Publications by authors named "Manfred Grabherr"

55Publications

Building de novo reference genome assemblies of complex eukaryotic microorganisms from single nuclei.

Authors:
Merce Montoliu-Nerin Marisol Sánchez-García Claudia Bergin Manfred Grabherr Barbara Ellis Verena Esther Kutschera Marcin Kierczak Hanna Johannesson Anna Rosling

Sci Rep 2020 Jan 28;10(1):1303. Epub 2020 Jan 28.

Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Uppsala, Sweden.

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January 2020

Investigation of the host transcriptional response to intracellular bacterial infection using Dictyostelium discoideum as a host model.

Authors:
Jonas Kjellin Maria Pränting Frauke Bach Roshan Vaid Bart Edelbroek Zhiru Li Marc P Hoeppner Manfred Grabherr Ralph R Isberg Monica Hagedorn Fredrik Söderbom

BMC Genomics 2019 Dec 10;20(1):961. Epub 2019 Dec 10.

Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.

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December 2019

Author Correction: Intra- and inter-individual metabolic profiling highlights carnitine and lysophosphatidylcholine pathways as key molecular defects in type 2 diabetes.

Authors:
Klev Diamanti Marco Cavalli Gang Pan Maria J Pereira Chanchal Kumar Stanko Skrtic Manfred Grabherr Ulf Risérus Jan W Eriksson Jan Komorowski Claes Wadelius

Sci Rep 2019 Nov 28;9(1):18158. Epub 2019 Nov 28.

Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.

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November 2019

Intra- and inter-individual metabolic profiling highlights carnitine and lysophosphatidylcholine pathways as key molecular defects in type 2 diabetes.

Authors:
Klev Diamanti Marco Cavalli Gang Pan Maria J Pereira Chanchal Kumar Stanko Skrtic Manfred Grabherr Ulf Risérus Jan W Eriksson Jan Komorowski Claes Wadelius

Sci Rep 2019 07 4;9(1):9653. Epub 2019 Jul 4.

Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.

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July 2019

Analyzing DNA methylation patterns in subjects diagnosed with schizophrenia using machine learning methods.

Authors:
Behrooz Torabi Moghadam Mitra Etemadikhah Grazyna Rajkowska Craig Stockmeier Manfred Grabherr Jan Komorowski Lars Feuk Eva Lindholm Carlström

J Psychiatr Res 2019 07 2;114:41-47. Epub 2019 Apr 2.

Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden. Electronic address:

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July 2019

ACES: a machine learning toolbox for clustering analysis and visualization.

Authors:
Jiangning Gao Görel Sundström Behrooz Torabi Moghadam Neda Zamani Manfred G Grabherr

BMC Genomics 2018 Dec 27;19(1):964. Epub 2018 Dec 27.

Department of medical biochemistry and microbiology, Uppsala University, Uppsala, Sweden.

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December 2018

Functional and evolutionary genomic inferences in through genome and population sequencing of American and European aspen.

Authors:
Yao-Cheng Lin Jing Wang Nicolas Delhomme Bastian Schiffthaler Görel Sundström Andrea Zuccolo Björn Nystedt Torgeir R Hvidsten Amanda de la Torre Rosa M Cossu Marc P Hoeppner Henrik Lantz Douglas G Scofield Neda Zamani Anna Johansson Chanaka Mannapperuma Kathryn M Robinson Niklas Mähler Ilia J Leitch Jaume Pellicer Eung-Jun Park Marc Van Montagu Yves Van de Peer Manfred Grabherr Stefan Jansson Pär K Ingvarsson Nathaniel R Street

Proc Natl Acad Sci U S A 2018 11 29;115(46):E10970-E10978. Epub 2018 Oct 29.

Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden;

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November 2018

Special Issue Introduction: The Wonders and Mysteries Next Generation Sequencing Technologies Help Reveal.

Authors:
Manfred G Grabherr Bozena Kaminska Jan Komorowski

Genes (Basel) 2018 Oct 18;9(10). Epub 2018 Oct 18.

Department of Cell and Molecular Biology, Uppsala University, 752 36 Uppsala, Sweden.

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October 2018

Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum.

Authors:
Zhen Liao Jonas Kjellin Marc P Hoeppner Manfred Grabherr Fredrik Söderbom

RNA Biol 2018 21;15(7):937-954. Epub 2018 Aug 21.

a Department of Cell and Molecular Biology , Uppsala University , Uppsala , Sweden.

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December 2018

Comparative omics and feeding manipulations in chicken indicate a shift of the endocrine role of visceral fat towards reproduction.

Authors:
Susanne Bornelöv Eyal Seroussi Sara Yosefi Sharon Benjamini Shoval Miyara Mark Ruzal Manfred Grabherr Nima Rafati Anna-Maja Molin Ken Pendavis Shane C Burgess Leif Andersson Miriam Friedman-Einat

BMC Genomics 2018 Apr 26;19(1):295. Epub 2018 Apr 26.

Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel.

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April 2018

Reading and editing the Pleurodeles waltl genome reveals novel features of tetrapod regeneration.

