Nicolae Sapoval

Affiliations

Department of Computer Science, Rice University, Houston, TX, USA.

Publications (21)

Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission.

bioRxiv : the preprint server for biology

Avec: Medhat Mahmoud , Michael D Jochum , Yunxi Liu , R A Leo Elworth , Qi Wang , Dreycey Albin , Huw Ogilvie , Michael D Lee , Sonia Villapol , Kyle M Hernandez , Irina Maljkovic Berry , Jonathan Foox , Afshin Beheshti , Krista Ternus , Kjersti M Aagaard , David Posada , Christopher E Mason , Fritz Sedlazeck , Todd J Treangen

Comprehensive Multi-omics Analysis Reveals Mitochondrial Stress as a Central Biological Hub for Spaceflight Impact.

Cell

Avec: Willian A da Silveira , Hossein Fazelinia , Sara Brin Rosenthal , Evagelia C Laiakis , Man S Kim , Cem Meydan , Yared Kidane , Komal S Rathi , Scott M Smith , Benjamin Stear , Yue Ying , Yuanchao Zhang , Jonathan Foox , Susana Zanello , Brian Crucian , Dong Wang , Adrienne Nugent , Helio A Costa , Sara R Zwart , Sonja Schrepfer , R A Leo Elworth , Todd Treangen , Matthew MacKay , Nandan S Gokhale , Stacy M Horner , Larry N Singh , Douglas C Wallace , Jeffrey S Willey , Jonathan C Schisler , Robert Meller , J Tyson McDonald , Kathleen M Fisch , Gary Hardiman , Deanne Taylor , Christopher E Mason , Sylvain V Costes , Afshin Beheshti

Lightweight taxonomic profiling of long-read sequenced metagenomes with Lemur and Magnet.

bioRxiv : the preprint server for biology

Avec: Yunxi Liu , Kristen Curry , Bryce Kille , Wenyu Huang , Natalie Kokroko , Michael G Nute , Alona Tyshaieva , Alexander T Dilthey , Erin Molloy , Todd J Treangen

Role of miR-2392 in driving SARS-CoV-2 infection.

Cell reports

Avec: J Tyson McDonald , Francisco J Enguita , Deanne Taylor , Robert J Griffin , Waldemar Priebe , Mark R Emmett , Mohammad M Sajadi , Anthony D Harris , Jean Clement , Joseph M Dybas , Nukhet Aykin-Burns , Joseph W Guarnieri , Larry N Singh , Peter Grabham , Stephen B Baylin , Aliza Yousey , Andrea N Pearson , Peter M Corry , Amanda Saravia-Butler , Thomas R Aunins , Sadhana Sharma , Prashant Nagpal , Cem Meydan , Jonathan Foox , Christopher Mozsary , Bianca Cerqueira , Viktorija Zaksas , Urminder Singh , Eve Syrkin Wurtele , Sylvain V Costes , Gustavo Gastão Davanzo , Diego Galeano , Alberto Paccanaro , Suzanne L Meinig , Robert S Hagan , Natalie M Bowman , Auteur inconnu , Matthew C Wolfgang , Selin Altinok , Todd J Treangen , Pedro M Moraes-Vieira , Charles Vanderburg , Douglas C Wallace , Jonathan C Schisler , Christopher E Mason , Anushree Chatterjee , Robert Meller , Afshin Beheshti

SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission.

Genome research

Avec: Medhat Mahmoud , Michael D Jochum , Yunxi Liu , R A Leo Elworth , Qi Wang , Dreycey Albin , Huw A Ogilvie , Michael D Lee , Sonia Villapol , Kyle M Hernandez , Irina Maljkovic Berry , Jonathan Foox , Afshin Beheshti , Krista Ternus , Kjersti M Aagaard , David Posada , Christopher E Mason , Fritz J Sedlazeck , Todd J Treangen

KOMB: K-core based de novo characterization of copy number variation in microbiomes.

