Daniela Puiu

Affiliations

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21211, USA.
Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21211, USA.

Publications (15)

The genome of the American groundhog,

F1000Research

Avec: Daniela Puiu , Aleksey Zimin , Alaina Shumate , Yuchen Ge , Jiabin Qiu , Manoj Bhaskaran , Steven L Salzberg

Major data analysis errors invalidate cancer microbiome findings.

mBio

Avec: Abraham Gihawi , Yuchen Ge , Jennifer Lu , Daniela Puiu , Amanda Xu , Colin S Cooper , Daniel S Brewer , Mihaela Pertea , Steven L Salzberg

A Genome Sequence for the Threatened Whitebark Pine.

bioRxiv : the preprint server for biology

Avec: David B Neale , Aleksey V Zimin , Amy Meltzer , Akriti Bhattarai , Maurice Amee , Laura Figueroa Corona , Brian J Allen , Daniela Puiu , Jessica Wright , Amanda R De La Torre , Patrick E McGuire , Winston Timp , Steven L Salzberg , Jill L Wegrzyn

A Genome Sequence for the Threatened Whitebark Pine.

G3 (Bethesda, Md.)

Avec: David B Neale , Aleksey V Zimin , Amy Meltzer , Akriti Bhattarai , Maurice Amee , Laura Figueroa Corona , Brian J Allen , Daniela Puiu , Jessica Wright , Amanda R De La Torre , Patrick E McGuire , Winston Timp , Steven L Salzberg , Jill L Wegrzyn

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

Author Correction: Assembly of a pan-genome from deep sequencing of 910 humans of African descent.

Nature genetics

Avec: Rachel M Sherman , Juliet Forman , Valentin Antonescu , Daniela Puiu , Michelle Daya , Nicholas Rafaels , Meher Preethi Boorgula , Sameer Chavan , Candelaria Vergara , Victor E Ortega , Albert M Levin , Celeste Eng , Maria Yazdanbakhsh , James G Wilson , Javier Marrugo , Leslie A Lange , L Keoki Williams , Harold Watson , Lorraine B Ware , Christopher O Olopade , Olufunmilayo Olopade , Ricardo R Oliveira , Carole Ober , Dan L Nicolae , Deborah A Meyers , Alvaro Mayorga , Jennifer Knight-Madden , Tina Hartert , Nadia N Hansel , Marilyn G Foreman , Jean G Ford , Mezbah U Faruque , Georgia M Dunston , Luis Caraballo , Esteban G Burchard , Eugene R Bleecker , Maria I Araujo , Edwin F Herrera-Paz , Monica Campbell , Cassandra Foster , Margaret A Taub , Terri H Beaty , Ingo Ruczinski , Rasika A Mathias , Kathleen C Barnes , Steven L Salzberg

Assembly of a pan-genome from deep sequencing of 910 humans of African descent.

Nature genetics

Avec: Rachel M Sherman , Juliet Forman , Valentin Antonescu , Daniela Puiu , Michelle Daya , Nicholas Rafaels , Meher Preethi Boorgula , Sameer Chavan , Candelaria Vergara , Victor E Ortega , Albert M Levin , Celeste Eng , Maria Yazdanbakhsh , James G Wilson , Javier Marrugo , Leslie A Lange , L Keoki Williams , Harold Watson , Lorraine B Ware , Christopher O Olopade , Olufunmilayo Olopade , Ricardo R Oliveira , Carole Ober , Dan L Nicolae , Deborah A Meyers , Alvaro Mayorga , Jennifer Knight-Madden , Tina Hartert , Nadia N Hansel , Marilyn G Foreman , Jean G Ford , Mezbah U Faruque , Georgia M Dunston , Luis Caraballo , Esteban G Burchard , Eugene R Bleecker , Maria I Araujo , Edwin F Herrera-Paz , Monica Campbell , Cassandra Foster , Margaret A Taub , Terri H Beaty , Ingo Ruczinski , Rasika A Mathias , Kathleen C Barnes , Steven L Salzberg

Genomic architecture of complex traits in loblolly pine.