Authors:
Ahmed Elewa Heng Wang Carlos Talavera-López Alberto Joven Gonçalo Brito Anoop Kumar L Shahul Hameed May Penrad-Mobayed Zeyu Yao Neda Zamani Yamen Abbas Ilgar Abdullayev Rickard Sandberg Manfred Grabherr Björn Andersson András Simon

Nat Commun 2017 12 22;8(1):2286. Epub 2017 Dec 22.

Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, SE-171 65, Sweden.

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December 2017

Characterization of the Giardia intestinalis secretome during interaction with human intestinal epithelial cells: The impact on host cells.

Authors:
Showgy Y Ma'ayeh Jingyi Liu Dimitra Peirasmaki Katarina Hörnaeus Sara Bergström Lind Manfred Grabherr Jonas Bergquist Staffan G Svärd

PLoS Negl Trop Dis 2017 12 11;11(12):e0006120. Epub 2017 Dec 11.

Department of Cell and Molecular Biology, Uppsala University, BMC, Uppsala, Sweden.

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December 2017

A practical guide to build assemblies for single tissues of non-model organisms: the example of a Neotropical frog.

Authors:
Santiago Montero-Mendieta Manfred Grabherr Henrik Lantz Ignacio De la Riva Jennifer A Leonard Matthew T Webster Carles Vilà

PeerJ 2017 1;5:e3702. Epub 2017 Sep 1.

Conservation and Evolutionary Genetics Group, Department of Integrative Ecology, Doñana Biological Station (EBD-CSIC), Consejo Superior de Investigaciones Científicas, Seville, Spain.

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September 2017

RNA-sequence data normalization through in silico prediction of reference genes: the bacterial response to DNA damage as case study.

Authors:
Bork A Berghoff Torgny Karlsson Thomas Källman E Gerhart H Wagner Manfred G Grabherr

BioData Min 2017 5;10:30. Epub 2017 Sep 5.

Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.

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September 2017

Evolution of the p53-MDM2 pathway.

Authors:
Emma Åberg Fulvio Saccoccia Manfred Grabherr Wai Ying Josefin Ore Per Jemth Greta Hultqvist

BMC Evol Biol 2017 08 3;17(1):177. Epub 2017 Aug 3.

Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123, Uppsala, Sweden.

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August 2017

PiiL: visualization of DNA methylation and gene expression data in gene pathways.

Authors:
Behrooz Torabi Moghadam Neda Zamani Jan Komorowski Manfred Grabherr

BMC Genomics 2017 08 2;18(1):571. Epub 2017 Aug 2.

Department of Medical Biochemistry and Microbiology/BILS, Genomics, Uppsala University, Uppsala, Sweden.

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August 2017

Correspondence on Lovell et al.: identification of chicken genes previously assumed to be evolutionarily lost.

Authors:
Susanne Bornelöv Eyal Seroussi Sara Yosefi Ken Pendavis Shane C Burgess Manfred Grabherr Miriam Friedman-Einat Leif Andersson

Genome Biol 2017 06 14;18(1):112. Epub 2017 Jun 14.

Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, SE-751 23, Sweden.

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June 2017

microTaboo: a general and practical solution to the k-disjoint problem.

Authors:
Mohammed Al-Jaff Eric Sandström Manfred Grabherr

BMC Bioinformatics 2017 May 2;18(1):228. Epub 2017 May 2.

Department of Medical Biochemistry and Microbiology, Uppsala University, 75123, Uppsala, Sweden.

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May 2017

Interactions of Freshwater Cyanobacteria with Bacterial Antagonists.

Authors:
Omneya Ahmed Osman Sara Beier Manfred Grabherr Stefan Bertilsson

Appl Environ Microbiol 2017 04 17;83(7). Epub 2017 Mar 17.

Department of Ecology and Genetics, Limnology, and Science for Life Laboratory, Uppsala University, Uppsala, Sweden

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April 2017

Combinatorial identification of DNA methylation patterns over age in the human brain.

Authors:
Behrooz Torabi Moghadam Michal Dabrowski Bozena Kaminska Manfred G Grabherr Jan Komorowski

BMC Bioinformatics 2016 Sep 23;17(1):393. Epub 2016 Sep 23.

Department of Cell and Molecular Biology, Computational and Systems Biology, Uppsala University, Uppsala, Sweden.

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September 2016

Coordinated Changes in Gene Expression Throughout Encystation of Giardia intestinalis.

Authors:
Elin Einarsson Karin Troell Marc P Hoeppner Manfred Grabherr Ulf Ribacke Staffan G Svärd

PLoS Negl Trop Dis 2016 Mar 25;10(3):e0004571. Epub 2016 Mar 25.

Department of Cell and Molecular Biology, BMC, Uppsala University, Uppsala, Sweden.

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March 2016

Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies).

Authors:
Nicolas Delhomme Görel Sundström Neda Zamani Henrik Lantz Yao-Cheng Lin Torgeir R Hvidsten Marc P Höppner Patric Jern Yves Van de Peer Joakim Lundeberg Manfred G Grabherr Nathaniel R Street

PLoS One 2015 28;10(9):e0139080. Epub 2015 Sep 28.

Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden.

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May 2016

Draft Genome Sequence of the Cellulolytic Fungus Chaetomium globosum.

Authors:
Christina A Cuomo Wendy A Untereiner Li-Jun Ma Manfred Grabherr Bruce W Birren

Genome Announc 2015 Feb 26;3(1). Epub 2015 Feb 26.

Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.

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February 2015

Evolution of Darwin's finches and their beaks revealed by genome sequencing.

Authors:
Sangeet Lamichhaney Jonas Berglund Markus Sällman Almén Khurram Maqbool Manfred Grabherr Alvaro Martinez-Barrio Marta Promerová Carl-Johan Rubin Chao Wang Neda Zamani B Rosemary Grant Peter R Grant Matthew T Webster Leif Andersson

Nature 2015 Feb 11;518(7539):371-5. Epub 2015 Feb 11.

1] Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden [2] Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden [3] Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843-4458, USA.

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February 2015

Function of Isolated Pancreatic Islets From Patients at Onset of Type 1 Diabetes: Insulin Secretion Can Be Restored After Some Days in a Nondiabetogenic Environment In Vitro: Results From the DiViD Study.

Authors:
Lars Krogvold Oskar Skog Görel Sundström Bjørn Edwin Trond Buanes Kristian F Hanssen Johnny Ludvigsson Manfred Grabherr Olle Korsgren Knut Dahl-Jørgensen

Diabetes 2015 Jul 12;64(7):2506-12. Epub 2015 Feb 12.

Paediatric Department, Oslo University Hospital and Faculty of Medicine, University of Oslo, Oslo, Norway.

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July 2015

Whiteboard: a framework for the programmatic visualization of complex biological analyses.

Authors:
Görel Sundström Neda Zamani Manfred G Grabherr Evan Mauceli

Bioinformatics 2015 Jun 5;31(12):2054-5. Epub 2015 Feb 5.

Department of Medical Biochemistry and Microbiology, Bioinformatics Infrastructure for Life Sciences, Uppsala University, 75123 Uppsala, Sweden, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden and Parabase Genomics, 27 Drydock Avenue, Boston MA 02210, USA.

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June 2015

Genome and physiology of the ascomycete filamentous fungus Xeromyces bisporus, the most xerophilic organism isolated to date.

Authors:
Su-Lin L Leong Henrik Lantz Olga V Pettersson Jens C Frisvad Ulf Thrane Hermann J Heipieper Jan Dijksterhuis Manfred Grabherr Mats Pettersson Christian Tellgren-Roth Johan Schnürer

Environ Microbiol 2015 Feb 7;17(2):496-513. Epub 2014 Oct 7.

Department of Microbiology, Swedish University of Agricultural Sciences, Box 7025, SE-75007, Uppsala, Sweden.

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February 2015

Modular and configurable optimal sequence alignment software: Cola.

Authors:
Neda Zamani Görel Sundström Marc P Höppner Manfred G Grabherr

Source Code Biol Med 2014 9;9:12. Epub 2014 Jun 9.

Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.

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June 2014

A universal genomic coordinate translator for comparative genomics.

Authors:
Neda Zamani Görel Sundström Jennifer R S Meadows Marc P Höppner Jacques Dainat Henrik Lantz Brian J Haas Manfred G Grabherr

BMC Bioinformatics 2014 Jun 30;15:227. Epub 2014 Jun 30.

Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.

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June 2014

An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts.

Authors:
Marc P Hoeppner Andrew Lundquist Mono Pirun Jennifer R S Meadows Neda Zamani Jeremy Johnson Görel Sundström April Cook Michael G FitzGerald Ross Swofford Evan Mauceli Behrooz Torabi Moghadam Anna Greka Jessica Alföldi Amr Abouelleil Lynne Aftuck Daniel Bessette Aaron Berlin Adam Brown Gary Gearin Annie Lui J Pendexter Macdonald Margaret Priest Terrance Shea Jason Turner-Maier Andrew Zimmer Eric S Lander Federica di Palma Kerstin Lindblad-Toh Manfred G Grabherr

PLoS One 2014 13;9(3):e91172. Epub 2014 Mar 13.

Science for Life Laboratories, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden; Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America.

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January 2016

Broad-scale phylogenomics provides insights into retrovirus-host evolution.

Authors:
Alexander Hayward Manfred Grabherr Patric Jern

Proc Natl Acad Sci U S A 2013 Dec 25;110(50):20146-51. Epub 2013 Nov 25.

Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala Biomedical Centre, SE-75123 Uppsala, Sweden.

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December 2013

Efficient cellular fractionation improves RNA sequencing analysis of mature and nascent transcripts from human tissues.

Authors:
Ammar Zaghlool Adam Ameur Linnea Nyberg Jonatan Halvardson Manfred Grabherr Lucia Cavelier Lars Feuk

BMC Biotechnol 2013 Nov 13;13:99. Epub 2013 Nov 13.

Department of Immunology, Genetics and Pathology, Rudbeck Laboratory and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.

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November 2013

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.

