Resources

  • Resource |

    Genome in a Bottle Consortium presents a high-confidence dataset for benchmarking small variant calls in human genomes.

    • Justin M. Zook
    • , Jennifer McDaniel
    • , Nathan D. Olson
    • , Justin Wagner
    • , Hemang Parikh
    • , Haynes Heaton
    • , Sean A. Irvine
    • , Len Trigg
    • , Rebecca Truty
    • , Cory Y. McLean
    • , Francisco M. De La Vega
    • , Chunlin Xiao
    • , Stephen Sherry
    •  & Marc Salit
  • Resource | | open

    A resource of >1,500 bacterial reference genomes sheds light on the human gut microbiome.

    • Yuanqiang Zou
    • , Wenbin Xue
    • , Guangwen Luo
    • , Ziqing Deng
    • , Panpan Qin
    • , Ruijin Guo
    • , Haipeng Sun
    • , Yan Xia
    • , Suisha Liang
    • , Ying Dai
    • , Daiwei Wan
    • , Rongrong Jiang
    • , Lili Su
    • , Qiang Feng
    • , Zhuye Jie
    • , Tongkun Guo
    • , Zhongkui Xia
    • , Chuan Liu
    • , Jinghong Yu
    • , Yuxiang Lin
    • , Shanmei Tang
    • , Guicheng Huo
    • , Xun Xu
    • , Yong Hou
    • , Xin Liu
    • , Jian Wang
    • , Huanming Yang
    • , Karsten Kristiansen
    • , Junhua Li
    • , Huijue Jia
    •  & Liang Xiao
  • Resource | | open

    A large bacterial strain collection and genome sequences will boost gut microbiome research.

    • Samuel C. Forster
    • , Nitin Kumar
    • , Blessing O. Anonye
    • , Alexandre Almeida
    • , Elisa Viciani
    • , Mark D. Stares
    • , Matthew Dunn
    • , Tapoka T. Mkandawire
    • , Ana Zhu
    • , Yan Shao
    • , Lindsay J. Pike
    • , Thomas Louie
    • , Hilary P. Browne
    • , Alex L. Mitchell
    • , B. Anne Neville
    • , Robert D. Finn
    •  & Trevor D. Lawley
  • Resource | | open

    Rumen microbiome biology gets a boost with the release of 410 high-quality reference genomes from the Hungate1000 project.

    • Rekha Seshadri
    • , Sinead C Leahy
    • , Graeme T Attwood
    • , Koon Hoong Teh
    • , Suzanne C Lambie
    • , Adrian L Cookson
    • , Emiley A Eloe-Fadrosh
    • , Georgios A Pavlopoulos
    • , Michalis Hadjithomas
    • , Neha J Varghese
    • , David Paez-Espino
    • , Hungate1000 project collaborators
    • , Nikola Palevich
    • , Peter H Janssen
    • , Ron S Ronimus
    • , Samantha Noel
    • , Priya Soni
    • , Kerri Reilly
    • , Todd Atherly
    • , Cherie Ziemer
    • , Andre-Denis Wright
    • , Suzanne Ishaq
    • , Michael Cotta
    • , Stephanie Thompson
    • , Katie Crosley
    • , Nest McKain
    • , R John Wallace
    • , Harry J Flint
    • , Jennifer C Martin
    • , Robert J Forster
    • , Robert J Gruninger
    • , Tim McAllister
    • , Rosalind Gilbert
    • , Diane Ouwerkerk
    • , Athol Klieve
    • , Rafat Al Jassim
    • , Stuart Denman
    • , Chris McSweeney
    • , Carly Rosewarne
    • , Satoshi Koike
    • , Yasuo Kobayashi
    • , Makoto Mitsumori
    • , Takumi Shinkai
    • , Silvio Cravero
    • , María Cerón Cucchi
    • , Rechelle Perry
    • , Gemma Henderson
    • , Christopher J Creevey
    • , Nicolas Terrapon
    • , Pascal Lapebie
    • , Elodie Drula
    • , Vincent Lombard
    • , Edward Rubin
    • , Nikos C Kyrpides
    • , Bernard Henrissat
    • , Tanja Woyke
    • , Natalia N Ivanova
    •  & William J Kelly
  • Resource |

    Large-scale integration of metabolite and protein structural data with existing networks of human metabolism provides insights into gene function and how drugs affect metabolic response.

    • Elizabeth Brunk
    • , Swagatika Sahoo
    • , Daniel C Zielinski
    • , Ali Altunkaya
    • , Andreas Dräger
    • , Nathan Mih
    • , Francesco Gatto
    • , Avlant Nilsson
    • , German Andres Preciat Gonzalez
    • , Maike Kathrin Aurich
    • , Andreas Prlić
    • , Anand Sastry
    • , Anna D Danielsdottir
    • , Almut Heinken
    • , Alberto Noronha
    • , Peter W Rose
    • , Stephen K Burley
    • , Ronan M T Fleming
    • , Jens Nielsen
    • , Ines Thiele
    •  & Bernhard O Palsson
  • Resource |

    A survey of cell envelope proteins and their interacting partners in E. coli by mass spectrometry reveals insights into essential bacterial processes.

