Katherine Rothamel

Affiliations

Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.

Publications (12)

Discovery of Widespread Host Protein Interactions with the Pre-replicated Genome of CHIKV Using VIR-CLASP.

Molecular cell

Avec: Byungil Kim , Sarah Arcos , Katherine Rothamel , Jeffrey Jian , Kristie L Rose , W Hayes McDonald , Yuqi Bian , Seth Reasoner , Nicholas J Barrows , Shelton Bradrick , Mariano A Garcia-Blanco , Manuel Ascano

Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions.

Research square

Avec: Joy S Xiang , Jasmine R Mueller , En-Ching Luo , Brian A Yee , Danielle Schafer , Jonathan C Schmok , Frederick E Tan , Katherine Rothamel , Rachael N McVicar , Elizabeth M Kwong , Ben A Croker , Krysten L Jones , Hsuan-Lin Her , Chun-Yuan Chen , Anthony Q Vu , Wenhao Jin , Samuel S Park , Phuong Le , Kristopher W Brannan , Eric R Kofman , Yanhua Li , Alexandra T Tankka , Kevin D Dong , Yan Song , Alex E Clark , Aaron F Carlin , Eric L Van Nostrand , Sandra L Leibel , Gene W Yeo

Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP.

Nature methods

Avec: Daniel A Lorenz , Hsuan-Lin Her , Kylie A Shen , Katie Rothamel , Kasey R Hutt , Allan C Nojadera , Stephanie C Bruns , Sergei A Manakov , Brian A Yee , Karen B Chapman , Gene W Yeo

HydRA: Deep-learning models for predicting RNA-binding capacity from protein interaction association context and protein sequence.

Molecular cell

Avec: Wenhao Jin , Kristopher W Brannan , Katannya Kapeli , Samuel S Park , Hui Qing Tan , Maya L Gosztyla , Mayuresh Mujumdar , Joshua Ahdout , Bryce Henroid , Katherine Rothamel , Joy S Xiang , Limsoon Wong , Gene W Yeo

Viral crosslinking and solid-phase purification enables discovery of ribonucleoprotein complexes on incoming RNA virus genomes.

Nature protocols

Avec: Byungil Kim , Sarah Arcos , Katherine Rothamel , Manuel Ascano

RNA Binding Proteins as Pioneer Determinants of Infection: Protective, Proviral, or Both?

Viruses

Avec: Samantha Lisy , Katherine Rothamel , Manuel Ascano

Large-scale map of RNA binding protein interactomes across the mRNA life-cycle.

bioRxiv : the preprint server for biology

Avec: Lena Street , Katherine Rothamel , Kristopher Brannan , Wenhao Jin , Benjamin Bokor , Kevin Dong , Kevin Rhine , Assael Madrigal , Norah Al-Azzam , Jenny Kim Kim , Yanzhe Ma , Ahmed Abdou , Erica Wolin , Ella Doron-Mandel , Joshua Ahdout , Mayuresh Mujumdar , Marko Jovanovic , Gene W Yeo

Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions.

bioRxiv : the preprint server for biology

Avec: Joy S Xiang , Jasmine R Mueller , En-Ching Luo , Brian A Yee , Danielle Schafer , Jonathan C Schmok , Frederick E Tan , Katherine Rothamel , Rachael N McVicar , Elizabeth M Kwong , Krysten L Jones , Hsuan-Lin Her , Chun-Yuan Chen , Anthony Q Vu , Wenhao Jin , Samuel S Park , Phuong Le , Kristopher W Brannan , Eric R Kofman , Yanhua Li , Alexandra T Tankka , Kevin D Dong , Yan Song , Aaron F Carlin , Eric L Van Nostrand , Sandra L Leibel , Gene W Yeo

Proteomic discovery of chemical probes that perturb protein complexes in human cells.

Molecular cell

Avec: Michael R Lazear , Jarrett R Remsberg , Martin G Jaeger , Katherine Rothamel , Hsuan-Lin Her , Kristen E DeMeester , Evert Njomen , Simon J Hogg , Jahan Rahman , Landon R Whitby , Sang Joon Won , Michael A Schafroth , Daisuke Ogasawara , Minoru Yokoyama , Garrett L Lindsey , Haoxin Li , Jason Germain , Sabrina Barbas , Joan Vaughan , Thomas W Hanigan , Vincent F Vartabedian , Christopher J Reinhardt , Melissa M Dix , Seong Joo Koo , Inha Heo , John R Teijaro , Gabriel M Simon , Brahma Ghosh , Omar Abdel-Wahab , Kay Ahn , Alan Saghatelian , Bruno Melillo , Stuart L Schreiber , Gene W Yeo , Benjamin F Cravatt

ELAVL1 primarily couples mRNA stability with the 3' UTRs of interferon-stimulated genes.

Cell reports

Avec: Katherine Rothamel , Sarah Arcos , Byungil Kim , Clara Reasoner , Samantha Lisy , Neelanjan Mukherjee , Manuel Ascano

PAR-dCLIP: Enabling detection of RNA binding protein target transcripts bound at 5' termini through the incorporation of a decapping step.