The New phytologist

Avec: Amanda R De La Torre , Daniela Puiu , Marc W Crepeau , Kristian Stevens , Steven L Salzberg , Charles H Langley , David B Neale

Guillain-Barré Syndrome Outbreak in Peru 2019 Associated With

Neurology(R) neuroimmunology & neuroinflammation

Avec: Ana P Ramos , Sonja E Leonhard , Susan K Halstead , Mireya A Cuba , Carlos C Castañeda , Jose A Dioses , Martin A Tipismana , Jesus T Abanto , Alejandro Llanos , Dawn Gourlay , Max Grogl , Mariana Ramos , Jesus D Rojas , Rina Meza , Daniela Puiu , Rachel M Sherman , Steven L Salzberg , Patricia J Simner , Hugh J Willison , Bart C Jacobs , David R Cornblath , Hugo F Umeres , Carlos A Pardo

High-quality genome and methylomes illustrate features underlying evolutionary success of oaks.

Nature communications

Avec: Victoria L Sork , Shawn J Cokus , Sorel T Fitz-Gibbon , Aleksey V Zimin , Daniela Puiu , Jesse A Garcia , Paul F Gugger , Claudia L Henriquez , Ying Zhen , Kirk E Lohmueller , Matteo Pellegrini , Steven L Salzberg

Quantifying constraint in the human mitochondrial genome.

Nature

Avec: Nicole J Lake , Kaiyue Ma , Wei Liu , Stephanie L Battle , Kristen M Laricchia , Grace Tiao , Daniela Puiu , Kenneth K Ng , Justin Cohen , Alison G Compton , Shannon Cowie , John Christodoulou , David R Thorburn , Hongyu Zhao , Dan E Arking , Shamil R Sunyaev , Monkol Lek

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

Dissecting the Polygenic Basis of Cold Adaptation Using Genome-Wide Association of Traits and Environmental Data in Douglas-fir.

Genes

Avec: Amanda R De La Torre , Benjamin Wilhite , Daniela Puiu , John Bradley St Clair , Marc W Crepeau , Steven L Salzberg , Charles H Langley , Brian Allen , David B Neale

Genome-wide association identifies candidate genes for drought tolerance in coast redwood and giant sequoia.

The Plant journal : for cell and molecular biology

Avec: Amanda R De La Torre , Manoj K Sekhwal , Daniela Puiu , Steven L Salzberg , Alison D Scott , Brian Allen , David B Neale , Alana R O Chin , Thomas N Buckley

