Analyses

  • Analysis | | open

    A multi-laboratory study finds that single-molecule FRET is a reproducible and reliable approach for determining accurate distances in dye-labeled DNA duplexes.

    • Björn Hellenkamp
    • , Sonja Schmid
    • , Olga Doroshenko
    • , Oleg Opanasyuk
    • , Ralf Kühnemuth
    • , Soheila Rezaei Adariani
    • , Benjamin Ambrose
    • , Mikayel Aznauryan
    • , Anders Barth
    • , Victoria Birkedal
    • , Mark E. Bowen
    • , Hongtao Chen
    • , Thorben Cordes
    • , Tobias Eilert
    • , Carel Fijen
    • , Christian Gebhardt
    • , Markus Götz
    • , Giorgos Gouridis
    • , Enrico Gratton
    • , Taekjip Ha
    • , Pengyu Hao
    • , Christian A. Hanke
    • , Andreas Hartmann
    • , Jelle Hendrix
    • , Lasse L. Hildebrandt
    • , Verena Hirschfeld
    • , Johannes Hohlbein
    • , Boyang Hua
    • , Christian G. Hübner
    • , Eleni Kallis
    • , Achillefs N. Kapanidis
    • , Jae-Yeol Kim
    • , Georg Krainer
    • , Don C. Lamb
    • , Nam Ki Lee
    • , Edward A. Lemke
    • , Brié Levesque
    • , Marcia Levitus
    • , James J. McCann
    • , Nikolaus Naredi-Rainer
    • , Daniel Nettels
    • , Thuy Ngo
    • , Ruoyi Qiu
    • , Nicole C. Robb
    • , Carlheinz Röcker
    • , Hugo Sanabria
    • , Michael Schlierf
    • , Tim Schröder
    • , Benjamin Schuler
    • , Henning Seidel
    • , Lisa Streit
    • , Johann Thurn
    • , Philip Tinnefeld
    • , Swati Tyagi
    • , Niels Vandenberk
    • , Andrés Manuel Vera
    • , Keith R. Weninger
    • , Bettina Wünsch
    • , Inna S. Yanez-Orozco
    • , Jens Michaelis
    • , Claus A. M. Seidel
    • , Timothy D. Craggs
    •  & Thorsten Hugel
  • Analysis |

    Reanalysis of DNA-immunoprecipitation-based data shows that modification-specific antibodies bind unmodified short tandem repeats, and IgG controls are needed to avoid false positives.

    • Antonio Lentini
    • , Cathrine Lagerwall
    • , Svante Vikingsson
    • , Heidi K. Mjoseng
    • , Karolos Douvlataniotis
    • , Hartmut Vogt
    • , Henrik Green
    • , Richard R. Meehan
    • , Mikael Benson
    •  & Colm E. Nestor
  • Analysis |

    This Analysis compares and contrasts methods for measuring the mechanical properties of cells by applying the different approaches to the same breast cancer cell line.

    • Pei-Hsun Wu
    • , Dikla Raz-Ben Aroush
    • , Atef Asnacios
    • , Wei-Chiang Chen
    • , Maxim E. Dokukin
    • , Bryant L. Doss
    • , Pauline Durand-Smet
    • , Andrew Ekpenyong
    • , Jochen Guck
    • , Nataliia V. Guz
    • , Paul A. Janmey
    • , Jerry S. H. Lee
    • , Nicole M. Moore
    • , Albrecht Ott
    • , Yeh-Chuin Poh
    • , Robert Ros
    • , Mathias Sander
    • , Igor Sokolov
    • , Jack R. Staunton
    • , Ning Wang
    • , Graeme Whyte
    •  & Denis Wirtz
  • Analysis |

    A direct comparison of 5′-end RNA-seq methods reveals strong performance by CAGE, and identifies differential transcriptional start site usage among brain-related samples.