Authors:
Brian J Haas Alexie Papanicolaou Moran Yassour Manfred Grabherr Philip D Blood Joshua Bowden Matthew Brian Couger David Eccles Bo Li Matthias Lieber Matthew D MacManes Michael Ott Joshua Orvis Nathalie Pochet Francesco Strozzi Nathan Weeks Rick Westerman Thomas William Colin N Dewey Robert Henschel Richard D LeDuc Nir Friedman Aviv Regev

Nat Protoc 2013 Aug 11;8(8):1494-512. Epub 2013 Jul 11.

Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA.

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August 2013

Unsupervised genome-wide recognition of local relationship patterns.

Authors:
Neda Zamani Pamela Russell Henrik Lantz Marc P Hoeppner Jennifer Rs Meadows Nagarjun Vijay Evan Mauceli Federica di Palma Kerstin Lindblad-Toh Patric Jern Manfred G Grabherr

BMC Genomics 2013 May 24;14:347. Epub 2013 May 24.

Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.

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May 2013

Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring.

Authors:
Sangeet Lamichhaney Alvaro Martinez Barrio Nima Rafati Görel Sundström Carl-Johan Rubin Elizabeth R Gilbert Jonas Berglund Anna Wetterbom Linda Laikre Matthew T Webster Manfred Grabherr Nils Ryman Leif Andersson

Proc Natl Acad Sci U S A 2012 Nov 7;109(47):19345-50. Epub 2012 Nov 7.

Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden.

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November 2012

The genomic basis of adaptive evolution in threespine sticklebacks.

Authors:
Felicity C Jones Manfred G Grabherr Yingguang Frank Chan Pamela Russell Evan Mauceli Jeremy Johnson Ross Swofford Mono Pirun Michael C Zody Simon White Ewan Birney Stephen Searle Jeremy Schmutz Jane Grimwood Mark C Dickson Richard M Myers Craig T Miller Brian R Summers Anne K Knecht Shannon D Brady Haili Zhang Alex A Pollen Timothy Howes Chris Amemiya Jen Baldwin Toby Bloom David B Jaffe Robert Nicol Jane Wilkinson Eric S Lander Federica Di Palma Kerstin Lindblad-Toh David M Kingsley

Nature 2012 Apr 4;484(7392):55-61. Epub 2012 Apr 4.

Department of Developmental Biology, Beckman Center B300, Stanford University School of Medicine, Stanford California 94305, USA.

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April 2012

Artificially designed promoters: understanding the role of spatial features and canonical binding sites in transcription.

Authors:
Martina Baumann Marc P Höppner Michael Meier Jens Pontiller Wolfgang Ernst Reingard Grabherr Evan Mauceli Manfred G Grabherr

Bioeng Bugs 2012 Mar-Apr;3(2):120-3. Epub 2012 Mar 1.

Department of Biotechnology; University of Natural Resources and Applied Life Sciences, Vienna, Austria.

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October 2012

The genome of the green anole lizard and a comparative analysis with birds and mammals.

Authors:
Jessica Alföldi Federica Di Palma Manfred Grabherr Christina Williams Lesheng Kong Evan Mauceli Pamela Russell Craig B Lowe Richard E Glor Jacob D Jaffe David A Ray Stephane Boissinot Andrew M Shedlock Christopher Botka Todd A Castoe John K Colbourne Matthew K Fujita Ricardo Godinez Moreno Boudewijn F ten Hallers David Haussler Andreas Heger David Heiman Daniel E Janes Jeremy Johnson Pieter J de Jong Maxim Y Koriabine Marcia Lara Peter A Novick Chris L Organ Sally E Peach Steven Poe David D Pollock Kevin de Queiroz Thomas Sanger Steve Searle Jeremy D Smith Zachary Smith Ross Swofford Jason Turner-Maier Juli Wade Sarah Young Amonida Zadissa Scott V Edwards Travis C Glenn Christopher J Schneider Jonathan B Losos Eric S Lander Matthew Breen Chris P Ponting Kerstin Lindblad-Toh

Nature 2011 Aug 31;477(7366):587-91. Epub 2011 Aug 31.

Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.

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August 2011

Exploiting nucleotide composition to engineer promoters.

Authors:
Manfred G Grabherr Jens Pontiller Evan Mauceli Wolfgang Ernst Martina Baumann Tara Biagi Ross Swofford Pamela Russell Michael C Zody Federica Di Palma Kerstin Lindblad-Toh Reingard M Grabherr

PLoS One 2011 18;6(5):e20136. Epub 2011 May 18.

Broad Institute, Cambridge, Massachusetts, United States of America.

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October 2011

Computational methods for transcriptome annotation and quantification using RNA-seq.

Authors:
Manuel Garber Manfred G Grabherr Mitchell Guttman Cole Trapnell

Nat Methods 2011 Jun 27;8(6):469-77. Epub 2011 May 27.

Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA.

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June 2011

Genome sequencing and assembly.

Authors:
Manfred G Grabherr Evan Mauceli Li-Jun Ma

Methods Mol Biol 2011 ;722:1-9

University of Massachusetts, Amkebt, MA, USA.

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September 2011

Full-length transcriptome assembly from RNA-Seq data without a reference genome.