    • Mohan Babu
    • , Cedoljub Bundalovic-Torma
    • , Charles Calmettes
    • , Sadhna Phanse
    • , Qingzhou Zhang
    • , Yue Jiang
    • , Zoran Minic
    • , Sunyoung Kim
    • , Jitender Mehla
    • , Alla Gagarinova
    • , Irina Rodionova
    • , Ashwani Kumar
    • , Hongbo Guo
    • , Olga Kagan
    • , Oxana Pogoutse
    • , Hiroyuki Aoki
    • , Viktor Deineko
    • , J Harry Caufield
    • , Erik Holtzapple
    • , Zhongge Zhang
    • , Ake Vastermark
    • , Yogee Pandya
    • , Christine Chieh-lin Lai
    • , Majida El Bakkouri
    • , Yogesh Hooda
    • , Megha Shah
    • , Dan Burnside
    • , Mohsen Hooshyar
    • , James Vlasblom
    • , Sessandra V Rajagopala
    • , Ashkan Golshani
    • , Stefan Wuchty
    • , Jack F Greenblatt
    • , Milton Saier
    • , Peter Uetz
    • , Trevor F Moraes
    • , John Parkinson
    •  & Andrew Emili
  • Resource |

    An atlas of microRNA expression patterns and regulators is produced by deep sequencing of short RNAs in human and mouse cells.

    • Derek de Rie
    • , Imad Abugessaisa
    • , Tanvir Alam
    • , Erik Arner
    • , Peter Arner
    • , Haitham Ashoor
    • , Gaby Åström
    • , Magda Babina
    • , Nicolas Bertin
    • , A Maxwell Burroughs
    • , Ailsa J Carlisle
    • , Carsten O Daub
    • , Michael Detmar
    • , Ruslan Deviatiiarov
    • , Alexandre Fort
    • , Claudia Gebhard
    • , Daniel Goldowitz
    • , Sven Guhl
    • , Thomas J Ha
    • , Jayson Harshbarger
    • , Akira Hasegawa
    • , Kosuke Hashimoto
    • , Meenhard Herlyn
    • , Peter Heutink
    • , Kelly J Hitchens
    • , Chung Chau Hon
    • , Edward Huang
    • , Yuri Ishizu
    • , Chieko Kai
    • , Takeya Kasukawa
    • , Peter Klinken
    • , Timo Lassmann
    • , Charles-Henri Lecellier
    • , Weonju Lee
    • , Marina Lizio
    • , Vsevolod Makeev
    • , Anthony Mathelier
    • , Yulia A Medvedeva
    • , Niklas Mejhert
    • , Christopher J Mungall
    • , Shohei Noma
    • , Mitsuhiro Ohshima
    • , Mariko Okada-Hatakeyama
    • , Helena Persson
    • , Patrizia Rizzu
    • , Filip Roudnicky
    • , Pål Sætrom
    • , Hiroki Sato
    • , Jessica Severin
    • , Jay W Shin
    • , Rolf K Swoboda
    • , Hiroshi Tarui
    • , Hiroo Toyoda
    • , Kristoffer Vitting-Seerup
    • , Louise Winteringham
    • , Yoko Yamaguchi
    • , Kayoko Yasuzawa
    • , Misako Yoneda
    • , Noriko Yumoto
    • , Susan Zabierowski
    • , Peter G Zhang
    • , Christine A Wells
    • , Kim M Summers
    • , Hideya Kawaji
    • , Albin Sandelin
    • , Michael Rehli
    • , The FANTOM Consortium
    • , Yoshihide Hayashizaki
    • , Piero Carninci
    • , Alistair R R Forrest
    •  & Michiel J L de Hoon
  • Resource |

    B-cell VH region repertoire sequencing of eight anatomical sites in six human donors reveals distinct networks of clone distribution.

    • Wenzhao Meng
    • , Bochao Zhang
    • , Gregory W Schwartz
    • , Aaron M Rosenfeld
    • , Daqiu Ren
    • , Joseph J C Thome
    • , Dustin J Carpenter
    • , Nobuhide Matsuoka
    • , Harvey Lerner
    • , Amy L Friedman
    • , Tomer Granot
    • , Donna L Farber
    • , Mark J Shlomchik
    • , Uri Hershberg
    •  & Eline T Luning Prak
  • Resource | | open

    Metagenomic and microbial sequence data are made easier to interpret with the addition of 1,003 genomes to the Genomic Encyclopedia of Bacteria and Archaea.

    • Supratim Mukherjee
    • , Rekha Seshadri
    • , Neha J Varghese
    • , Emiley A Eloe-Fadrosh
    • , Jan P Meier-Kolthoff
    • , Markus Göker
    • , R Cameron Coates
    • , Michalis Hadjithomas
    • , Georgios A Pavlopoulos
    • , David Paez-Espino
    • , Yasuo Yoshikuni
    • , Axel Visel
    • , William B Whitman
    • , George M Garrity
    • , Jonathan A Eisen
    • , Philip Hugenholtz
    • , Amrita Pati
    • , Natalia N Ivanova
    • , Tanja Woyke
    • , Hans-Peter Klenk
    •  & Nikos C Kyrpides
  • Resource |

    A proteomic atlas of a model legume and its rhizobial symbiont provides a resource for understanding symbiotic nitrogen fixation.