    • Xian Adiconis
    • , Adam L. Haber
    • , Sean K. Simmons
    • , Ami Levy Moonshine
    • , Zhe Ji
    • , Michele A. Busby
    • , Xi Shi
    • , Justin Jacques
    • , Madeline A. Lancaster
    • , Jen Q. Pan
    • , Aviv Regev
    •  & Joshua Z. Levin
  • Analysis |

    This analysis describes the results of three Cell Tracking Challenge editions for examining the performance of cell segmentation and tracking algorithms and provides practical feedback for users and developers.

    • Vladimír Ulman
    • , Martin Maška
    • , Klas E G Magnusson
    • , Olaf Ronneberger
    • , Carsten Haubold
    • , Nathalie Harder
    • , Pavel Matula
    • , Petr Matula
    • , David Svoboda
    • , Miroslav Radojevic
    • , Ihor Smal
    • , Karl Rohr
    • , Joakim Jaldén
    • , Helen M Blau
    • , Oleh Dzyubachyk
    • , Boudewijn Lelieveldt
    • , Pengdong Xiao
    • , Yuexiang Li
    • , Siu-Yeung Cho
    • , Alexandre C Dufour
    • , Jean-Christophe Olivo-Marin
    • , Constantino C Reyes-Aldasoro
    • , Jose A Solis-Lemus
    • , Robert Bensch
    • , Thomas Brox
    • , Johannes Stegmaier
    • , Ralf Mikut
    • , Steffen Wolf
    • , Fred A Hamprecht
    • , Tiago Esteves
    • , Pedro Quelhas
    • , Ömer Demirel
    • , Lars Malmström
    • , Florian Jug
    • , Pavel Tomancak
    • , Erik Meijering
    • , Arrate Muñoz-Barrutia
    • , Michal Kozubek
    •  & Carlos Ortiz-de-Solorzano
  • Analysis | | open

    The Critical Assessment of Metagenome Interpretation (CAMI) community initiative presents results from its first challenge, a rigorous benchmarking of software for metagenome assembly, binning and taxonomic profiling.

    • Alexander Sczyrba
    • , Peter Hofmann
    • , Peter Belmann
    • , David Koslicki
    • , Stefan Janssen
    • , Johannes Dröge
    • , Ivan Gregor
    • , Stephan Majda
    • , Jessika Fiedler
    • , Eik Dahms
    • , Andreas Bremges
    • , Adrian Fritz
    • , Ruben Garrido-Oter
    • , Tue Sparholt Jørgensen
    • , Nicole Shapiro
    • , Philip D Blood
    • , Alexey Gurevich
    • , Yang Bai
    • , Dmitrij Turaev
    • , Matthew Z DeMaere
    • , Rayan Chikhi
    • , Niranjan Nagarajan
    • , Christopher Quince
    • , Fernando Meyer
    • , Monika Balvočiūtė
    • , Lars Hestbjerg Hansen
    • , Søren J Sørensen
    • , Burton K H Chia
    • , Bertrand Denis
    • , Jeff L Froula
    • , Zhong Wang
    • , Robert Egan
    • , Dongwan Don Kang
    • , Jeffrey J Cook
    • , Charles Deltel
    • , Michael Beckstette
    • , Claire Lemaitre
    • , Pierre Peterlongo
    • , Guillaume Rizk
    • , Dominique Lavenier
    • , Yu-Wei Wu
    • , Steven W Singer
    • , Chirag Jain
    • , Marc Strous
    • , Heiner Klingenberg
    • , Peter Meinicke
    • , Michael D Barton
    • , Thomas Lingner
    • , Hsin-Hung Lin
    • , Yu-Chieh Liao
    • , Genivaldo Gueiros Z Silva
    • , Daniel A Cuevas
    • , Robert A Edwards
    • , Surya Saha
    • , Vitor C Piro
    • , Bernhard Y Renard
    • , Mihai Pop
    • , Hans-Peter Klenk
    • , Markus Göker
    • , Nikos C Kyrpides
    • , Tanja Woyke
    • , Julia A Vorholt
    • , Paul Schulze-Lefert
    • , Edward M Rubin
    • , Aaron E Darling
    • , Thomas Rattei
    •  & Alice C McHardy
  • Analysis |

    This study compares naive human pluripotent stem cells, either reprogrammed directly from somatic cells or converted from primed cells, under a variety of culture conditions.