Authors:
Manfred G Grabherr Brian J Haas Moran Yassour Joshua Z Levin Dawn A Thompson Ido Amit Xian Adiconis Lin Fan Raktima Raychowdhury Qiandong Zeng Zehua Chen Evan Mauceli Nir Hacohen Andreas Gnirke Nicholas Rhind Federica di Palma Bruce W Birren Chad Nusbaum Kerstin Lindblad-Toh Nir Friedman Aviv Regev

Nat Biotechnol 2011 May 15;29(7):644-52. Epub 2011 May 15.

Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA.

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May 2011

Obligate biotrophy features unraveled by the genomic analysis of rust fungi.

Authors:
Sébastien Duplessis Christina A Cuomo Yao-Cheng Lin Andrea Aerts Emilie Tisserant Claire Veneault-Fourrey David L Joly Stéphane Hacquard Joëlle Amselem Brandi L Cantarel Readman Chiu Pedro M Coutinho Nicolas Feau Matthew Field Pascal Frey Eric Gelhaye Jonathan Goldberg Manfred G Grabherr Chinnappa D Kodira Annegret Kohler Ursula Kües Erika A Lindquist Susan M Lucas Rohit Mago Evan Mauceli Emmanuelle Morin Claude Murat Jasmyn L Pangilinan Robert Park Matthew Pearson Hadi Quesneville Nicolas Rouhier Sharadha Sakthikumar Asaf A Salamov Jeremy Schmutz Benjamin Selles Harris Shapiro Philippe Tanguay Gerald A Tuskan Bernard Henrissat Yves Van de Peer Pierre Rouzé Jeffrey G Ellis Peter N Dodds Jacqueline E Schein Shaobin Zhong Richard C Hamelin Igor V Grigoriev Les J Szabo Francis Martin

Proc Natl Acad Sci U S A 2011 May 2;108(22):9166-71. Epub 2011 May 2.

Unité Mixte de Recherche 1136, Institut National de la Recherche Agronomique/Nancy Université, Interactions Arbres/Micro-organismes, Centre de Nancy, 54280 Champenoux, France.

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May 2011

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium.

Authors:
Li-Jun Ma H Charlotte van der Does Katherine A Borkovich Jeffrey J Coleman Marie-Josée Daboussi Antonio Di Pietro Marie Dufresne Michael Freitag Manfred Grabherr Bernard Henrissat Petra M Houterman Seogchan Kang Won-Bo Shim Charles Woloshuk Xiaohui Xie Jin-Rong Xu John Antoniw Scott E Baker Burton H Bluhm Andrew Breakspear Daren W Brown Robert A E Butchko Sinead Chapman Richard Coulson Pedro M Coutinho Etienne G J Danchin Andrew Diener Liane R Gale Donald M Gardiner Stephen Goff Kim E Hammond-Kosack Karen Hilburn Aurélie Hua-Van Wilfried Jonkers Kemal Kazan Chinnappa D Kodira Michael Koehrsen Lokesh Kumar Yong-Hwan Lee Liande Li John M Manners Diego Miranda-Saavedra Mala Mukherjee Gyungsoon Park Jongsun Park Sook-Young Park Robert H Proctor Aviv Regev M Carmen Ruiz-Roldan Divya Sain Sharadha Sakthikumar Sean Sykes David C Schwartz B Gillian Turgeon Ilan Wapinski Olen Yoder Sarah Young Qiandong Zeng Shiguo Zhou James Galagan Christina A Cuomo H Corby Kistler Martijn Rep

Nature 2010 Mar;464(7287):367-73

The Broad Institute, Cambridge, Massachusetts 02141, USA.

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March 2010

Genome-wide synteny through highly sensitive sequence alignment: Satsuma.

Authors:
Manfred G Grabherr Pamela Russell Miriah Meyer Evan Mauceli Jessica Alföldi Federica Di Palma Kerstin Lindblad-Toh

Bioinformatics 2010 May 5;26(9):1145-51. Epub 2010 Mar 5.

Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA.

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May 2010

Identification of repetitive elements in the genome of Oreochromis niloticus: tilapia repeat masker.

Authors:
Andrey Shirak Manfred Grabherr Federica Di Palma Kerstin Lindblad-Toh Gideon Hulata Micha Ron Tom D Kocher Eyal Seroussi

Mar Biotechnol (NY) 2010 Apr 21;12(2):121-5. Epub 2009 Nov 21.

Agricultural Research Organization, Institute of Animal Science, Bet Dagan, 50250, Israel.

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April 2010

High-throughput sequencing of microdissected chromosomal regions.

Authors:
Anja Weise Bernd Timmermann Manfred Grabherr Martin Werber Patricia Heyn Nadezda Kosyakova Thomas Liehr Heidemarie Neitzel Kateryna Konrat Christiane Bommer Carola Dietrich Anna Rajab Richard Reinhardt Stefan Mundlos Tom H Lindner Katrin Hoffmann

Eur J Hum Genet 2010 Apr 4;18(4):457-62. Epub 2009 Nov 4.

Institute of Human Genetics and Anthropology, Jena, Germany.