    • Harald Marx
    • , Catherine E Minogue
    • , Dhileepkumar Jayaraman
    • , Alicia L Richards
    • , Nicholas W Kwiecien
    • , Alireza F Siahpirani
    • , Shanmugam Rajasekar
    • , Junko Maeda
    • , Kevin Garcia
    • , Angel R Del Valle-Echevarria
    • , Jeremy D Volkening
    • , Michael S Westphall
    • , Sushmita Roy
    • , Michael R Sussman
    • , Jean-Michel Ané
    •  & Joshua J Coon
  • Resource |

    Proteomics, lipidomics and metabolomics of single gene deletion yeast strains sheds light on mitochondrial protein biology.

    • Jonathan A Stefely
    • , Nicholas W Kwiecien
    • , Elyse C Freiberger
    • , Alicia L Richards
    • , Adam Jochem
    • , Matthew J P Rush
    • , Arne Ulbrich
    • , Kyle P Robinson
    • , Paul D Hutchins
    • , Mike T Veling
    • , Xiao Guo
    • , Zachary A Kemmerer
    • , Kyle J Connors
    • , Edna A Trujillo
    • , Jacob Sokol
    • , Harald Marx
    • , Michael S Westphall
    • , Alexander S Hebert
    • , David J Pagliarini
    •  & Joshua J Coon
  • Resource | | open

    The global genetic diversity of cassava and related Manihot species is revealed by sequencing of 53 cultivated and wild accessions and genotyping of 268 African cassavas, providing a vital resource for breeding.

    • Jessen V Bredeson
    • , Jessica B Lyons
    • , Simon E Prochnik
    • , G Albert Wu
    • , Cindy M Ha
    • , Eric Edsinger-Gonzales
    • , Jane Grimwood
    • , Jeremy Schmutz
    • , Ismail Y Rabbi
    • , Chiedozie Egesi
    • , Poasa Nauluvula
    • , Vincent Lebot
    • , Joseph Ndunguru
    • , Geoffrey Mkamilo
    • , Rebecca S Bart
    • , Tim L Setter
    • , Roslyn M Gleadow
    • , Peter Kulakow
    • , Morag E Ferguson
    • , Steve Rounsley
    •  & Daniel S Rokhsar
  • Resource |

    A large-scale quantification of Escherichia coli proteomes across 22 experimental conditions.

    • Alexander Schmidt
    • , Karl Kochanowski
    • , Silke Vedelaar
    • , Erik Ahrné
    • , Benjamin Volkmer
    • , Luciano Callipo
    • , Kèvin Knoops
    • , Manuel Bauer
    • , Ruedi Aebersold
    •  & Matthias Heinemann
  • Resource |

    A well-characterized library of experimental kinase inhibitors provides leads for targeting the untargeted kinome.

    • Jonathan M Elkins
    • , Vita Fedele
    • , Marta Szklarz
    • , Kamal R Abdul Azeez
    • , Eidarus Salah
    • , Jowita Mikolajczyk
    • , Sergei Romanov
    • , Nikolai Sepetov
    • , Xi-Ping Huang
    • , Bryan L Roth
    • , Ayman Al Haj Zen
    • , Denis Fourches
    • , Eugene Muratov
    • , Alex Tropsha
    • , Joel Morris
    • , Beverly A Teicher
    • , Mark Kunkel
    • , Eric Polley
    • , Karen E Lackey
    • , Francis L Atkinson
    • , John P Overington
    • , Paul Bamborough
    • , Susanne Müller
    • , Daniel J Price
    • , Timothy M Willson
    • , David H Drewry
    • , Stefan Knapp
    •  & William J Zuercher
  • Resource |

    The mouse gut microbiome is catalogued and compared to the human microbiome.

    • Liang Xiao
    • , Qiang Feng
    • , Suisha Liang
    • , Si Brask Sonne
    • , Zhongkui Xia
    • , Xinmin Qiu
    • , Xiaoping Li
    • , Hua Long
    • , Jianfeng Zhang
    • , Dongya Zhang
    • , Chuan Liu
    • , Zhiwei Fang
    • , Joyce Chou
    • , Jacob Glanville
    • , Qin Hao
    • , Dorota Kotowska
    • , Camilla Colding
    • , Tine Rask Licht
    • , Donghai Wu
    • , Jun Yu
    • , Joseph Jao Yiu Sung
    • , Qiaoyi Liang
    • , Junhua Li
    • , Huijue Jia
    • , Zhou Lan
    • , Valentina Tremaroli
    • , Piotr Dworzynski
    • , H Bjørn Nielsen
    • , Fredrik Bäckhed
    • , Joël Doré
    • , Emmanuelle Le Chatelier
    • , S Dusko Ehrlich
    • , John C Lin
    • , Manimozhiyan Arumugam
    • , Jun Wang
    • , Lise Madsen
    •  & Karsten Kristiansen
  • Resource |

    Comprehensive analysis of changes in protein acetylation in response to lysine deacetylase inhibitors uncovers inhibitor specificities.

    • Christian Schölz
    • , Brian T Weinert
    • , Sebastian A Wagner
    • , Petra Beli
    • , Yasuyuki Miyake
    • , Jun Qi
    • , Lars J Jensen
    • , Werner Streicher
    • , Anna R McCarthy
    • , Nicholas J Westwood
    • , Sonia Lain
    • , Jürgen Cox
    • , Patrick Matthias
    • , Matthias Mann
    • , James E Bradner
    •  & Chunaram Choudhary
  • Resource |

    Comprehensive analysis of the binding specificities of C2H2 zinc finger proteins reveals their DNA recognition code.

