Simone Rubinacci

Affiliations

Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.

Publications (16)

Assessing the impact of post-mortem damage and contamination on imputation performance in ancient DNA.

Scientific reports

Avec: Antonio Garrido Marques , Simone Rubinacci , Anna-Sapfo Malaspinas , Olivier Delaneau , Bárbara Sousa da Mota

XSI-a genotype compression tool for compressive genomics in large biobanks.

Bioinformatics (Oxford, England)

Avec: Rick Wertenbroek , Simone Rubinacci , Ioannis Xenarios , Yann Thoma , Olivier Delaneau

Accurate rare variant phasing of whole-genome and whole-exome sequencing data in the UK Biobank.

Nature genetics

Avec: Robin J Hofmeister , Diogo M Ribeiro , Simone Rubinacci , Olivier Delaneau

Imputation of low-coverage sequencing data from 150,119 UK Biobank genomes.

Nature genetics

Avec: Simone Rubinacci , Robin J Hofmeister , Bárbara Sousa da Mota , Olivier Delaneau

Genotype imputation using the Positional Burrows Wheeler Transform.

PLoS genetics

Avec: Simone Rubinacci , Olivier Delaneau , Jonathan Marchini

μ- PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data.

Bioinformatics (Oxford, England)

Avec: Davide Cozzi , Massimiliano Rossi , Simone Rubinacci , Travis Gagie , Dominik Köppl , Christina Boucher , Paola Bonizzoni

Mapache: a flexible pipeline to map ancient DNA.

Bioinformatics (Oxford, England)

Avec: Samuel Neuenschwander , Diana I Cruz Dávalos , Lucas Anchieri , Bárbara Sousa da Mota , Davide Bozzi , Simone Rubinacci , Olivier Delaneau , Simon Rasmussen , Anna-Sapfo Malaspinas

High-throughput SARS-CoV-2 and host genome sequencing from single nasopharyngeal swabs.

medRxiv : the preprint server for health sciences

Avec: John E Gorzynski , Hannah N De Jong , David Amar , Chris R Hughes , Alexander Ioannidis , Rob Bierman , Darren Liu , Yosuke Tanigawa , Amy Kistler , Jack Kamm , Jaehee Kim , Lorenzo Cappello , Norma F Neff , Simone Rubinacci , Olivier Delaneau , Massa J Shoura , Kinya Seo , Anna Kirillova , Archana Raja , Shirley Sutton , ChunHong Huang , Malaya Kumar Sahoo , Kalyan C Mallempati , Gonzalo Montero-Martin , Kazutoyo Osoegawa , David Jimenez-Morales , Nathaniel Watson , Nathan Hammond , Ruchi Joshi , Marcelo Fernandez-Vina , Jeffrey W Christle , Matthew T Wheeler , Phil Febbo , Kyle Farh , Gary Schroth , F Desouza , Julia Palacios , Julia Salzman , Benjamin A Pinsky , Manuel A Rivas , Carlos D Bustamante , Euan A Ashley , Victoria N Parikh

The molecular basis, genetic control and pleiotropic effects of local gene co-expression.

Nature communications

Avec: Diogo M Ribeiro , Simone Rubinacci , Anna Ramisch , Robin J Hofmeister , Emmanouil T Dermitzakis , Olivier Delaneau

A Genomics England haplotype reference panel and imputation of UK Biobank.

Nature genetics

Avec: Sinan Shi , Simone Rubinacci , Sile Hu , Loukas Moutsianas , Alex Stuckey , Anna C Need , Pier Francesco Palamara , Mark Caulfield , Jonathan Marchini , Simon Myers

Parent-of-Origin inference for biobanks.

Nature communications

Avec: Robin J Hofmeister , Simone Rubinacci , Diogo M Ribeiro , Alfonso Buil , Zoltán Kutalik , Olivier Delaneau

Imputation of ancient human genomes.

Nature communications

Avec: Bárbara Sousa da Mota , Simone Rubinacci , Diana Ivette Cruz Dávalos , Carlos Eduardo G Amorim , Martin Sikora , Niels N Johannsen , Marzena H Szmyt , Piotr Włodarczak , Anita Szczepanek , Marcin M Przybyła , Hannes Schroeder , Morten E Allentoft , Eske Willerslev , Anna-Sapfo Malaspinas , Olivier Delaneau

Efficient phasing and imputation of low-coverage sequencing data using large reference panels.

Nature genetics

Avec: Simone Rubinacci , Diogo M Ribeiro , Robin J Hofmeister , Olivier Delaneau

Deconvoluting complex correlates of COVID-19 severity with a multi-omic pandemic tracking strategy.

