Accueil
Alaina Shumate
Alaina Shumate
Affiliations
Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America.
Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, United States of America.
ORCID: 0000-0002-4450-1857
Publications (15)
Improved transcriptome assembly using a hybrid of long and short reads with StringTie.
PLoS computational biology
Avec:
Alaina Shumate
,
Brandon Wong
,
Geo Pertea
,
Mihaela Pertea
LiftoffTools: a toolkit for comparing gene annotations mapped between genome assemblies.
F1000Research
Avec:
Alaina Shumate
,
Steven Salzberg
Evaluating Disaster Damages and Operational Status of Health-Care Facilities During the Emergency Response Phase of Hurricane Maria in Puerto Rico.
Disaster medicine and public health preparedness
Avec:
E A Irvin-Barnwell
,
M Cruz
,
C Maniglier-Poulet
,
J Cabrera
,
J Rivera Diaz
,
R De La Cruz Perez
,
C Forrester
,
A Shumate
,
J Mutter
,
L Graziano
,
L Rivera Gonzalez
,
J Malilay
,
M Raheem
Novel fluorescent GPCR biosensor detects retinal equilibrium binding to opsin and active G protein and arrestin signaling conformations.
The Journal of biological chemistry
Avec:
Christopher T Schafer
,
Anthony Shumate
,
David L Farrens
The complete sequence of a human Y chromosome.
Nature
Avec:
Arang Rhie
,
Sergey Nurk
,
Monika Cechova
,
Savannah J Hoyt
,
Dylan J Taylor
,
Nicolas Altemose
,
Paul W Hook
,
Sergey Koren
,
Mikko Rautiainen
,
Ivan A Alexandrov
,
Jamie Allen
,
Mobin Asri
,
Andrey V Bzikadze
,
Nae-Chyun Chen
,
Chen-Shan Chin
,
Mark Diekhans
,
Paul Flicek
,
Giulio Formenti
,
Arkarachai Fungtammasan
,
Carlos Garcia Giron
,
Erik Garrison
,
Ariel Gershman
,
Jennifer L Gerton
,
Patrick G S Grady
,
Andrea Guarracino
,
Leanne Haggerty
,
Reza Halabian
,
Nancy F Hansen
,
Robert Harris
,
Gabrielle A Hartley
,
William T Harvey
,
Marina Haukness
,
Jakob Heinz
,
Thibaut Hourlier
,
Robert M Hubley
,
Sarah E Hunt
,
Stephen Hwang
,
Miten Jain
,
Rupesh K Kesharwani
,
Alexandra P Lewis
,
Heng Li
,
Glennis A Logsdon
,
Julian K Lucas
,
Wojciech Makalowski
,
Christopher Markovic
,
Fergal J Martin
,
Ann M Mc Cartney
,
Rajiv C McCoy
,
Jennifer McDaniel
,
Brandy M McNulty
,
Paul Medvedev
,
Alla Mikheenko
,
Katherine M Munson
,
Terence D Murphy
,
Hugh E Olsen
,
Nathan D Olson
,
Luis F Paulin
,
David Porubsky
,
Tamara Potapova
,
Fedor Ryabov
,
Steven L Salzberg
,
Michael E G Sauria
,
Fritz J Sedlazeck
,
Kishwar Shafin
,
Valery A Shepelev
,
Alaina Shumate
,
Jessica M Storer
,
Likhitha Surapaneni
,
Angela M Taravella Oill
,
Françoise Thibaud-Nissen
,
Winston Timp
,
Marta Tomaszkiewicz
,
Mitchell R Vollger
,
Brian P Walenz
,
Allison C Watwood
,
Matthias H Weissensteiner
,
Aaron M Wenger
,
Melissa A Wilson
,
Samantha Zarate
,
Yiming Zhu
,
Justin M Zook
,
Evan E Eichler
,
Rachel J O'Neill
,
Michael C Schatz
,
Karen H Miga
,
Kateryna D Makova
,
Adam M Phillippy
CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure.
Genome biology
Avec:
Ales Varabyou
,
Markus J Sommer
,
Beril Erdogdu
,
Ida Shinder
,
Ilia Minkin
,
Kuan-Hao Chao
,
Sukhwan Park
,
Jakob Heinz
,
Christopher Pockrandt
,
Alaina Shumate
,
Natalia Rincon
,
Daniela Puiu
,
Martin Steinegger
,
Steven L Salzberg
,
Mihaela Pertea
Chromosome-Scale Assembly of the Bread Wheat Genome Reveals Thousands of Additional Gene Copies.
Genetics
Avec:
Michael Alonge
,
Alaina Shumate
,
Daniela Puiu
,
Aleksey V Zimin
,
Steven L Salzberg
Assembly and annotation of an Ashkenazi human reference genome.
Genome biology
Avec:
Alaina Shumate
,
Aleksey V Zimin
,
Rachel M Sherman
,
Daniela Puiu
,
Justin M Wagner
,
Nathan D Olson
,
Mihaela Pertea
,
Marc L Salit
,
Justin M Zook
,
Steven L Salzberg
Liftoff: accurate mapping of gene annotations.