    • Hamed S Najafabadi
    • , Sanie Mnaimneh
    • , Frank W Schmitges
    • , Michael Garton
    • , Kathy N Lam
    • , Ally Yang
    • , Mihai Albu
    • , Matthew T Weirauch
    • , Ernest Radovani
    • , Philip M Kim
    • , Jack Greenblatt
    • , Brendan J Frey
    •  & Timothy R Hughes
  • Resource | | open

    Resequencing of 302 soybean accessions and GWAS provide a comprehensive resource for soybean geneticists and breeders.

    • Zhengkui Zhou
    • , Yu Jiang
    • , Zheng Wang
    • , Zhiheng Gou
    • , Jun Lyu
    • , Weiyu Li
    • , Yanjun Yu
    • , Liping Shu
    • , Yingjun Zhao
    • , Yanming Ma
    • , Chao Fang
    • , Yanting Shen
    • , Tengfei Liu
    • , Congcong Li
    • , Qing Li
    • , Mian Wu
    • , Min Wang
    • , Yunshuai Wu
    • , Yang Dong
    • , Wenting Wan
    • , Xiao Wang
    • , Zhaoli Ding
    • , Yuedong Gao
    • , Hui Xiang
    • , Baoge Zhu
    • , Suk-Ha Lee
    • , Wen Wang
    •  & Zhixi Tian
  • Resource |

    A comprehensive analysis of RNA sequencing and single-nucleotide polymorphism (SNP) array data provides new insights into the biology of 675 human cancer cell lines

    • Christiaan Klijn
    • , Steffen Durinck
    • , Eric W Stawiski
    • , Peter M Haverty
    • , Zhaoshi Jiang
    • , Hanbin Liu
    • , Jeremiah Degenhardt
    • , Oleg Mayba
    • , Florian Gnad
    • , Jinfeng Liu
    • , Gregoire Pau
    • , Jens Reeder
    • , Yi Cao
    • , Kiran Mukhyala
    • , Suresh K Selvaraj
    • , Mamie Yu
    • , Gregory J Zynda
    • , Matthew J Brauer
    • , Thomas D Wu
    • , Robert C Gentleman
    • , Gerard Manning
    • , Robert L Yauch
    • , Richard Bourgon
    • , David Stokoe
    • , Zora Modrusan
    • , Richard M Neve
    • , Frederic J de Sauvage
    • , Jeffrey Settleman
    • , Somasekar Seshagiri
    •  & Zemin Zhang
  • Resource |

    Efforts to improve the efficiency of photosynthesis in crop plants will benefit from a resource of transcriptomic and metabolomic data on maize and rice.

    • Lin Wang
    • , Angelika Czedik-Eysenberg
    • , Rachel A Mertz
    • , Yaqing Si
    • , Takayuki Tohge
    • , Adriano Nunes-Nesi
    • , Stephanie Arrivault
    • , Lauren K Dedow
    • , Douglas W Bryant
    • , Wen Zhou
    • , Jiajia Xu
    • , Sarit Weissmann
    • , Anthony Studer
    • , Pinghua Li
    • , Cankui Zhang
    • , Therese LaRue
    • , Ying Shao
    • , Zehong Ding
    • , Qi Sun
    • , Rohan V Patel
    • , Robert Turgeon
    • , Xinguang Zhu
    • , Nicholas J Provart
    • , Todd C Mockler
    • , Alisdair R Fernie
    • , Mark Stitt
    • , Peng Liu
    •  & Thomas P Brutnell
  • Resource |

    Li et al. provide the largest catalog of genes in the human gut microbiome based on samples from >1,200 individuals across three continents.

    • Junhua Li
    • , Huijue Jia
    • , Xianghang Cai
    • , Huanzi Zhong
    • , Qiang Feng
    • , Shinichi Sunagawa
    • , Manimozhiyan Arumugam
    • , Jens Roat Kultima
    • , Edi Prifti
    • , Trine Nielsen
    • , Agnieszka Sierakowska Juncker
    • , Chaysavanh Manichanh
    • , Bing Chen
    • , Wenwei Zhang
    • , Florence Levenez
    • , Juan Wang
    • , Xun Xu
    • , Liang Xiao
    • , Suisha Liang
    • , Dongya Zhang
    • , Zhaoxi Zhang
    • , Weineng Chen
    • , Hailong Zhao
    • , Jumana Yousuf Al-Aama
    • , Sherif Edris
    • , Huanming Yang
    • , Jian Wang
    • , Torben Hansen
    • , Henrik Bjørn Nielsen
    • , Søren Brunak
    • , Karsten Kristiansen
    • , Francisco Guarner
    • , Oluf Pedersen
    • , Joel Doré
    • , S Dusko Ehrlich
    • , MetaHIT Consortium
    • , Nicolas Pons
    • , Emmanuelle Le Chatelier
    • , Jean-Michel Batto
    • , Sean Kennedy
    • , Florence Haimet
    • , Yohanan Winogradski
    • , Eric Pelletier
    • , Denis LePaslier
    • , François Artiguenave
    • , Thomas Bruls
    • , Jean Weissenbach
    • , Keith Turner
    • , Julian Parkhill
    • , Maria Antolin
    • , Francesc Casellas
    • , Natalia Borruel
    • , Encarna Varela
    • , Antonio Torrejon
    • , Gérard Denariaz
    • , Muriel Derrien
    • , Johan E T van Hylckama Vlieg
    • , Patrick Viega
    • , Raish Oozeer
    • , Jan Knoll
    • , Maria Rescigno
    • , Christian Brechot
    • , Christine M'Rini
    • , Alexandre Mérieux
    • , Takuji Yamada
    • , Sebastian Tims
    • , Erwin G Zoetendal
    • , Michiel Kleerebezem
    • , Willem M de Vos
    • , Antonella Cultrone
    • , Marion Leclerc
    • , Catherine Juste
    • , Eric Guedon
    • , Christine Delorme
    • , Séverine Layec
    • , Ghalia Khaci
    • , Maarten van de Guchte
    • , Gaetana Vandemeulebrouck
    • , Alexandre Jamet
    • , Rozenn Dervyn
    • , Nicolas Sanchez
    • , Hervé Blottière
    • , Emmanuelle Maguin
    • , Pierre Renault
    • , Julien Tap
    • , Daniel R Mende
    • , Peer Bork
    •  & Jun Wang
  • Resource |