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April 2010

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans.

Authors:
Brian J Haas Sophien Kamoun Michael C Zody Rays H Y Jiang Robert E Handsaker Liliana M Cano Manfred Grabherr Chinnappa D Kodira Sylvain Raffaele Trudy Torto-Alalibo Tolga O Bozkurt Audrey M V Ah-Fong Lucia Alvarado Vicky L Anderson Miles R Armstrong Anna Avrova Laura Baxter Jim Beynon Petra C Boevink Stephanie R Bollmann Jorunn I B Bos Vincent Bulone Guohong Cai Cahid Cakir James C Carrington Megan Chawner Lucio Conti Stefano Costanzo Richard Ewan Noah Fahlgren Michael A Fischbach Johanna Fugelstad Eleanor M Gilroy Sante Gnerre Pamela J Green Laura J Grenville-Briggs John Griffith Niklaus J Grünwald Karolyn Horn Neil R Horner Chia-Hui Hu Edgar Huitema Dong-Hoon Jeong Alexandra M E Jones Jonathan D G Jones Richard W Jones Elinor K Karlsson Sridhara G Kunjeti Kurt Lamour Zhenyu Liu Lijun Ma Daniel Maclean Marcus C Chibucos Hayes McDonald Jessica McWalters Harold J G Meijer William Morgan Paul F Morris Carol A Munro Keith O'Neill Manuel Ospina-Giraldo Andrés Pinzón Leighton Pritchard Bernard Ramsahoye Qinghu Ren Silvia Restrepo Sourav Roy Ari Sadanandom Alon Savidor Sebastian Schornack David C Schwartz Ulrike D Schumann Ben Schwessinger Lauren Seyer Ted Sharpe Cristina Silvar Jing Song David J Studholme Sean Sykes Marco Thines Peter J I van de Vondervoort Vipaporn Phuntumart Stephan Wawra Rob Weide Joe Win Carolyn Young Shiguo Zhou William Fry Blake C Meyers Pieter van West Jean Ristaino Francine Govers Paul R J Birch Stephen C Whisson Howard S Judelson Chad Nusbaum

Nature 2009 Sep 9;461(7262):393-8. Epub 2009 Sep 9.

Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA.

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September 2009

Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication.

Authors:
Li-Jun Ma Ashraf S Ibrahim Christopher Skory Manfred G Grabherr Gertraud Burger Margi Butler Marek Elias Alexander Idnurm B Franz Lang Teruo Sone Ayumi Abe Sarah E Calvo Luis M Corrochano Reinhard Engels Jianmin Fu Wilhelm Hansberg Jung-Mi Kim Chinnappa D Kodira Michael J Koehrsen Bo Liu Diego Miranda-Saavedra Sinead O'Leary Lucila Ortiz-Castellanos Russell Poulter Julio Rodriguez-Romero José Ruiz-Herrera Yao-Qing Shen Qiandong Zeng James Galagan Bruce W Birren Christina A Cuomo Brian L Wickes

PLoS Genet 2009 Jul 3;5(7):e1000549. Epub 2009 Jul 3.

The Broad Institute of MIT and Harvard, Cambridge, MA, USA.

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July 2009

Evolution of pathogenicity and sexual reproduction in eight Candida genomes.

Authors:
Geraldine Butler Matthew D Rasmussen Michael F Lin Manuel A S Santos Sharadha Sakthikumar Carol A Munro Esther Rheinbay Manfred Grabherr Anja Forche Jennifer L Reedy Ino Agrafioti Martha B Arnaud Steven Bates Alistair J P Brown Sascha Brunke Maria C Costanzo David A Fitzpatrick Piet W J de Groot David Harris Lois L Hoyer Bernhard Hube Frans M Klis Chinnappa Kodira Nicola Lennard Mary E Logue Ronny Martin Aaron M Neiman Elissavet Nikolaou Michael A Quail Janet Quinn Maria C Santos Florian F Schmitzberger Gavin Sherlock Prachi Shah Kevin A T Silverstein Marek S Skrzypek David Soll Rodney Staggs Ian Stansfield Michael P H Stumpf Peter E Sudbery Thyagarajan Srikantha Qiandong Zeng Judith Berman Matthew Berriman Joseph Heitman Neil A R Gow Michael C Lorenz Bruce W Birren Manolis Kellis Christina A Cuomo

Nature 2009 Jun;459(7247):657-62

UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.

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June 2009

A cis-acting regulatory mutation causes premature hair graying and susceptibility to melanoma in the horse.

Authors:
Gerli Rosengren Pielberg Anna Golovko Elisabeth Sundström Ino Curik Johan Lennartsson Monika H Seltenhammer Thomas Druml Matthew Binns Carolyn Fitzsimmons Gabriella Lindgren Kaj Sandberg Roswitha Baumung Monika Vetterlein Sara Strömberg Manfred Grabherr Claire Wade Kerstin Lindblad-Toh Fredrik Pontén Carl-Henrik Heldin Johann Sölkner Leif Andersson

Nat Genet 2008 Aug 20;40(8):1004-9. Epub 2008 Jul 20.