Nature communications

Avec: Victoria N Parikh , Alexander G Ioannidis , David Jimenez-Morales , John E Gorzynski , Hannah N De Jong , Xiran Liu , Jonasel Roque , Victoria P Cepeda-Espinoza , Kazutoyo Osoegawa , Chris Hughes , Shirley C Sutton , Nathan Youlton , Ruchi Joshi , David Amar , Yosuke Tanigawa , Douglas Russo , Justin Wong , Jessie T Lauzon , Jacob Edelson , Daniel Mas Montserrat , Yongchan Kwon , Simone Rubinacci , Olivier Delaneau , Lorenzo Cappello , Jaehee Kim , Massa J Shoura , Archana N Raja , Nathaniel Watson , Nathan Hammond , Elizabeth Spiteri , Kalyan C Mallempati , Gonzalo Montero-Martín , Jeffrey Christle , Jennifer Kim , Anna Kirillova , Kinya Seo , Yong Huang , Chunli Zhao , Sonia Moreno-Grau , Steven G Hershman , Karen P Dalton , Jimmy Zhen , Jack Kamm , Karan D Bhatt , Alina Isakova , Maurizio Morri , Thanmayi Ranganath , Catherine A Blish , Angela J Rogers , Kari Nadeau , Samuel Yang , Andra Blomkalns , Ruth O'Hara , Norma F Neff , Christopher DeBoever , Sándor Szalma , Matthew T Wheeler , Christian M Gates , Kyle Farh , Gary P Schroth , Phil Febbo , Francis deSouza , Omar E Cornejo , Marcelo Fernandez-Vina , Amy Kistler , Julia A Palacios , Benjamin A Pinsky , Carlos D Bustamante , Manuel A Rivas , Euan A Ashley

A resampling-based approach to share reference panels.

Nature computational science

Avec: Théo Cavinato , Simone Rubinacci , Anna-Sapfo Malaspinas , Olivier Delaneau

A blended genome and exome sequencing method captures genetic variation in an unbiased, high-quality, and cost-effective manner.

bioRxiv : the preprint server for biology

Avec: Toni A Boltz , Benjamin B Chu , Calwing Liao , Julia M Sealock , Robert Ye , Lerato Majara , Jack M Fu , Susan Service , Lingyu Zhan , Sarah E Medland , Sinéad B Chapman , Simone Rubinacci , Matthew DeFelice , Jonna L Grimsby , Tamrat Abebe , Melkam Alemayehu , Fred K Ashaba , Elizabeth G Atkinson , Tim Bigdeli , Amanda B Bradway , Harrison Brand , Lori B Chibnik , Abebaw Fekadu , Michael Gatzen , Bizu Gelaye , Stella Gichuru , Marissa L Gildea , Toni C Hill , Hailiang Huang , Kalyn M Hubbard , Wilfred E Injera , Roxanne James , Moses Joloba , Christopher Kachulis , Phillip R Kalmbach , Rogers Kamulegeya , Gabriel Kigen , Soyeon Kim , Nastassja Koen , Edith K Kwobah , Joseph Kyebuzibwa , Seungmo Lee , Niall J Lennon , Penelope A Lind , Esteban A Lopera-Maya , Johnstone Makale , Serghei Mangul , Justin McMahon , Pierre Mowlem , Henry Musinguzi , Rehema M Mwema , Noeline Nakasujja , Carter P Newman , Lethukuthula L Nkambule , Conor R O'Neil , Ana Maria Olivares , Catherine M Olsen , Linnet Ongeri , Sophie J Parsa , Adele Pretorius , Raj Ramesar , Faye L Reagan , Chiara Sabatti , Jacquelyn A Schneider , Welelta Shiferaw , Anne Stevenson , Erik Stricker , Rocky E Stroud , Jessie Tang , David Whiteman , Mary T Yohannes , Mingrui Yu , Kai Yuan , Auteur inconnu , Dickens Akena , Lukoye Atwoli , Symon M Kariuki , Karestan C Koenen , Charles R J C Newton , Dan J Stein , Solomon Teferra , Zukiswa Zingela , Carlos N Pato , Michele T Pato , Carlos Lopez-Jaramillo , Nelson Freimer , Roel A Ophoff , Loes M Olde Loohuis , Michael E Talkowski , Benjamin M Neale , Daniel P Howrigan , Alicia R Martin