Computational and structural biotechnology journal

Avec: Advait Balaji , Charlie Seto , R A Leo Elworth , Yilei Fu , Michael G Nute , Tor Savidge , Santiago Segarra , Todd J Treangen

An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates.

F1000Research

Avec: Ann M Mc Cartney , Medhat Mahmoud , Michael Jochum , Daniel Paiva Agustinho , Barry Zorman , Ahmad Al Khleifat , Fawaz Dabbaghie , Rupesh K Kesharwani , Moritz Smolka , Moez Dawood , Dreycey Albin , Elbay Aliyev , Hakeem Almabrazi , Ahmed Arslan , Advait Balaji , Sairam Behera , Kimberley Billingsley , Daniel L Cameron , Joyjit Daw , Eric T Dawson , Wouter De Coster , Haowei Du , Christopher Dunn , Rocio Esteban , Angad Jolly , Divya Kalra , Chunxiao Liao , Yunxi Liu , Tsung-Yu Lu , James M Havrilla , Michael M Khayat , Maximillian Marin , Jean Monlong , Stephen Price , Alejandro Rafael Gener , Jingwen Ren , Sagayamary Sagayaradj , Claude Sinner , Daniela C Soto , Arda Soylev , Arun Subramaniyan , Najeeb Syed , Neha Tadimeti , Pamella Tater , Pankaj Vats , Justin Vaughn , Kimberly Walker , Gaojianyong Wang , Qiandong Zeng , Shangzhe Zhang , Tingting Zhao , Bryce Kille , Evan Biederstedt , Mark Chaisson , Adam English , Zev Kronenberg , Todd J Treangen , Timothy Hefferon , Chen-Shan Chin , Ben Busby , Fritz J Sedlazeck

Accelerating SARS-CoV-2 low frequency variant calling on ultra deep sequencing datasets.

ArXiv

Avec: Bryce Kille , Yunxi Liu , Michael Nute , Lawrence Rauchwerger , Nancy Amato , Todd J Treangen

Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters.

Virus evolution

Avec: Pilar Gallego-García , Nair Varela , Nuria Estévez-Gómez , Loretta De Chiara , Iria Fernández-Silva , Diana Valverde , Todd J Treangen , Benito Regueiro , Jorge Julio Cabrera-Alvargonzález , Víctor Del Campo , Sonia Pérez , David Posada

Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens.

Nature communications

Avec: Michael X Wang , Esther G Lou , Eddie Kim , Prashant Kalvapalle , Bryce Kille , R A Leo Elworth , Yunxi Liu , Yilei Fu , Lauren B Stadler , Todd J Treangen

The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms.

F1000Research

Avec: Kimberly Walker , Divya Kalra , Rebecca Lowdon , Guangyi Chen , David Molik , Daniela C Soto , Fawaz Dabbaghie , Ahmad Al Khleifat , Medhat Mahmoud , Luis F Paulin , Muhammad Sohail Raza , Susanne P Pfeifer , Daniel Paiva Agustinho , Elbay Aliyev , Pavel Avdeyev , Enrico R Barrozo , Sairam Behera , Kimberley Billingsley , Li Chuin Chong , Deepak Choubey , Wouter De Coster , Yilei Fu , Alejandro R Gener , Timothy Hefferon , David Morgan Henke , Wolfram Höps , Anastasia Illarionova , Michael D Jochum , Maria Jose , Rupesh K Kesharwani , Sree Rohit Raj Kolora , Jędrzej Kubica , Priya Lakra , Damaris Lattimer , Chia-Sin Liew , Bai-Wei Lo , Chunhsuan Lo , Anneri Lötter , Sina Majidian , Suresh Kumar Mendem , Rajarshi Mondal , Hiroko Ohmiya , Nasrin Parvin , Carolina Peralta , Chi-Lam Poon , Ramanandan Prabhakaran , Marie Saitou , Aditi Sammi , Philippe Sanio , Najeeb Syed , Todd Treangen , Gaojianyong Wang , Tiancheng Xu , Jianzhi Yang , Shangzhe Zhang , Weiyu Zhou , Fritz J Sedlazeck , Ben Busby