    • Xiaodong Liu
    • , Christian M Nefzger
    • , Fernando J Rossello
    • , Joseph Chen
    • , Anja S Knaupp
    • , Jaber Firas
    • , Ethan Ford
    • , Jahnvi Pflueger
    • , Jacob M Paynter
    • , Hun S Chy
    • , Carmel M O'Brien
    • , Cheng Huang
    • , Ketan Mishra
    • , Margeaux Hodgson-Garms
    • , Natasha Jansz
    • , Sarah M Williams
    • , Marnie E Blewitt
    • , Susan K Nilsson
    • , Ralf B Schittenhelm
    • , Andrew L Laslett
    • , Ryan Lister
    •  & Jose M Polo
  • Analysis |

    Six tools to call chromatin interactions and seven tools for topologically associating domain calling are systematically compared with real and simulated data. The strengths and weaknesses of each tool are discussed.

    • Mattia Forcato
    • , Chiara Nicoletti
    • , Koustav Pal
    • , Carmen Maria Livi
    • , Francesco Ferrari
    •  & Silvio Bicciato
  • Analysis |

    A comparison framework applied to 15 single-cell RNA-seq protocols reveals differences in accuracy and sensitivity and discusses the utility of RNA spike-in standards.

    • Valentine Svensson
    • , Kedar Nath Natarajan
    • , Lam-Ha Ly
    • , Ricardo J Miragaia
    • , Charlotte Labalette
    • , Iain C Macaulay
    • , Ana Cvejic
    •  & Sarah A Teichmann
  • Analysis |

    Benchmarking on synthetic data reveals differences between common RNA-seq alignment software tools, particularly for complex genomic regions.

    • Giacomo Baruzzo
    • , Katharina E Hayer
    • , Eun Ji Kim
    • , Barbara Di Camillo
    • , Garret A FitzGerald
    •  & Gregory R Grant
  • Analysis |

    This Analysis provides a head-to-head comparison of >40 monomeric fluorescent proteins in terms of photophysical properties, photostability and performance in fusions to help users choose the best-performing tools.

    • Paula J Cranfill
    • , Brittney R Sell
    • , Michelle A Baird
    • , John R Allen
    • , Zeno Lavagnino
    • , H Martijn de Gruiter
    • , Gert-Jan Kremers
    • , Michael W Davidson
    • , Alessandro Ustione
    •  & David W Piston
  • Analysis |

    A comparison of seven dCas9-based transcriptional activators shows that VPR, SAM, and Suntag perform best in cell lines from a variety of organisms.

    • Alejandro Chavez
    • , Marcelle Tuttle
    • , Benjamin W Pruitt
    • , Ben Ewen-Campen
    • , Raj Chari
    • , Dmitry Ter-Ovanesyan
    • , Sabina J Haque
    • , Ryan J Cecchi
    • , Emma J K Kowal
    • , Joanna Buchthal
    • , Benjamin E Housden
    • , Norbert Perrimon
    • , James J Collins
    •  & George Church
  • Analysis | | open

    The Quest for Orthologs consortium compares the performance of a large number of established orthology inference methods on 20 benchmarks and provides a free web tool for methods developers to facilitate further benchmarking.