Réseau de co-auteurs

Olivier Delaneau 13 collaborations

Robin J Hofmeister 5 collaborations

Anna-Sapfo Malaspinas 4 collaborations

Bárbara Sousa da Mota 4 collaborations

Diogo M Ribeiro 4 collaborations

Jonathan Marchini 2 collaborations

John E Gorzynski 2 collaborations

Hannah N De Jong 2 collaborations

David Amar 2 collaborations

Yosuke Tanigawa 2 collaborations

Amy Kistler 2 collaborations

Jack Kamm 2 collaborations

Jaehee Kim 2 collaborations

Lorenzo Cappello 2 collaborations

Norma F Neff 2 collaborations

Massa J Shoura 2 collaborations

Kinya Seo 2 collaborations

Anna Kirillova 2 collaborations

Kalyan C Mallempati 2 collaborations

Kazutoyo Osoegawa 2 collaborations

David Jimenez-Morales 2 collaborations

Nathaniel Watson 2 collaborations

Nathan Hammond 2 collaborations

Ruchi Joshi 2 collaborations

Marcelo Fernandez-Vina 2 collaborations

Matthew T Wheeler 2 collaborations

Phil Febbo 2 collaborations

Kyle Farh 2 collaborations

Benjamin A Pinsky 2 collaborations

Manuel A Rivas 2 collaborations

Carlos D Bustamante 2 collaborations

Euan A Ashley 2 collaborations

Victoria N Parikh 2 collaborations

Antonio Garrido Marques 1 collaboration

Rick Wertenbroek 1 collaboration

Ioannis Xenarios 1 collaboration

Yann Thoma 1 collaboration

Davide Cozzi 1 collaboration

Massimiliano Rossi 1 collaboration

Travis Gagie 1 collaboration

Dominik Köppl 1 collaboration

Christina Boucher 1 collaboration

Paola Bonizzoni 1 collaboration

Samuel Neuenschwander 1 collaboration

Diana I Cruz Dávalos 1 collaboration

Lucas Anchieri 1 collaboration

Davide Bozzi 1 collaboration

Simon Rasmussen 1 collaboration

Chris R Hughes 1 collaboration

Alexander Ioannidis 1 collaboration

Rob Bierman 1 collaboration

Darren Liu 1 collaboration

Archana Raja 1 collaboration

Shirley Sutton 1 collaboration

ChunHong Huang 1 collaboration

Malaya Kumar Sahoo 1 collaboration

Gonzalo Montero-Martin 1 collaboration

Jeffrey W Christle 1 collaboration

Gary Schroth 1 collaboration

F Desouza 1 collaboration

Julia Palacios 1 collaboration

Julia Salzman 1 collaboration

Anna Ramisch 1 collaboration

Emmanouil T Dermitzakis 1 collaboration

Sinan Shi 1 collaboration

Sile Hu 1 collaboration

Loukas Moutsianas 1 collaboration

Alex Stuckey 1 collaboration

Anna C Need 1 collaboration

Pier Francesco Palamara 1 collaboration

Mark Caulfield 1 collaboration

Simon Myers 1 collaboration

Alfonso Buil 1 collaboration

Zoltán Kutalik 1 collaboration

Diana Ivette Cruz Dávalos 1 collaboration

Carlos Eduardo G Amorim 1 collaboration

Martin Sikora 1 collaboration

Niels N Johannsen 1 collaboration

Marzena H Szmyt 1 collaboration

Piotr Włodarczak 1 collaboration

Anita Szczepanek 1 collaboration

Marcin M Przybyła 1 collaboration

Hannes Schroeder 1 collaboration

Morten E Allentoft 1 collaboration

Eske Willerslev 1 collaboration

Alexander G Ioannidis 1 collaboration

Xiran Liu 1 collaboration

Jonasel Roque 1 collaboration

Victoria P Cepeda-Espinoza 1 collaboration

Chris Hughes 1 collaboration

Shirley C Sutton 1 collaboration

Nathan Youlton 1 collaboration

Douglas Russo 1 collaboration

Justin Wong 1 collaboration

Jessie T Lauzon 1 collaboration

Jacob Edelson 1 collaboration

Daniel Mas Montserrat 1 collaboration

Yongchan Kwon 1 collaboration

Archana N Raja 1 collaboration

Elizabeth Spiteri 1 collaboration

Gonzalo Montero-Martín 1 collaboration

Jeffrey Christle 1 collaboration

Jennifer Kim 1 collaboration

Yong Huang 1 collaboration

Chunli Zhao 1 collaboration

Sonia Moreno-Grau 1 collaboration

Steven G Hershman 1 collaboration