Bioinformatics (Oxford, England)
Avec:
Alaina Shumate
,
Steven L Salzberg
Curated variation benchmarks for challenging medically relevant autosomal genes.
Nature biotechnology
Avec:
Justin Wagner
,
Nathan D Olson
,
Lindsay Harris
,
Jennifer McDaniel
,
Haoyu Cheng
,
Arkarachai Fungtammasan
,
Yih-Chii Hwang
,
Richa Gupta
,
Aaron M Wenger
,
William J Rowell
,
Ziad M Khan
,
Jesse Farek
,
Yiming Zhu
,
Aishwarya Pisupati
,
Medhat Mahmoud
,
Chunlin Xiao
,
Byunggil Yoo
,
Sayed Mohammad Ebrahim Sahraeian
,
Danny E Miller
,
David Jáspez
,
José M Lorenzo-Salazar
,
Adrián Muñoz-Barrera
,
Luis A Rubio-Rodríguez
,
Carlos Flores
,
Giuseppe Narzisi
,
Uday Shanker Evani
,
Wayne E Clarke
,
Joyce Lee
,
Christopher E Mason
,
Stephen E Lincoln
,
Karen H Miga
,
Mark T W Ebbert
,
Alaina Shumate
,
Heng Li
,
Chen-Shan Chin
,
Justin M Zook
,
Fritz J Sedlazeck
Epigenetic patterns in a complete human genome.
Science (New York, N.Y.)
Avec:
Ariel Gershman
,
Michael E G Sauria
,
Xavi Guitart
,
Mitchell R Vollger
,
Paul W Hook
,
Savannah J Hoyt
,
Miten Jain
,
Alaina Shumate
,
Roham Razaghi
,
Sergey Koren
,
Nicolas Altemose
,
Gina V Caldas
,
Glennis A Logsdon
,
Arang Rhie
,
Evan E Eichler
,
Michael C Schatz
,
Rachel J O'Neill
,
Adam M Phillippy
,
Karen H Miga
,
Winston Timp
Combining DNA and protein alignments to improve genome annotation with LiftOn.
bioRxiv : the preprint server for biology
Avec:
Kuan-Hao Chao
,
Jakob M Heinz
,
Celine Hoh
,
Alan Mao
,
Alaina Shumate
,
Mihaela Pertea
,
Steven L Salzberg
Functional integrity of membrane protein rhodopsin solubilized by styrene-maleic acid copolymer.
Biophysical journal
Avec:
Stephanie G Pitch
,
Weekie Yao
,
Istvan Szundi
,
Jonathan Fay
,
Eefei Chen
,
Anthony Shumate
,
David S Kliger
,
David L Farrens
The genome of the American groundhog,
F1000Research
Avec:
Daniela Puiu
,
Aleksey Zimin
,
Alaina Shumate
,
Yuchen Ge
,
Jiabin Qiu
,
Manoj Bhaskaran
,
Steven L Salzberg
A reference-quality, fully annotated genome from a Puerto Rican individual.
Genetics
Avec:
Aleksey V Zimin
,
Alaina Shumate
,
Ida Shinder
,
Jakob Heinz
,
Daniela Puiu
,
Mihaela Pertea
,
Steven L Salzberg
Réseau de co-auteurs
Steven L Salzberg
8 collaborations
Mihaela Pertea
5 collaborations
Daniela Puiu
5 collaborations
Jakob Heinz
3 collaborations
Nathan D Olson
3 collaborations
Justin M Zook
3 collaborations
Karen H Miga
3 collaborations
Aleksey V Zimin
3 collaborations
Anthony Shumate
2 collaborations
David L Farrens
2 collaborations
Arang Rhie
2 collaborations
Savannah J Hoyt
2 collaborations
Nicolas Altemose
2 collaborations
Paul W Hook
2 collaborations
Sergey Koren
2 collaborations
Chen-Shan Chin
2 collaborations
Arkarachai Fungtammasan
2 collaborations
Ariel Gershman
2 collaborations
Miten Jain
2 collaborations
Heng Li
2 collaborations
Glennis A Logsdon
2 collaborations
Jennifer McDaniel
2 collaborations
Michael E G Sauria
2 collaborations
Fritz J Sedlazeck
2 collaborations
Winston Timp
2 collaborations
Mitchell R Vollger
2 collaborations
Aaron M Wenger
2 collaborations
Yiming Zhu
2 collaborations
Evan E Eichler
2 collaborations
Rachel J O'Neill
2 collaborations
Michael C Schatz
2 collaborations
Adam M Phillippy
2 collaborations
Ida Shinder
2 collaborations
Kuan-Hao Chao
2 collaborations
Brandon Wong
1 collaboration
Geo Pertea
1 collaboration
Steven Salzberg
1 collaboration
E A Irvin-Barnwell
1 collaboration
M Cruz
1 collaboration
C Maniglier-Poulet
1 collaboration
J Cabrera
1 collaboration
J Rivera Diaz
1 collaboration
R De La Cruz Perez
1 collaboration
C Forrester
1 collaboration
A Shumate
1 collaboration
J Mutter
1 collaboration
L Graziano
1 collaboration
L Rivera Gonzalez
1 collaboration
J Malilay
1 collaboration