    • Adrian M Altenhoff
    • , Brigitte Boeckmann
    • , Salvador Capella-Gutierrez
    • , Daniel A Dalquen
    • , Todd DeLuca
    • , Kristoffer Forslund
    • , Jaime Huerta-Cepas
    • , Benjamin Linard
    • , Cécile Pereira
    • , Leszek P Pryszcz
    • , Fabian Schreiber
    • , Alan Sousa da Silva
    • , Damian Szklarczyk
    • , Clément-Marie Train
    • , Peer Bork
    • , Odile Lecompte
    • , Christian von Mering
    • , Ioannis Xenarios
    • , Kimmen Sjölander
    • , Lars Juhl Jensen
    • , Maria J Martin
    • , Matthieu Muffato
    • , Quest for Orthologs consortium
    • , Adrian M Altenhoff
    • , Brigitte Boeckmann
    • , Salvador Capella-Gutierrez
    • , Todd DeLuca
    • , Kristoffer Forslund
    • , Jaime Huerta-Cepas
    • , Benjamin Linard
    • , Cécile Pereira
    • , Leszek P Pryszcz
    • , Fabian Schreiber
    • , Alan Sousa da Silva
    • , Damian Szklarczyk
    • , Clément-Marie Train
    • , Odile Lecompte
    • , Ioannis Xenarios
    • , Kimmen Sjölander
    • , Maria J Martin
    • , Matthieu Muffato
    • , Toni Gabaldón
    • , Suzanna E Lewis
    • , Paul D Thomas
    • , Erik Sonnhammer
    • , Christophe Dessimoz
    • , Toni Gabaldón
    • , Suzanna E Lewis
    • , Paul D Thomas
    • , Erik Sonnhammer
    •  & Christophe Dessimoz
  • Analysis | | open

    The HPN-DREAM community challenge assessed the ability of computational methods to infer causal molecular networks, focusing specifically on the task of inferring causal protein signaling networks in cancer cell lines.