KombOver: Efficient k-core and K-truss based characterization of perturbations within the human gut microbiome.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

Avec: Marko Tanevski , Todd J Treangen

The Great Deceiver: miR-2392's Hidden Role in Driving SARS-CoV-2 Infection.

bioRxiv : the preprint server for biology

Avec: J Tyson McDonald , Francisco Javier Enguita , Deanne Taylor , Robert J Griffin , Waldemar Priebe , Mark R Emmett , Mohammad M Sajadi , Anthony D Harris , Jean Clement , Joseph M Dybas , Nukhet Aykin-Burns , Joseph W Guarnieri , Larry N Singh , Peter Grabham , Stephen B Baylin , Aliza Yousey , Andrea N Pearson , Peter M Corry , Amanda Saravia-Butler , Thomas R Aunins , Sadhana Sharma , Prashant Nagpal , Cem Meydan , Jonathan Foox , Christopher Mozsary , Bianca Cerqueira , Viktorija Zaksas , Urminder Singh , Eve Syrkin Wurtele , Sylvain V Costes , Gustavo Gastão Davanzo , Diego Galeano , Alberto Paccanaro , Suzanne L Meinig , Robert S Hagan , Natalie M Bowman , Auteur inconnu , Matthew C Wolfgang , Selin Altinok , Todd J Treangen , Pedro M Moraes-Vieira , Charles Vanderburg , Douglas C Wallace , Jonathan Schisler , Christopher E Mason , Anushree Chatterjee , Robert Meller , Afshin Beheshti

Current progress and open challenges for applying deep learning across the biosciences.

Nature communications

Avec: Amirali Aghazadeh , Michael G Nute , Dinler A Antunes , Advait Balaji , Richard Baraniuk , C J Barberan , Ruth Dannenfelser , Chen Dun , Mohammadamin Edrisi , R A Leo Elworth , Bryce Kille , Anastasios Kyrillidis , Luay Nakhleh , Cameron R Wolfe , Zhi Yan , Vicky Yao , Todd J Treangen

Direct comparison of RT-ddPCR and targeted amplicon sequencing for SARS-CoV-2 mutation monitoring in wastewater.

The Science of the total environment

Avec: Esther G Lou , Camille McCall , Lauren Bauhs , Russell Carlson-Stadler , Prashant Kalvapalle , Yanlai Lai , Kyle Palmer , Ryker Penn , Whitney Rich , Madeline Wolken , Pamela Brown , Katherine B Ensor , Loren Hopkins , Todd J Treangen , Lauren B Stadler

Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater.

Nature communications

Avec: Yunxi Liu , Esther G Lou , Loren Hopkins , Katherine B Ensor , Rebecca Schneider , Lauren B Stadler , Todd J Treangen

Crykey: Rapid Identification of SARS-CoV-2 Cryptic Mutations in Wastewater.

medRxiv : the preprint server for health sciences

Avec: Yunxi Liu , Pilar Gallego-García , Laura Tomás , David Posada , Todd J Treangen , Lauren B Stadler

Crykey: Rapid identification of SARS-CoV-2 cryptic mutations in wastewater.