M Raheem
1 collaboration
Christopher T Schafer
1 collaboration
Sergey Nurk
1 collaboration
Monika Cechova
1 collaboration
Dylan J Taylor
1 collaboration
Mikko Rautiainen
1 collaboration
Ivan A Alexandrov
1 collaboration
Jamie Allen
1 collaboration
Mobin Asri
1 collaboration
Andrey V Bzikadze
1 collaboration
Nae-Chyun Chen
1 collaboration
Mark Diekhans
1 collaboration
Paul Flicek
1 collaboration
Giulio Formenti
1 collaboration
Carlos Garcia Giron
1 collaboration
Erik Garrison
1 collaboration
Jennifer L Gerton
1 collaboration
Patrick G S Grady
1 collaboration
Andrea Guarracino
1 collaboration
Leanne Haggerty
1 collaboration
Reza Halabian
1 collaboration
Nancy F Hansen
1 collaboration
Robert Harris
1 collaboration
Gabrielle A Hartley
1 collaboration
William T Harvey
1 collaboration
Marina Haukness
1 collaboration
Thibaut Hourlier
1 collaboration
Robert M Hubley
1 collaboration
Sarah E Hunt
1 collaboration
Stephen Hwang
1 collaboration
Rupesh K Kesharwani
1 collaboration
Alexandra P Lewis
1 collaboration
Julian K Lucas
1 collaboration
Wojciech Makalowski
1 collaboration
Christopher Markovic
1 collaboration
Fergal J Martin
1 collaboration
Ann M Mc Cartney
1 collaboration
Rajiv C McCoy
1 collaboration
Brandy M McNulty
1 collaboration
Paul Medvedev
1 collaboration
Alla Mikheenko
1 collaboration
Katherine M Munson
1 collaboration
Terence D Murphy
1 collaboration
Hugh E Olsen
1 collaboration
Luis F Paulin
1 collaboration
David Porubsky
1 collaboration
Tamara Potapova
1 collaboration
Fedor Ryabov
1 collaboration
Kishwar Shafin
1 collaboration
Valery A Shepelev
1 collaboration
Jessica M Storer
1 collaboration
Likhitha Surapaneni
1 collaboration
Angela M Taravella Oill
1 collaboration
Françoise Thibaud-Nissen
1 collaboration
Marta Tomaszkiewicz
1 collaboration
Brian P Walenz
1 collaboration
Allison C Watwood
1 collaboration
Matthias H Weissensteiner
1 collaboration
Melissa A Wilson
1 collaboration
Samantha Zarate
1 collaboration
Kateryna D Makova
1 collaboration
Ales Varabyou
1 collaboration
Markus J Sommer
1 collaboration
Beril Erdogdu
1 collaboration
Ilia Minkin
1 collaboration
Sukhwan Park
1 collaboration
Christopher Pockrandt
1 collaboration
Natalia Rincon
1 collaboration
Martin Steinegger
1 collaboration
Michael Alonge
1 collaboration
Rachel M Sherman
1 collaboration
Justin M Wagner
1 collaboration
Marc L Salit
1 collaboration
Justin Wagner
1 collaboration
Lindsay Harris
1 collaboration
Haoyu Cheng
1 collaboration
Yih-Chii Hwang
1 collaboration
Richa Gupta
1 collaboration
William J Rowell
1 collaboration
Ziad M Khan
1 collaboration
Jesse Farek
1 collaboration
Aishwarya Pisupati
1 collaboration
Medhat Mahmoud
1 collaboration
Chunlin Xiao
1 collaboration
Byunggil Yoo
1 collaboration
Sayed Mohammad Ebrahim Sahraeian
1 collaboration
Danny E Miller
1 collaboration
David Jáspez
1 collaboration
José M Lorenzo-Salazar
1 collaboration
Adrián Muñoz-Barrera
1 collaboration
Luis A Rubio-Rodríguez
1 collaboration
Carlos Flores
1 collaboration
Giuseppe Narzisi
1 collaboration
Uday Shanker Evani
1 collaboration
Wayne E Clarke
1 collaboration
Joyce Lee
1 collaboration
Christopher E Mason
1 collaboration
Stephen E Lincoln
1 collaboration
Mark T W Ebbert
1 collaboration
Xavi Guitart
1 collaboration
Roham Razaghi
1 collaboration
Gina V Caldas
1 collaboration
Jakob M Heinz
1 collaboration
Celine Hoh
1 collaboration
Alan Mao
1 collaboration
Stephanie G Pitch
1 collaboration
Weekie Yao
1 collaboration
Istvan Szundi
1 collaboration
Jonathan Fay
1 collaboration
Eefei Chen
1 collaboration
David S Kliger
1 collaboration
Aleksey Zimin
1 collaboration
Yuchen Ge
1 collaboration
Jiabin Qiu
1 collaboration
Manoj Bhaskaran
1 collaboration