Réseau de co-auteurs

Steven L Salzberg 14 collaborations

David B Neale 5 collaborations

Aleksey V Zimin 5 collaborations

Amanda R De La Torre 5 collaborations

Alaina Shumate 4 collaborations

Rachel M Sherman 4 collaborations

Mihaela Pertea 3 collaborations

Yuchen Ge 2 collaborations

Amy Meltzer 2 collaborations

Akriti Bhattarai 2 collaborations

Maurice Amee 2 collaborations

Laura Figueroa Corona 2 collaborations

Brian J Allen 2 collaborations

Jessica Wright 2 collaborations

Patrick E McGuire 2 collaborations

Winston Timp 2 collaborations

Jill L Wegrzyn 2 collaborations

Juliet Forman 2 collaborations

Valentin Antonescu 2 collaborations

Michelle Daya 2 collaborations

Nicholas Rafaels 2 collaborations

Meher Preethi Boorgula 2 collaborations

Sameer Chavan 2 collaborations

Candelaria Vergara 2 collaborations

Victor E Ortega 2 collaborations

Albert M Levin 2 collaborations

Celeste Eng 2 collaborations

Maria Yazdanbakhsh 2 collaborations

James G Wilson 2 collaborations

Javier Marrugo 2 collaborations

Leslie A Lange 2 collaborations

L Keoki Williams 2 collaborations

Harold Watson 2 collaborations

Lorraine B Ware 2 collaborations

Christopher O Olopade 2 collaborations

Olufunmilayo Olopade 2 collaborations

Ricardo R Oliveira 2 collaborations

Carole Ober 2 collaborations

Dan L Nicolae 2 collaborations

Deborah A Meyers 2 collaborations

Alvaro Mayorga 2 collaborations

Jennifer Knight-Madden 2 collaborations

Tina Hartert 2 collaborations

Nadia N Hansel 2 collaborations

Marilyn G Foreman 2 collaborations

Jean G Ford 2 collaborations

Mezbah U Faruque 2 collaborations

Georgia M Dunston 2 collaborations

Luis Caraballo 2 collaborations

Esteban G Burchard 2 collaborations

Eugene R Bleecker 2 collaborations

Maria I Araujo 2 collaborations

Edwin F Herrera-Paz 2 collaborations

Monica Campbell 2 collaborations

Cassandra Foster 2 collaborations

Margaret A Taub 2 collaborations

Terri H Beaty 2 collaborations

Ingo Ruczinski 2 collaborations

Rasika A Mathias 2 collaborations

Kathleen C Barnes 2 collaborations

Marc W Crepeau 2 collaborations

Charles H Langley 2 collaborations

Brian Allen 2 collaborations

Aleksey Zimin 1 collaboration

Jiabin Qiu 1 collaboration

Manoj Bhaskaran 1 collaboration

Abraham Gihawi 1 collaboration

Jennifer Lu 1 collaboration

Amanda Xu 1 collaboration

Colin S Cooper 1 collaboration

Daniel S Brewer 1 collaboration

Ales Varabyou 1 collaboration

Markus J Sommer 1 collaboration

Beril Erdogdu 1 collaboration

Ida Shinder 1 collaboration

Ilia Minkin 1 collaboration

Kuan-Hao Chao 1 collaboration

Sukhwan Park 1 collaboration

Jakob Heinz 1 collaboration

Christopher Pockrandt 1 collaboration

Natalia Rincon 1 collaboration

Martin Steinegger 1 collaboration

Kristian Stevens 1 collaboration

Ana P Ramos 1 collaboration

Sonja E Leonhard 1 collaboration

Susan K Halstead 1 collaboration

Mireya A Cuba 1 collaboration

Carlos C Castañeda 1 collaboration

Jose A Dioses 1 collaboration

Martin A Tipismana 1 collaboration

Jesus T Abanto 1 collaboration

Alejandro Llanos 1 collaboration

Dawn Gourlay 1 collaboration

Max Grogl 1 collaboration

Mariana Ramos 1 collaboration

Jesus D Rojas 1 collaboration

Rina Meza 1 collaboration

Patricia J Simner 1 collaboration

Hugh J Willison 1 collaboration

Bart C Jacobs 1 collaboration

David R Cornblath 1 collaboration

Hugo F Umeres 1 collaboration

Carlos A Pardo 1 collaboration

Victoria L Sork 1 collaboration

Shawn J Cokus 1 collaboration

Sorel T Fitz-Gibbon 1 collaboration

Jesse A Garcia 1 collaboration

Paul F Gugger 1 collaboration

Claudia L Henriquez 1 collaboration

Ying Zhen 1 collaboration

Kirk E Lohmueller 1 collaboration

Matteo Pellegrini 1 collaboration

Nicole J Lake 1 collaboration

Kaiyue Ma 1 collaboration

Wei Liu 1 collaboration

Stephanie L Battle 1 collaboration

Kristen M Laricchia 1 collaboration

Grace Tiao 1 collaboration

Kenneth K Ng 1 collaboration

Justin Cohen 1 collaboration

Alison G Compton 1 collaboration

Shannon Cowie 1 collaboration

John Christodoulou 1 collaboration

David R Thorburn 1 collaboration

Hongyu Zhao 1 collaboration

Dan E Arking 1 collaboration

Shamil R Sunyaev 1 collaboration

Monkol Lek 1 collaboration

Michael Alonge 1 collaboration

Justin M Wagner 1 collaboration

Nathan D Olson 1 collaboration

Marc L Salit 1 collaboration

Justin M Zook 1 collaboration

Benjamin Wilhite 1 collaboration

John Bradley St Clair 1 collaboration

Manoj K Sekhwal 1 collaboration

Alison D Scott 1 collaboration

Alana R O Chin 1 collaboration

Thomas N Buckley 1 collaboration