    • Steven M Hill
    • , Laura M Heiser
    • , Thomas Cokelaer
    • , Michael Unger
    • , Nicole K Nesser
    • , Daniel E Carlin
    • , Yang Zhang
    • , Artem Sokolov
    • , Evan O Paull
    • , Chris K Wong
    • , Kiley Graim
    • , Adrian Bivol
    • , Haizhou Wang
    • , Fan Zhu
    • , Bahman Afsari
    • , Ludmila V Danilova
    • , Alexander V Favorov
    • , Wai Shing Lee
    • , Dane Taylor
    • , Chenyue W Hu
    • , Byron L Long
    • , David P Noren
    • , Alexander J Bisberg
    • , The HPN-DREAM Consortium
    • , Bahman Afsari
    • , Rami Al-Ouran
    • , Bernat Anton
    • , Tomasz Arodz
    • , Omid Askari Sichani
    • , Neda Bagheri
    • , Noah Berlow
    • , Alexander J Bisberg
    • , Adrian Bivol
    • , Anwesha Bohler
    • , Jaume Bonet
    • , Richard Bonneau
    • , Gungor Budak
    • , Razvan Bunescu
    • , Mehmet Caglar
    • , Binghuang Cai
    • , Chunhui Cai
    • , Daniel E Carlin
    • , Azzurra Carlon
    • , Lujia Chen
    • , Mark F Ciaccio
    • , Thomas Cokelaer
    • , Gregory Cooper
    • , Chad J Creighton
    • , Seyed-Mohammad-Hadi Daneshmand
    • , Alberto de la Fuente
    • , Barbara Di Camillo
    • , Ludmila V Danilova
    • , Joyeeta Dutta-Moscato
    • , Kevin Emmett
    • , Chris Evelo
    • , Mohammad-Kasim H Fassia
    • , Alexander V Favorov
    • , Elana J Fertig
    • , Justin D Finkle
    • , Francesca Finotello
    • , Stephen Friend
    • , Xi Gao
    • , Jean Gao
    • , Javier Garcia-Garcia
    • , Samik Ghosh
    • , Alberto Giaretta
    • , Kiley Graim
    • , Joe W Gray
    • , Ruth Großeholz
    • , Yuanfang Guan
    • , Justin Guinney
    • , Christoph Hafemeister
    • , Oliver Hahn
    • , Saad Haider
    • , Takeshi Hase
    • , Laura M Heiser
    • , Steven M Hill
    • , Jay Hodgson
    • , Bruce Hoff
    • , Chih Hao Hsu
    • , Chenyue W Hu
    • , Ying Hu
    • , Xun Huang
    • , Mahdi Jalili
    • , Xia Jiang
    • , Tim Kacprowski
    • , Lars Kaderali
    • , Mingon Kang
    • , Venkateshan Kannan
    • , Michael Kellen
    • , Kaito Kikuchi
    • , Dong-Chul Kim
    • , Hiroaki Kitano
    • , Bettina Knapp
    • , George Komatsoulis
    • , Heinz Koeppl
    • , Andreas Krämer
    • , Miron Bartosz Kursa
    • , Martina Kutmon
    • , Wai Shing Lee
    • , Yichao Li
    • , Xiaoyu Liang
    • , Zhaoqi Liu
    • , Yu Liu
    • , Byron L Long
    • , Songjian Lu
    • , Xinghua Lu
    • , Marco Manfrini
    • , Marta R A Matos
    • , Daoud Meerzaman
    • , Gordon B Mills
    • , Wenwen Min
    • , Sach Mukherjee
    • , Christian Lorenz Müller
    • , Richard E Neapolitan
    • , Nicole K Nesser
    • , David P Noren
    • , Thea Norman
    • , Baldo Oliva
    • , Stephen Obol Opiyo
    • , Ranadip Pal
    • , Aljoscha Palinkas
    • , Evan O Paull
    • , Joan Planas-Iglesias
    • , Daniel Poglayen
    • , Amina A Qutub
    • , Julio Saez-Rodriguez
    • , Francesco Sambo
    • , Tiziana Sanavia
    • , Ali Sharifi-Zarchi
    • , Janusz Slawek
    • , Artem Sokolov
    • , Mingzhou Song
    • , Paul T Spellman
    • , Adam Streck
    • , Gustavo Stolovitzky
    • , Sonja Strunz
    • , Joshua M Stuart
    • , Dane Taylor
    • , Jesper Tegnér
    • , Kirste Thobe
    • , Gianna Maria Toffolo
    • , Emanuele Trifoglio
    • , Michael Unger
    • , Qian Wan
    • , Haizhou Wang
    • , Lonnie Welch
    • , Chris K Wong
    • , Jia J Wu
    • , Albert Y Xue
    • , Ryota Yamanaka
    • , Chunhua Yan
    • , Sakellarios Zairis
    • , Michael Zengerling
    • , Hector Zenil
    • , Shihua Zhang
    • , Yang Zhang
    • , Fan Zhu
    • , Zhike Zi
    • , Gordon B Mills
    • , Joe W Gray
    • , Michael Kellen
    • , Thea Norman
    • , Stephen Friend
    • , Amina A Qutub
    • , Elana J Fertig
    • , Yuanfang Guan
    • , Mingzhou Song
    • , Joshua M Stuart
    • , Paul T Spellman
    • , Heinz Koeppl
    • , Gustavo Stolovitzky
    • , Julio Saez-Rodriguez
    •  & Sach Mukherjee
  • Analysis |

    This comparison of ten computational methods for detecting transcription factor binding sites in DNase hypersensitive regions in the genome determines which methods work consistently well, how DNase-seq experimental artifacts should be corrected for and which score is best for ranking methods.

    • Eduardo G Gusmao
    • , Manuel Allhoff
    • , Martin Zenke
    •  & Ivan G Costa
  • Analysis |

    This analysis compares 13 clustering methods on 24 data sets using the freely accessible ClustEval platform and presents guidelines for how to choose tools and set parameters for clustering biomedical data

    • Christian Wiwie
    • , Jan Baumbach
    •  & Richard Röttger
  • Analysis |

    A quantitative mass spectrometry–based standard operating procedure to classify antibody performance in immunoprecipitation is assessed in a multilaboratory study.

