sadik 1 collaboration

Christopher R Baker 1 collaboration

Dhruv Patel 1 collaboration

Tim Jeffers 1 collaboration

Julie Sievert 1 collaboration

Yuko Yoshinaga 1 collaboration

Judith A Owiti 1 collaboration

Vasanth R Singan 1 collaboration

Stephanie DeGraaf 1 collaboration

Matthew J Blow 1 collaboration

Maria J Harrison 1 collaboration

Axel Visel 1 collaboration

Christer Jansson 1 collaboration

Krishna K Niyogi 1 collaboration

Ronan C O'Malley 1 collaboration

Jerry Lee 1 collaboration

Stephanie Hilz 1 collaboration

Andrew J Sedgewick 1 collaboration

Bethany E Perez White 1 collaboration

Michael J Kesling 1 collaboration

Thaddeus Mully 1 collaboration

Justin Golovato 1 collaboration

Matthew Gray 1 collaboration

Esther A Kim 1 collaboration

Hani Sbitany 1 collaboration

Charles J Vaske 1 collaboration

Alejandra Martínez-Berdeja 1 collaboration

Zijun Zhao 1 collaboration

Ruby Ghadially 1 collaboration

Roberto R Ricardo-Gonzalez 1 collaboration

Liang Chen 1 collaboration

Christopher P Cook 1 collaboration

Ralf Schmidt 1 collaboration

Andrew Sedgewick 1 collaboration

Sakeen W Kashem 1 collaboration

Timothy C McCalmont 1 collaboration

Alexander Marson 1 collaboration

Silvia B V Ramos 1 collaboration

David Wu 1 collaboration

Sijia Wang 1 collaboration

Michelle Yuan 1 collaboration

Jamie Chan 1 collaboration

Abdullah El Kurdi 1 collaboration

David Han 1 collaboration

Hira Ali 1 collaboration

Blaize D'Angio 1 collaboration

Aaron Mayer 1 collaboration

Maha Rahim 1 collaboration

Ayano Kondo 1 collaboration

Daniel Klufas 1 collaboration

A Hunter Shain 1 collaboration

Gregory Simpson 1 collaboration

Roberto Ricardo-Gonzalez 1 collaboration