    Yeast-two hybrid screening of E. coli proteins and integration with protein structure and genetic interaction data provides an extensive interactome resource.

    • Seesandra V Rajagopala
    • , Patricia Sikorski
    • , Ashwani Kumar
    • , Roberto Mosca
    • , James Vlasblom
    • , Roland Arnold
    • , Jonathan Franca-Koh
    • , Suman B Pakala
    • , Sadhna Phanse
    • , Arnaud Ceol
    • , Roman Häuser
    • , Gabriella Siszler
    • , Stefan Wuchty
    • , Andrew Emili
    • , Mohan Babu
    • , Patrick Aloy
    • , Rembert Pieper
    •  & Peter Uetz
  • Resource | | open

    Genome sequences of the Chinese hamster and six Chinese hamster ovary cell lines provide a resource to aid in improving production of recombinant proteins.

    • Nathan E Lewis
    • , Xin Liu
    • , Yuxiang Li
    • , Harish Nagarajan
    • , George Yerganian
    • , Edward O'Brien
    • , Aarash Bordbar
    • , Anne M Roth
    • , Jeffrey Rosenbloom
    • , Chao Bian
    • , Min Xie
    • , Wenbin Chen
    • , Ning Li
    • , Deniz Baycin-Hizal
    • , Haythem Latif
    • , Jochen Forster
    • , Michael J Betenbaugh
    • , Iman Famili
    • , Xun Xu
    • , Jun Wang
    •  & Bernhard O Palsson
  • Resource |

    The metabolic modeling community has curated information from five models to create the most comprehensive model of human metabolism to date.

    • Ines Thiele
    • , Neil Swainston
    • , Ronan M T Fleming
    • , Andreas Hoppe
    • , Swagatika Sahoo
    • , Maike K Aurich
    • , Hulda Haraldsdottir
    • , Monica L Mo
    • , Ottar Rolfsson
    • , Miranda D Stobbe
    • , Stefan G Thorleifsson
    • , Rasmus Agren
    • , Christian Bölling
    • , Sergio Bordel
    • , Arvind K Chavali
    • , Paul Dobson
    • , Warwick B Dunn
    • , Lukas Endler
    • , David Hala
    • , Michael Hucka
    • , Duncan Hull
    • , Daniel Jameson
    • , Neema Jamshidi
    • , Jon J Jonsson
    • , Nick Juty
    • , Sarah Keating
    • , Intawat Nookaew
    • , Nicolas Le Novère
    • , Naglis Malys
    • , Alexander Mazein
    • , Jason A Papin
    • , Nathan D Price
    • , Evgeni Selkov Sr
    • , Martin I Sigurdsson
    • , Evangelos Simeonidis
    • , Nikolaus Sonnenschein
    • , Kieran Smallbone
    • , Anatoly Sorokin
    • , Johannes H G M van Beek
    • , Dieter Weichart
    • , Igor Goryanin
    • , Jens Nielsen
    • , Hans V Westerhoff
    • , Douglas B Kell
    • , Pedro Mendes
    •  & Bernhard Ø Palsson
  • Resource |

    A collection of TALENs targeted to 18,740 human protein-coding genes will facilitate genetic engineering of human cells.

    • Yongsub Kim
    • , Jiyeon Kweon
    • , Annie Kim
    • , Jae Kyung Chon
    • , Ji Yeon Yoo
    • , Hye Joo Kim
    • , Sojung Kim
    • , Choongil Lee
    • , Euihwan Jeong
    • , Eugene Chung
    • , Doyoung Kim
    • , Mi Seon Lee
    • , Eun Mi Go
    • , Hye Jung Song
    • , Hwangbeom Kim
    • , Namjin Cho
    • , Duhee Bang
    • , Seokjoong Kim
    •  & Jin-Soo Kim
  • Resource |

    Transcription activator–like effector nucleases (TALENs) enable genetic modification at specific sites in a genome. Reyon et al. present a method for high-throughput generation of TALENs, facilitating large-scale genome engineering.