Department of Medical Biochemistry and Microbiology, Uppsala University, Box 597, SE-751 24 Uppsala, Sweden.

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August 2008

Evolution of genes and genomes on the Drosophila phylogeny.

Authors:
Andrew G Clark Michael B Eisen Douglas R Smith Casey M Bergman Brian Oliver Therese A Markow Thomas C Kaufman Manolis Kellis William Gelbart Venky N Iyer Daniel A Pollard Timothy B Sackton Amanda M Larracuente Nadia D Singh Jose P Abad Dawn N Abt Boris Adryan Montserrat Aguade Hiroshi Akashi Wyatt W Anderson Charles F Aquadro David H Ardell Roman Arguello Carlo G Artieri Daniel A Barbash Daniel Barker Paolo Barsanti Phil Batterham Serafim Batzoglou Dave Begun Arjun Bhutkar Enrico Blanco Stephanie A Bosak Robert K Bradley Adrianne D Brand Michael R Brent Angela N Brooks Randall H Brown Roger K Butlin Corrado Caggese Brian R Calvi A Bernardo de Carvalho Anat Caspi Sergio Castrezana Susan E Celniker Jean L Chang Charles Chapple Sourav Chatterji Asif Chinwalla Alberto Civetta Sandra W Clifton Josep M Comeron James C Costello Jerry A Coyne Jennifer Daub Robert G David Arthur L Delcher Kim Delehaunty Chuong B Do Heather Ebling Kevin Edwards Thomas Eickbush Jay D Evans Alan Filipski Sven 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Nature 2007 Nov;450(7167):203-18

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.

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November 2007

Genome sequence of Aedes aegypti, a major arbovirus vector.

Authors:
Vishvanath Nene Jennifer R Wortman Daniel Lawson Brian Haas Chinnappa Kodira Zhijian Jake Tu Brendan Loftus Zhiyong Xi Karyn Megy Manfred Grabherr Quinghu Ren Evgeny M Zdobnov Neil F Lobo Kathryn S Campbell Susan E Brown Maria F Bonaldo Jingsong Zhu Steven P Sinkins David G Hogenkamp Paolo Amedeo Peter Arensburger Peter W Atkinson Shelby Bidwell Jim Biedler Ewan Birney Robert V Bruggner Javier Costas Monique R Coy Jonathan Crabtree Matt Crawford Becky Debruyn David Decaprio Karin Eiglmeier Eric Eisenstadt Hamza El-Dorry William M Gelbart Suely L Gomes Martin Hammond Linda I Hannick James R Hogan Michael H Holmes David Jaffe J Spencer Johnston Ryan C Kennedy Hean Koo Saul Kravitz Evgenia V Kriventseva David Kulp Kurt Labutti Eduardo Lee Song Li Diane D Lovin Chunhong Mao Evan Mauceli Carlos F M Menck Jason R Miller Philip Montgomery Akio Mori Ana L Nascimento Horacio F Naveira Chad Nusbaum Sinéad O'leary Joshua Orvis Mihaela Pertea Hadi Quesneville Kyanne R Reidenbach Yu-Hui Rogers Charles W Roth Jennifer R Schneider Michael Schatz Martin Shumway Mario Stanke Eric O Stinson Jose M C Tubio Janice P Vanzee Sergio Verjovski-Almeida Doreen Werner Owen White Stefan Wyder Qiandong Zeng Qi Zhao Yongmei Zhao Catherine A Hill Alexander S Raikhel Marcelo B Soares Dennis L Knudson Norman H Lee James Galagan Steven L Salzberg Ian T Paulsen George Dimopoulos Frank H Collins Bruce Birren Claire M Fraser-Liggett David W Severson

Science 2007 Jun 17;316(5832):1718-23. Epub 2007 May 17.

Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.

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June 2007

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences.

Authors:
Tarjei S Mikkelsen Matthew J Wakefield Bronwen Aken Chris T Amemiya Jean L Chang Shannon Duke Manuel Garber Andrew J Gentles Leo Goodstadt Andreas Heger Jerzy Jurka Michael Kamal Evan Mauceli Stephen M J Searle Ted Sharpe Michelle L Baker Mark A Batzer Panayiotis V Benos Katherine Belov Michele Clamp April Cook James Cuff Radhika Das Lance Davidow Janine E Deakin Melissa J Fazzari Jacob L Glass Manfred Grabherr John M Greally Wanjun Gu Timothy A Hore Gavin A Huttley Michael Kleber Randy L Jirtle Edda Koina Jeannie T Lee Shaun Mahony Marco A Marra Robert D Miller Robert D Nicholls Mayumi Oda Anthony T Papenfuss Zuly E Parra David D Pollock David A Ray Jacqueline E Schein Terence P Speed Katherine Thompson John L VandeBerg Claire M Wade Jerilyn A Walker Paul D Waters Caleb Webber Jennifer R Weidman Xiaohui Xie Michael C Zody Jennifer A Marshall Graves Chris P Ponting Matthew Breen Paul B Samollow Eric S Lander Kerstin Lindblad-Toh

Nature 2007 May;447(7141):167-77

Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.