Methods in enzymology

Avec: Samantha Lisy , Katherine Rothamel , Yelena Perevalova-Pinzul , Manuel Ascano

The YTHDF Proteins Shape the Brain Gene Signatures of Alzheimer's Disease.

bioRxiv : the preprint server for biology

Avec: Shinya Tasaki , Denis R Avey , Nicola A Kearns , Artemis Iatrou , Chunjiang Yu , Sashini De Tissera , Himanshu Vyas , Jishu Xu , Daniel J Flood , Katherine Rothamel , Aliza P Wingo , Thomas S Wingo , Nicholas T Seyfried , Philip L De Jager , Gene Yeo , Chris Gaiteri , David A Bennett , Yanling Wang

Réseau de co-auteurs

Gene W Yeo 6 collaborations

Manuel Ascano 5 collaborations

Hsuan-Lin Her 4 collaborations

Wenhao Jin 4 collaborations

Byungil Kim 3 collaborations

Sarah Arcos 3 collaborations

Joy S Xiang 3 collaborations

Brian A Yee 3 collaborations

Samuel S Park 3 collaborations

Kristopher W Brannan 3 collaborations

Samantha Lisy 3 collaborations

Jasmine R Mueller 2 collaborations

En-Ching Luo 2 collaborations

Danielle Schafer 2 collaborations

Jonathan C Schmok 2 collaborations

Frederick E Tan 2 collaborations

Rachael N McVicar 2 collaborations

Elizabeth M Kwong 2 collaborations

Krysten L Jones 2 collaborations

Chun-Yuan Chen 2 collaborations

Anthony Q Vu 2 collaborations

Phuong Le 2 collaborations

Eric R Kofman 2 collaborations

Yanhua Li 2 collaborations

Alexandra T Tankka 2 collaborations

Kevin D Dong 2 collaborations

Yan Song 2 collaborations

Aaron F Carlin 2 collaborations

Eric L Van Nostrand 2 collaborations

Sandra L Leibel 2 collaborations

Mayuresh Mujumdar 2 collaborations

Joshua Ahdout 2 collaborations

Jeffrey Jian 1 collaboration

Kristie L Rose 1 collaboration

W Hayes McDonald 1 collaboration

Yuqi Bian 1 collaboration

Seth Reasoner 1 collaboration

Nicholas J Barrows 1 collaboration

Shelton Bradrick 1 collaboration

Mariano A Garcia-Blanco 1 collaboration

Ben A Croker 1 collaboration

Alex E Clark 1 collaboration

Daniel A Lorenz 1 collaboration

Kylie A Shen 1 collaboration

Katie Rothamel 1 collaboration

Kasey R Hutt 1 collaboration

Allan C Nojadera 1 collaboration

Stephanie C Bruns 1 collaboration

Sergei A Manakov 1 collaboration

Karen B Chapman 1 collaboration

Katannya Kapeli 1 collaboration

Hui Qing Tan 1 collaboration

Maya L Gosztyla 1 collaboration

Bryce Henroid 1 collaboration

Limsoon Wong 1 collaboration

Lena Street 1 collaboration

Kristopher Brannan 1 collaboration

Benjamin Bokor 1 collaboration

Kevin Dong 1 collaboration

Kevin Rhine 1 collaboration

Assael Madrigal 1 collaboration

Norah Al-Azzam 1 collaboration

Jenny Kim Kim 1 collaboration

Yanzhe Ma 1 collaboration

Ahmed Abdou 1 collaboration

Erica Wolin 1 collaboration

Ella Doron-Mandel 1 collaboration

Marko Jovanovic 1 collaboration

Michael R Lazear 1 collaboration

Jarrett R Remsberg 1 collaboration

Martin G Jaeger 1 collaboration

Kristen E DeMeester 1 collaboration

Evert Njomen 1 collaboration

Simon J Hogg 1 collaboration

Jahan Rahman 1 collaboration

Landon R Whitby 1 collaboration

Sang Joon Won 1 collaboration

Michael A Schafroth 1 collaboration

Daisuke Ogasawara 1 collaboration

Minoru Yokoyama 1 collaboration

Garrett L Lindsey 1 collaboration

Haoxin Li 1 collaboration

Jason Germain 1 collaboration

Sabrina Barbas 1 collaboration

Joan Vaughan 1 collaboration

Thomas W Hanigan 1 collaboration

Vincent F Vartabedian 1 collaboration

Christopher J Reinhardt 1 collaboration

Melissa M Dix 1 collaboration

Seong Joo Koo 1 collaboration

Inha Heo 1 collaboration

John R Teijaro 1 collaboration

Gabriel M Simon 1 collaboration

Brahma Ghosh 1 collaboration

Omar Abdel-Wahab 1 collaboration

Kay Ahn 1 collaboration

Alan Saghatelian 1 collaboration

Bruno Melillo 1 collaboration

Stuart L Schreiber 1 collaboration

Benjamin F Cravatt 1 collaboration

Clara Reasoner 1 collaboration

Neelanjan Mukherjee 1 collaboration

Yelena Perevalova-Pinzul 1 collaboration

Shinya Tasaki 1 collaboration

Denis R Avey 1 collaboration

Nicola A Kearns 1 collaboration

Artemis Iatrou 1 collaboration

Chunjiang Yu 1 collaboration

Sashini De Tissera 1 collaboration

Himanshu Vyas 1 collaboration

Jishu Xu 1 collaboration

Daniel J Flood 1 collaboration

Aliza P Wingo 1 collaboration

Thomas S Wingo 1 collaboration

Nicholas T Seyfried 1 collaboration

Philip L De Jager 1 collaboration

Gene Yeo 1 collaboration

Chris Gaiteri 1 collaboration

David A Bennett 1 collaboration

Yanling Wang 1 collaboration