    • Deepak Reyon
    • , Shengdar Q Tsai
    • , Cyd Khayter
    • , Jennifer A Foden
    • , Jeffry D Sander
    •  & J Keith Joung
  • Resource |

    PARP inhibitors have recently entered phase 3 clinical trials as cancer therapeutics, but the specificity of many of these compounds is unknown. Wahlberg et al. used biochemical approaches to show that most PARP inhibitors target multiple PARP family members.

    • Elisabet Wahlberg
    • , Tobias Karlberg
    • , Ekaterina Kouznetsova
    • , Natalia Markova
    • , Antonio Macchiarulo
    • , Ann-Gerd Thorsell
    • , Ewa Pol
    • , Åsa Frostell
    • , Torun Ekblad
    • , Delal Öncü
    • , Björn Kull
    • , Graeme Michael Robertson
    • , Roberto Pellicciari
    • , Herwig Schüler
    •  & Johan Weigelt
  • Resource |

    A catalog of genetic variation in a crop species facilitates marker-assisted breeding, gene mapping and analysis of elite traits. Xu et al. resequenced 40 cultivated and 10 wild rice accessions to >15 × coverage, yielding 6.5 million single-nucleotide polymorphisms and 808,000 small insertions and deletions.

    • Xun Xu
    • , Xin Liu
    • , Song Ge
    • , Jeffrey D Jensen
    • , Fengyi Hu
    • , Xin Li
    • , Yang Dong
    • , Ryan N Gutenkunst
    • , Lin Fang
    • , Lei Huang
    • , Jingxiang Li
    • , Weiming He
    • , Guojie Zhang
    • , Xiaoming Zheng
    • , Fumin Zhang
    • , Yingrui Li
    • , Chang Yu
    • , Karsten Kristiansen
    • , Xiuqing Zhang
    • , Jian Wang
    • , Mark Wright
    • , Susan McCouch
    • , Rasmus Nielsen
    • , Jun Wang
    •  & Wen Wang
  • Resource |

    The International Stem Cell Initiative compares 125 ethnically diverse human embryonic stem cell lines at early and late passage. Data on karotype, single-nucleotide polymorphisms and methylation shed light on how the cells adapt to long-term culture.

    • The International Stem Cell Initiative
    • , Katherine Amps
    • , Peter W Andrews
    • , George Anyfantis
    • , Lyle Armstrong
    • , Stuart Avery
    • , Hossein Baharvand
    • , Julie Baker
    • , Duncan Baker
    • , Maria B Munoz
    • , Stephen Beil
    • , Nissim Benvenisty
    • , Dalit Ben-Yosef
    • , Juan-Carlos Biancotti
    • , Alexis Bosman
    • , Romulo Martin Brena
    • , Daniel Brison
    • , Gunilla Caisander
    • , María V Camarasa
    • , Jieming Chen
    • , Eric Chiao
    • , Young Min Choi
    • , Andre B H Choo
    • , Daniel Collins
    • , Alan Colman
    • , Jeremy M Crook
    • , George Q Daley
    • , Anne Dalton
    • , Paul A De Sousa
    • , Chris Denning
    • , Janet Downie
    • , Petr Dvorak
    • , Karen D Montgomery
    • , Anis Feki
    • , Angela Ford
    • , Victoria Fox
    • , Ana M Fraga
    • , Tzvia Frumkin
    • , Lin Ge
    • , Paul J Gokhale
    • , Tamar Golan-Lev
    • , Hamid Gourabi
    • , Michal Gropp
    • , Lu Guangxiu
    • , Ales Hampl
    • , Katie Harron
    • , Lyn Healy
    • , Wishva Herath
    • , Frida Holm
    • , Outi Hovatta
    • , Johan Hyllner
    • , Maneesha S Inamdar
    • , Astrid Kresentia Irwanto
    • , Tetsuya Ishii
    • , Marisa Jaconi
    • , Ying Jin
    • , Susan Kimber
    • , Sergey Kiselev
    • , Barbara B Knowles
    • , Oded Kopper
    • , Valeri Kukharenko
    • , Anver Kuliev
    • , Maria A Lagarkova
    • , Peter W Laird
    • , Majlinda Lako
    • , Andrew L Laslett
    • , Neta Lavon
    • , Dong Ryul Lee
    • , Jeoung Eun Lee
    • , Chunliang Li
    • , Linda S Lim
    • , Tenneille E Ludwig
    • , Yu Ma
    • , Edna Maltby
    • , Ileana Mateizel
    • , Yoav Mayshar
    • , Maria Mileikovsky
    • , Stephen L Minger
    • , Takamichi Miyazaki
    • , Shin Yong Moon
    • , Harry Moore
    • , Christine Mummery
    • , Andras Nagy
    • , Norio Nakatsuji
    • , Kavita Narwani
    • , Steve K W Oh
    • , Sun Kyung Oh
    • , Cia Olson
    • , Timo Otonkoski
    • , Fei Pan
    • , In-Hyun Park
    • , Steve Pells
    • , Martin F Pera
    • , Lygia V Pereira
    • , Ouyang Qi
    • , Grace Selva Raj
    • , Benjamin Reubinoff
    • , Alan Robins
    • , Paul Robson
    • , Janet Rossant
    • , Ghasem H Salekdeh
    • , Thomas C Schulz
    • , Karen Sermon
    • , Jameelah Sheik Mohamed
    • , Hui Shen
    • , Eric Sherrer
    • , Kuldip Sidhu
    • , Shirani Sivarajah
    • , Heli Skottman
    • , Claudia Spits
    • , Glyn N Stacey
    • , Raimund Strehl
    • , Nick Strelchenko
    • , Hirofumi Suemori
    • , Bowen Sun
    • , Riitta Suuronen
    • , Kazutoshi Takahashi
    • , Timo Tuuri
    • , Parvathy Venu
    • , Yuri Verlinsky
    • , Dorien Ward-van Oostwaard
    • , Daniel J Weisenberger
    • , Yue Wu
    • , Shinya Yamanaka
    • , Lorraine Young
    •  & Qi Zhou
  • Resource |