Karen P Dalton 1 collaboration

Jimmy Zhen 1 collaboration

Karan D Bhatt 1 collaboration

Alina Isakova 1 collaboration

Maurizio Morri 1 collaboration

Thanmayi Ranganath 1 collaboration

Catherine A Blish 1 collaboration

Angela J Rogers 1 collaboration

Kari Nadeau 1 collaboration

Samuel Yang 1 collaboration

Andra Blomkalns 1 collaboration

Ruth O'Hara 1 collaboration

Christopher DeBoever 1 collaboration

Sándor Szalma 1 collaboration

Christian M Gates 1 collaboration

Gary P Schroth 1 collaboration

Francis deSouza 1 collaboration

Omar E Cornejo 1 collaboration

Julia A Palacios 1 collaboration

Théo Cavinato 1 collaboration

Toni A Boltz 1 collaboration

Benjamin B Chu 1 collaboration

Calwing Liao 1 collaboration

Julia M Sealock 1 collaboration

Robert Ye 1 collaboration

Lerato Majara 1 collaboration

Jack M Fu 1 collaboration

Susan Service 1 collaboration

Lingyu Zhan 1 collaboration

Sarah E Medland 1 collaboration

Sinéad B Chapman 1 collaboration

Matthew DeFelice 1 collaboration

Jonna L Grimsby 1 collaboration

Tamrat Abebe 1 collaboration

Melkam Alemayehu 1 collaboration

Fred K Ashaba 1 collaboration

Elizabeth G Atkinson 1 collaboration

Tim Bigdeli 1 collaboration

Amanda B Bradway 1 collaboration

Harrison Brand 1 collaboration

Lori B Chibnik 1 collaboration

Abebaw Fekadu 1 collaboration

Michael Gatzen 1 collaboration

Bizu Gelaye 1 collaboration

Stella Gichuru 1 collaboration

Marissa L Gildea 1 collaboration

Toni C Hill 1 collaboration

Hailiang Huang 1 collaboration

Kalyn M Hubbard 1 collaboration

Wilfred E Injera 1 collaboration

Roxanne James 1 collaboration

Moses Joloba 1 collaboration

Christopher Kachulis 1 collaboration

Phillip R Kalmbach 1 collaboration

Rogers Kamulegeya 1 collaboration

Gabriel Kigen 1 collaboration

Soyeon Kim 1 collaboration

Nastassja Koen 1 collaboration

Edith K Kwobah 1 collaboration

Joseph Kyebuzibwa 1 collaboration

Seungmo Lee 1 collaboration

Niall J Lennon 1 collaboration

Penelope A Lind 1 collaboration

Esteban A Lopera-Maya 1 collaboration

Johnstone Makale 1 collaboration

Serghei Mangul 1 collaboration

Justin McMahon 1 collaboration

Pierre Mowlem 1 collaboration

Henry Musinguzi 1 collaboration

Rehema M Mwema 1 collaboration

Noeline Nakasujja 1 collaboration

Carter P Newman 1 collaboration

Lethukuthula L Nkambule 1 collaboration

Conor R O'Neil 1 collaboration

Ana Maria Olivares 1 collaboration

Catherine M Olsen 1 collaboration

Linnet Ongeri 1 collaboration

Sophie J Parsa 1 collaboration

Adele Pretorius 1 collaboration

Raj Ramesar 1 collaboration

Faye L Reagan 1 collaboration

Chiara Sabatti 1 collaboration

Jacquelyn A Schneider 1 collaboration

Welelta Shiferaw 1 collaboration

Anne Stevenson 1 collaboration

Erik Stricker 1 collaboration

Rocky E Stroud 1 collaboration

Jessie Tang 1 collaboration

David Whiteman 1 collaboration

Mary T Yohannes 1 collaboration

Mingrui Yu 1 collaboration

Kai Yuan 1 collaboration

None None 1 collaboration

Dickens Akena 1 collaboration

Lukoye Atwoli 1 collaboration

Symon M Kariuki 1 collaboration

Karestan C Koenen 1 collaboration

Charles R J C Newton 1 collaboration

Dan J Stein 1 collaboration

Solomon Teferra 1 collaboration

Zukiswa Zingela 1 collaboration

Carlos N Pato 1 collaboration

Michele T Pato 1 collaboration

Carlos Lopez-Jaramillo 1 collaboration

Nelson Freimer 1 collaboration

Roel A Ophoff 1 collaboration

Loes M Olde Loohuis 1 collaboration

Michael E Talkowski 1 collaboration

Benjamin M Neale 1 collaboration

Daniel P Howrigan 1 collaboration

Alicia R Martin 1 collaboration