Nature communications

Avec: Yunxi Liu , Pilar Gallego-García , Laura Tomás , David Posada , Todd J Treangen , Lauren B Stadler

Infectious Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Exhaled Aerosols and Efficacy of Masks During Early Mild Infection.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Avec: Oluwasanmi O Adenaiye , Jianyu Lai , P Jacob Bueno de Mesquita , Filbert Hong , Somayeh Youssefi , Jennifer German , S H Sheldon Tai , Barbara Albert , Maria Schanz , Stuart Weston , Jun Hang , Christian Fung , Hye Kyung Chung , Kristen K Coleman , Todd Treangen , Irina Maljkovic Berry , Kristin Mullins , Matthew Frieman , Tianzhou Ma , Donald K Milton

QuaID: Enabling Earlier Detection of Recently Emerged SARS-CoV-2 Variants of Concern in Wastewater.

medRxiv : the preprint server for health sciences

Avec: Yunxi Liu , Esther G Lou , Loren Hopkins , Katherine B Ensor , Rebecca Schneider , Lauren B Stadler , Todd J Treangen

Olivar: automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens.

bioRxiv : the preprint server for biology

Avec: Michael X Wang , Esther G Lou , Eddie Kim , Prashant Kalvapalle , Bryce Kille , R A Leo Elworth , Yunxi Liu , Yilei Fu , Lauren B Stadler , Todd J Treangen