    Davis et al. extend their previous efforts to use inhibitor-kinase interactions to understand kinase inhibitor selectivity by profiling the binding of 72 kinase inhibitors to 442 human kinase catalytic domains. The data reveal group-specific differences in selectivity and suggest the feasibility of developing reasonably specific inhibitors for most kinases.

    • Mindy I Davis
    • , Jeremy P Hunt
    • , Sanna Herrgard
    • , Pietro Ciceri
    • , Lisa M Wodicka
    • , Gabriel Pallares
    • , Michael Hocker
    • , Daniel K Treiber
    •  & Patrick P Zarrinkar
  • Resource |

    The promiscuity of most kinase inhibitors can cause drug toxicity and complicate the interpretation of experiments. Rather than assessing kinase-compound binding, Anastassiadis et al. use functional assays to profile the activities of 178 commercially available kinase inhibitors against 300 recombinant human protein kinases.

    • Theonie Anastassiadis
    • , Sean W Deacon
    • , Karthik Devarajan
    • , Haiching Ma
    •  & Jeffrey R Peterson
  • Resource |

    Prosser et al. describe a resource of mouse embryonic stem cell clones harboring deletions that target 392 microRNA loci.. Because the targeting cassettes can be readily replaced by reporter genes, conditional alleles and other variants, the lines should facilitate a broad range of studies into microRNA function.

    • Haydn M Prosser
    • , Hiroko Koike-Yusa
    • , James D Cooper
    • , Frances C Law
    •  & Allan Bradley
  • Resource |

    Essential genes have been effectively studied using temperature-sensitive alleles in yeast. Li et al. construct a large collection of temperature-sensitive yeast mutants and show how it enables high-throughput analyses of the function of essential genes.

    • Zhijian Li
    • , Franco J Vizeacoumar
    • , Sondra Bahr
    • , Jingjing Li
    • , Jonas Warringer
    • , Frederick S Vizeacoumar
    • , Renqiang Min
    • , Benjamin VanderSluis
    • , Jeremy Bellay
    • , Michael DeVit
    • , James A Fleming
    • , Andrew Stephens
    • , Julian Haase
    • , Zhen-Yuan Lin
    • , Anastasia Baryshnikova
    • , Hong Lu
    • , Zhun Yan
    • , Ke Jin
    • , Sarah Barker
    • , Alessandro Datti
    • , Guri Giaever
    • , Corey Nislow
    • , Chris Bulawa
    • , Chad L Myers
    • , Michael Costanzo
    • , Anne-Claude Gingras
    • , Zhaolei Zhang
    • , Anders Blomberg
    • , Kerry Bloom
    • , Brenda Andrews
    •  & Charles Boone
  • Resource |

    Previous work has suggested that induced pluripotent stem cells (iPSCs) are inferior to embryonic stem cells (ESCs) with respect to in vitro differentiation, raising questions about the utility of iPSCs for disease modeling. Characterization of a test set of 16 human iPSC lines shows that they perform as well as ESCs in differentiating to motor neurons.

    • Gabriella L Boulting
    • , Evangelos Kiskinis
    • , Gist F Croft
    • , Mackenzie W Amoroso
    • , Derek H Oakley
    • , Brian J Wainger
    • , Damian J Williams
    • , David J Kahler
    • , Mariko Yamaki
    • , Lance Davidow
    • , Christopher T Rodolfa
    • , John T Dimos
    • , Shravani Mikkilineni
    • , Amy B MacDermott
    • , Clifford J Woolf
    • , Christopher E Henderson
    • , Hynek Wichterle
    •  & Kevin Eggan
  • Resource |

    Reconstructing a metabolic model from the genome sequence of an organism is a useful but arduous approach for predicting phenotypes. Henry et al. describe a resource that automates most of this process and apply it to create >100 new metabolic models of microbes.

    • Christopher S Henry
    • , Matthew DeJongh
    • , Aaron A Best
    • , Paul M Frybarger
    • , Ben Linsay
    •  & Rick L Stevens
  • Resource |

    Tang et al. present the first large-scale, gene-specific library of knockout mice. They disrupt 472 genes encoding secreted or transmembrane proteins and report the results of a comprehensive phenotypic analysis.

    • Tracy Tang
    • , Li Li
    • , Jerry Tang
    • , Yun Li
    • , Wei Yu Lin
    • , Flavius Martin
    • , Deanna Grant
    • , Mark Solloway
    • , Leon Parker
    • , Weilan Ye
    • , William Forrest
    • , Nico Ghilardi
    • , Tamas Oravecz
    • , Kenneth A Platt
    • , Dennis S Rice
    • , Gwenn M Hansen
    • , Alejandro Abuin
    • , Derek E Eberhart
    • , Paul Godowski
    • , Kathleen H Holt
    • , Andrew Peterson
    • , Brian P Zambrowicz
    •  & Frederic J de Sauvage
  • Resource |

    Genome-wide single-gene deletion libraries can be important tools for understanding the molecular workings of an organism, but have only been created for a single eukaryotic species, Saccharomyces cerevisiae. Now, Kim et al. present a second collection of deletion mutants that covers 98.4% of the genes of Schizosaccharomyces pombe, allowing a systematic comparison of gene essentiality and knockout phenotypes between two eukaryotic species.