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May 2007

Genome sequence, comparative analysis and haplotype structure of the domestic dog.

Authors:
Kerstin Lindblad-Toh Claire M Wade Tarjei S Mikkelsen Elinor K Karlsson David B Jaffe Michael Kamal Michele Clamp Jean L Chang Edward J Kulbokas Michael C Zody Evan Mauceli Xiaohui Xie Matthew Breen Robert K Wayne Elaine A Ostrander Chris P Ponting Francis Galibert Douglas R Smith Pieter J DeJong Ewen Kirkness Pablo Alvarez Tara Biagi William Brockman Jonathan Butler Chee-Wye Chin April Cook James Cuff Mark J Daly David DeCaprio Sante Gnerre Manfred Grabherr Manolis Kellis Michael Kleber Carolyne Bardeleben Leo Goodstadt Andreas Heger Christophe Hitte Lisa Kim Klaus-Peter Koepfli Heidi G Parker John P Pollinger Stephen M J Searle Nathan B Sutter Rachael Thomas Caleb Webber Jennifer Baldwin Adal Abebe Amr Abouelleil Lynne Aftuck Mostafa Ait-Zahra Tyler Aldredge Nicole Allen Peter An Scott Anderson Claudel Antoine Harindra Arachchi Ali Aslam Laura Ayotte Pasang Bachantsang Andrew Barry Tashi Bayul Mostafa Benamara Aaron Berlin Daniel Bessette Berta Blitshteyn Toby Bloom Jason Blye Leonid Boguslavskiy Claude Bonnet Boris Boukhgalter Adam Brown Patrick Cahill Nadia Calixte Jody Camarata Yama Cheshatsang Jeffrey Chu Mieke Citroen Alville Collymore Patrick Cooke Tenzin Dawoe Riza Daza Karin Decktor Stuart DeGray Norbu Dhargay Kimberly Dooley Kathleen Dooley Passang Dorje Kunsang Dorjee Lester Dorris Noah Duffey Alan Dupes Osebhajajeme Egbiremolen Richard Elong Jill Falk Abderrahim Farina Susan Faro Diallo Ferguson Patricia Ferreira Sheila Fisher Mike FitzGerald Karen Foley Chelsea Foley Alicia Franke Dennis Friedrich Diane Gage Manuel Garber Gary Gearin Georgia Giannoukos Tina Goode Audra Goyette Joseph Graham Edward Grandbois Kunsang Gyaltsen Nabil Hafez Daniel Hagopian Birhane Hagos Jennifer Hall Claire Healy Ryan Hegarty Tracey Honan Andrea Horn Nathan Houde Leanne Hughes Leigh Hunnicutt M Husby Benjamin Jester Charlien Jones Asha Kamat Ben Kanga Cristyn Kells Dmitry Khazanovich Alix Chinh Kieu Peter Kisner Mayank Kumar Krista Lance Thomas Landers Marcia Lara William Lee Jean-Pierre Leger Niall Lennon Lisa Leuper Sarah LeVine Jinlei Liu Xiaohong Liu Yeshi Lokyitsang Tashi Lokyitsang Annie Lui Jan Macdonald John Major Richard Marabella Kebede Maru Charles Matthews Susan McDonough Teena Mehta James Meldrim Alexandre Melnikov Louis Meneus Atanas Mihalev Tanya Mihova Karen Miller Rachel Mittelman Valentine Mlenga Leonidas Mulrain Glen Munson Adam Navidi Jerome Naylor Tuyen Nguyen Nga Nguyen Cindy Nguyen Thu Nguyen Robert Nicol Nyima Norbu Choe Norbu Nathaniel Novod Tenchoe Nyima Peter Olandt Barry O'Neill Keith O'Neill Sahal Osman Lucien Oyono Christopher Patti Danielle Perrin Pema Phunkhang Fritz Pierre Margaret Priest Anthony Rachupka Sujaa Raghuraman Rayale Rameau Verneda Ray Christina Raymond Filip Rege Cecil Rise Julie Rogers Peter Rogov Julie Sahalie Sampath Settipalli Theodore Sharpe Terrance Shea Mechele Sheehan Ngawang Sherpa Jianying Shi Diana Shih Jessie Sloan Cherylyn Smith Todd Sparrow John Stalker Nicole Stange-Thomann Sharon Stavropoulos Catherine Stone Sabrina Stone Sean Sykes Pierre Tchuinga Pema Tenzing Senait Tesfaye Dawa Thoulutsang Yama Thoulutsang Kerri Topham Ira Topping Tsamla Tsamla Helen Vassiliev Vijay Venkataraman Andy Vo Tsering Wangchuk Tsering Wangdi Michael Weiand Jane Wilkinson Adam Wilson Shailendra Yadav Shuli Yang Xiaoping Yang Geneva Young Qing Yu Joanne Zainoun Lisa Zembek Andrew Zimmer Eric S Lander

Nature 2005 Dec;438(7069):803-19

Broad Institute of Harvard and MIT, 320 Charles Street, Cambridge, Massachusetts 02141, USA.

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December 2005