Réseau de co-auteurs

Todd J Treangen 18 collaborations

Yunxi Liu 11 collaborations

R A Leo Elworth 7 collaborations

Lauren B Stadler 7 collaborations

Bryce Kille 6 collaborations

Jonathan Foox 5 collaborations

Afshin Beheshti 5 collaborations

David Posada 5 collaborations

Christopher E Mason 5 collaborations

Esther G Lou 5 collaborations

Medhat Mahmoud 4 collaborations

Yilei Fu 4 collaborations

Michael D Jochum 3 collaborations

Dreycey Albin 3 collaborations

Irina Maljkovic Berry 3 collaborations

Cem Meydan 3 collaborations

Todd Treangen 3 collaborations

Larry N Singh 3 collaborations

Douglas C Wallace 3 collaborations

Robert Meller 3 collaborations

J Tyson McDonald 3 collaborations

Deanne Taylor 3 collaborations

Sylvain V Costes 3 collaborations

Michael G Nute 3 collaborations

Fritz J Sedlazeck 3 collaborations

Advait Balaji 3 collaborations

Pilar Gallego-García 3 collaborations

Prashant Kalvapalle 3 collaborations

Katherine B Ensor 3 collaborations

Loren Hopkins 3 collaborations

Qi Wang 2 collaborations

Michael D Lee 2 collaborations

Sonia Villapol 2 collaborations

Kyle M Hernandez 2 collaborations

Krista Ternus 2 collaborations

Kjersti M Aagaard 2 collaborations

Jonathan C Schisler 2 collaborations

Robert J Griffin 2 collaborations

Waldemar Priebe 2 collaborations

Mark R Emmett 2 collaborations

Mohammad M Sajadi 2 collaborations

Anthony D Harris 2 collaborations

Jean Clement 2 collaborations

Joseph M Dybas 2 collaborations

Nukhet Aykin-Burns 2 collaborations

Joseph W Guarnieri 2 collaborations

Peter Grabham 2 collaborations

Stephen B Baylin 2 collaborations

Aliza Yousey 2 collaborations

Andrea N Pearson 2 collaborations

Peter M Corry 2 collaborations

Amanda Saravia-Butler 2 collaborations

Thomas R Aunins 2 collaborations

Sadhana Sharma 2 collaborations

Prashant Nagpal 2 collaborations

Christopher Mozsary 2 collaborations

Bianca Cerqueira 2 collaborations

Viktorija Zaksas 2 collaborations

Urminder Singh 2 collaborations

Eve Syrkin Wurtele 2 collaborations

Gustavo Gastão Davanzo 2 collaborations

Diego Galeano 2 collaborations

Alberto Paccanaro 2 collaborations

Suzanne L Meinig 2 collaborations

Robert S Hagan 2 collaborations

Natalie M Bowman 2 collaborations

None None 2 collaborations

Matthew C Wolfgang 2 collaborations

Selin Altinok 2 collaborations

Pedro M Moraes-Vieira 2 collaborations

Charles Vanderburg 2 collaborations

Anushree Chatterjee 2 collaborations

Daniel Paiva Agustinho 2 collaborations

Ahmad Al Khleifat 2 collaborations

Fawaz Dabbaghie 2 collaborations

Rupesh K Kesharwani 2 collaborations

Elbay Aliyev 2 collaborations

Sairam Behera 2 collaborations

Kimberley Billingsley 2 collaborations

Wouter De Coster 2 collaborations

Divya Kalra 2 collaborations

Daniela C Soto 2 collaborations

Najeeb Syed 2 collaborations

Kimberly Walker 2 collaborations

Gaojianyong Wang 2 collaborations

Shangzhe Zhang 2 collaborations

Timothy Hefferon 2 collaborations

Ben Busby 2 collaborations

Michael X Wang 2 collaborations

Eddie Kim 2 collaborations

Rebecca Schneider 2 collaborations

Laura Tomás 2 collaborations

Huw Ogilvie 1 collaboration

Fritz Sedlazeck 1 collaboration

Willian A da Silveira 1 collaboration

Hossein Fazelinia 1 collaboration

Sara Brin Rosenthal 1 collaboration

Evagelia C Laiakis 1 collaboration

Man S Kim 1 collaboration

Yared Kidane 1 collaboration

Komal S Rathi 1 collaboration

Scott M Smith 1 collaboration

Benjamin Stear 1 collaboration

Yue Ying 1 collaboration

Yuanchao Zhang 1 collaboration

Susana Zanello 1 collaboration

Brian Crucian 1 collaboration

Dong Wang 1 collaboration

Adrienne Nugent 1 collaboration

Helio A Costa 1 collaboration

Sara R Zwart 1 collaboration

Sonja Schrepfer 1 collaboration

Matthew MacKay 1 collaboration

Nandan S Gokhale 1 collaboration

Stacy M Horner 1 collaboration

Jeffrey S Willey 1 collaboration

Kathleen M Fisch 1 collaboration

Gary Hardiman 1 collaboration

Kristen Curry 1 collaboration

Wenyu Huang 1 collaboration

Natalie Kokroko 1 collaboration

Alona Tyshaieva 1 collaboration

Alexander T Dilthey 1 collaboration

Erin Molloy 1 collaboration

Francisco J Enguita 1 collaboration

Huw A Ogilvie 1 collaboration