    • Dong-Uk Kim
    • , Jacqueline Hayles
    • , Dongsup Kim
    • , Valerie Wood
    • , Han-Oh Park
    • , Misun Won
    • , Hyang-Sook Yoo
    • , Trevor Duhig
    • , Miyoung Nam
    • , Georgia Palmer
    • , Sangjo Han
    • , Linda Jeffery
    • , Seung-Tae Baek
    • , Hyemi Lee
    • , Young Sam Shim
    • , Minho Lee
    • , Lila Kim
    • , Kyung-Sun Heo
    • , Eun Joo Noh
    • , Ah-Reum Lee
    • , Young-Joo Jang
    • , Kyung-Sook Chung
    • , Shin-Jung Choi
    • , Jo-Young Park
    • , Youngwoo Park
    • , Hwan Mook Kim
    • , Song-Kyu Park
    • , Hae-Joon Park
    • , Eun-Jung Kang
    • , Hyong Bai Kim
    • , Hyun-Sam Kang
    • , Hee-Moon Park
    • , Kyunghoon Kim
    • , Kiwon Song
    • , Kyung Bin Song
    • , Paul Nurse
    •  & Kwang-Lae Hoe
  • Resource |

    Cultured human embryonic stem cells often acquire chromosomal abnormalities that could be detrimental in certain applications. Närvä et al. report the highest-resolution genetic analysis of these cells to date and identify genes whose expression is altered by culture-induced genetic changes.

    • Elisa Närvä
    • , Reija Autio
    • , Nelly Rahkonen
    • , Lingjia Kong
    • , Neil Harrison
    • , Danny Kitsberg
    • , Lodovica Borghese
    • , Joseph Itskovitz-Eldor
    • , Omid Rasool
    • , Petr Dvorak
    • , Outi Hovatta
    • , Timo Otonkoski
    • , Timo Tuuri
    • , Wei Cui
    • , Oliver Brüstle
    • , Duncan Baker
    • , Edna Maltby
    • , Harry D Moore
    • , Nissim Benvenisty
    • , Peter W Andrews
    • , Olli Yli-Harja
    •  & Riitta Lahesmaa
  • Resource |

    Lee et al. have created the largest functional gene network for plants by combining existing data on Arabidopsis thaliana with data gathered from other organisms. Although the genetics of many A. thaliana traits has been thoroughly studied, the authors succeed in discovering new genes associated with root development and drought resistance.

    • Insuk Lee
    • , Bindu Ambaru
    • , Pranjali Thakkar
    • , Edward M Marcotte
    •  & Seung Y Rhee
  • Resource |

    We have yet to identify the functions of the majority of genes of Plasmodium falciparum, the causative agent of malaria. Hu et al. profile transcriptional changes after chemically induced growth perturbations to assemble a protein network that predicts P. faliciparum gene function.

    • Guangan Hu
    • , Ana Cabrera
    • , Maya Kono
    • , Sachel Mok
    • , Balbir K Chaal
    • , Silvia Haase
    • , Klemens Engelberg
    • , Sabna Cheemadan
    • , Tobias Spielmann
    • , Peter R Preiser
    • , Tim-W Gilberger
    •  & Zbynek Bozdech
  • Resource |

    Sequencing a person's genome may reveal large DNA insertions and other structural rearrangements, but assessing their effects requires pinpointing them to nucleotide resolution. Lam et al. use a library of previously discovered rearrangements to map and analyze genetic variation.

    • Hugo Y K Lam
    • , Xinmeng Jasmine Mu
    • , Adrian M Stütz
    • , Andrea Tanzer
    • , Philip D Cayting
    • , Michael Snyder
    • , Philip M Kim
    • , Jan O Korbel
    •  & Mark B Gerstein
  • Resource |

    Cho et al. reconstruct the regulatory and functional architecture of the E. coli genome by integrating data from several high-throughput measurements. The detailed map will allow the development of improved models of the networks that control the bacterium's transcription and translation.

    • Byung-Kwan Cho
    • , Karsten Zengler
    • , Yu Qiu
    • , Young Seoub Park
    • , Eric M Knight
    • , Christian L Barrett
    • , Yuan Gao
    •  & Bernhard Ø Palsson
  • Resource |

    Cytochrome P450 enzymes metabolize drugs and contribute to harmful drug-drug interactions. To decipher p450 activities, Veith et al. screen 17,000 compounds, including >1,000 FDA-approved drugs, against five important P450 isozymes and identify chemical structures that are enriched in compounds active against specific isozymes.

    • Henrike Veith
    • , Noel Southall
    • , Ruili Huang
    • , Tim James
    • , Darren Fayne
    • , Natalia Artemenko
    • , Min Shen
    • , James Inglese
    • , Christopher P Austin
    • , David G Lloyd
    •  & Douglas S Auld