Charlie Seto 1 collaboration

Tor Savidge 1 collaboration

Santiago Segarra 1 collaboration

Ann M Mc Cartney 1 collaboration

Michael Jochum 1 collaboration

Barry Zorman 1 collaboration

Moritz Smolka 1 collaboration

Moez Dawood 1 collaboration

Hakeem Almabrazi 1 collaboration

Ahmed Arslan 1 collaboration

Daniel L Cameron 1 collaboration

Joyjit Daw 1 collaboration

Eric T Dawson 1 collaboration

Haowei Du 1 collaboration

Christopher Dunn 1 collaboration

Rocio Esteban 1 collaboration

Angad Jolly 1 collaboration

Chunxiao Liao 1 collaboration

Tsung-Yu Lu 1 collaboration

James M Havrilla 1 collaboration

Michael M Khayat 1 collaboration

Maximillian Marin 1 collaboration

Jean Monlong 1 collaboration

Stephen Price 1 collaboration

Alejandro Rafael Gener 1 collaboration

Jingwen Ren 1 collaboration

Sagayamary Sagayaradj 1 collaboration

Claude Sinner 1 collaboration

Arda Soylev 1 collaboration

Arun Subramaniyan 1 collaboration

Neha Tadimeti 1 collaboration

Pamella Tater 1 collaboration

Pankaj Vats 1 collaboration

Justin Vaughn 1 collaboration

Qiandong Zeng 1 collaboration

Tingting Zhao 1 collaboration

Evan Biederstedt 1 collaboration

Mark Chaisson 1 collaboration

Adam English 1 collaboration

Zev Kronenberg 1 collaboration

Chen-Shan Chin 1 collaboration

Michael Nute 1 collaboration

Lawrence Rauchwerger 1 collaboration

Nancy Amato 1 collaboration

Nair Varela 1 collaboration

Nuria Estévez-Gómez 1 collaboration

Loretta De Chiara 1 collaboration

Iria Fernández-Silva 1 collaboration

Diana Valverde 1 collaboration

Benito Regueiro 1 collaboration

Jorge Julio Cabrera-Alvargonzález 1 collaboration

Víctor Del Campo 1 collaboration

Sonia Pérez 1 collaboration

Rebecca Lowdon 1 collaboration

Guangyi Chen 1 collaboration

David Molik 1 collaboration

Luis F Paulin 1 collaboration

Muhammad Sohail Raza 1 collaboration

Susanne P Pfeifer 1 collaboration

Pavel Avdeyev 1 collaboration

Enrico R Barrozo 1 collaboration

Li Chuin Chong 1 collaboration

Deepak Choubey 1 collaboration

Alejandro R Gener 1 collaboration

David Morgan Henke 1 collaboration

Wolfram Höps 1 collaboration

Anastasia Illarionova 1 collaboration

Maria Jose 1 collaboration

Sree Rohit Raj Kolora 1 collaboration

Jędrzej Kubica 1 collaboration

Priya Lakra 1 collaboration

Damaris Lattimer 1 collaboration

Chia-Sin Liew 1 collaboration

Bai-Wei Lo 1 collaboration

Chunhsuan Lo 1 collaboration

Anneri Lötter 1 collaboration

Sina Majidian 1 collaboration

Suresh Kumar Mendem 1 collaboration

Rajarshi Mondal 1 collaboration

Hiroko Ohmiya 1 collaboration

Nasrin Parvin 1 collaboration

Carolina Peralta 1 collaboration

Chi-Lam Poon 1 collaboration

Ramanandan Prabhakaran 1 collaboration

Marie Saitou 1 collaboration

Aditi Sammi 1 collaboration

Philippe Sanio 1 collaboration

Tiancheng Xu 1 collaboration

Jianzhi Yang 1 collaboration

Weiyu Zhou 1 collaboration

Marko Tanevski 1 collaboration

Francisco Javier Enguita 1 collaboration

Jonathan Schisler 1 collaboration

Amirali Aghazadeh 1 collaboration

Dinler A Antunes 1 collaboration

Richard Baraniuk 1 collaboration

C J Barberan 1 collaboration

Ruth Dannenfelser 1 collaboration

Chen Dun 1 collaboration

Mohammadamin Edrisi 1 collaboration

Anastasios Kyrillidis 1 collaboration

Luay Nakhleh 1 collaboration

Cameron R Wolfe 1 collaboration

Zhi Yan 1 collaboration

Vicky Yao 1 collaboration

Camille McCall 1 collaboration

Lauren Bauhs 1 collaboration

Russell Carlson-Stadler 1 collaboration

Yanlai Lai 1 collaboration

Kyle Palmer 1 collaboration

Ryker Penn 1 collaboration

Whitney Rich 1 collaboration

Madeline Wolken 1 collaboration

Pamela Brown 1 collaboration

Oluwasanmi O Adenaiye 1 collaboration

Jianyu Lai 1 collaboration

P Jacob Bueno de Mesquita 1 collaboration

Filbert Hong 1 collaboration

Somayeh Youssefi 1 collaboration

Jennifer German 1 collaboration

S H Sheldon Tai 1 collaboration

Barbara Albert 1 collaboration

Maria Schanz 1 collaboration

Stuart Weston 1 collaboration

Jun Hang 1 collaboration

Christian Fung 1 collaboration

Hye Kyung Chung 1 collaboration

Kristen K Coleman 1 collaboration

Kristin Mullins 1 collaboration

Matthew Frieman 1 collaboration

Tianzhou Ma 1 collaboration

Donald K Milton 1 collaboration