    • Edyta Marcon
    • , Harshika Jain
    • , Anandi Bhattacharya
    • , Hongbo Guo
    • , Sadhna Phanse
    • , Shuye Pu
    • , Gregory Byram
    • , Ben C Collins
    • , Evan Dowdell
    • , Maria Fenner
    • , Xinghua Guo
    • , Ashley Hutchinson
    • , Jacob J Kennedy
    • , Bryan Krastins
    • , Brett Larsen
    • , Zhen-Yuan Lin
    • , Mary F Lopez
    • , Peter Loppnau
    • , Shane Miersch
    • , Tin Nguyen
    • , Jonathan B Olsen
    • , Marcin Paduch
    • , Mani Ravichandran
    • , Alma Seitova
    • , Gouri Vadali
    • , Maryann S Vogelsang
    • , Jeffrey R Whiteaker
    • , Guoqing Zhong
    • , Nan Zhong
    • , Lei Zhao
    • , Ruedi Aebersold
    • , Cheryl H Arrowsmith
    • , Andrew Emili
    • , Lori Frappier
    • , Anne-Claude Gingras
    • , Matthias Gstaiger
    • , Amanda G Paulovich
    • , Shohei Koide
    • , Anthony A Kossiakoff
    • , Sachdev S Sidhu
    • , Shoshana J Wodak
    • , Susanne Gräslund
    • , Jack F Greenblatt
    •  & Aled M Edwards
  • Analysis |

    This Analysis reports a comparison of current software packages for single-molecule localization in localization-based super-resolution imaging. Performance of the participating software on synthetic, biologically inspired ground-truth data was assessed by multiple criteria.

    • Daniel Sage
    • , Hagai Kirshner
    • , Thomas Pengo
    • , Nico Stuurman
    • , Junhong Min
    • , Suliana Manley
    •  & Michael Unser
  • Analysis | | open

    The first report of the ICGC-TCGA DREAM Somatic Mutation Calling Challenge introduces the BAMSurgeon tool for accurate tumor simulation and reports the performance of 248 submissions in calling single-nucleotide variants from three pairs of synthetic tumor–normal genome benchmarks.

    • Adam D Ewing
    • , Kathleen E Houlahan
    • , Yin Hu
    • , Kyle Ellrott
    • , Cristian Caloian
    • , Takafumi N Yamaguchi
    • , J Christopher Bare
    • , Christine P'ng
    • , Daryl Waggott
    • , Veronica Y Sabelnykova
    • , ICGC-TCGA DREAM Somatic Mutation Calling Challenge participants
    • , Liu Xi
    • , Ninad Dewal
    • , Yu Fan
    • , Wenyi Wang
    • , David Wheeler
    • , Andreas Wilm
    • , Grace Hui Ting
    • , Chenhao Li
    • , Denis Bertrand
    • , Niranjan Nagarajan
    • , Qing-Rong Chen
    • , Chih-Hao Hsu
    • , Ying Hu
    • , Chunhua Yan
    • , Warren Kibbe
    • , Daoud Meerzaman
    • , Kristian Cibulskis
    • , Mara Rosenberg
    • , Louis Bergelson
    • , Adam Kiezun
    • , Amie Radenbaugh
    • , Anne-Sophie Sertier
    • , Anthony Ferrari
    • , Laurie Tonton
    • , Kunal Bhutani
    • , Nancy F Hansen
    • , Difei Wang
    • , Lei Song
    • , Zhongwu Lai
    • , Yang Liao
    • , Wei Shi
    • , José Carbonell-Caballero
    • , Joaquín Dopazo
    • , Cheryl C K Lau
    • , Justin Guinney
    • , Michael R Kellen
    • , Thea C Norman
    • , David Haussler
    • , Stephen H Friend
    • , Gustavo Stolovitzky
    • , Adam A Margolin
    • , Joshua M Stuart
    •  & Paul C Boutros
  • Analysis |

    12 microRNA expression profiling platforms are compared for their reproducibility, sensitivity, accuracy and specificity, and the strengths and weaknesses of each platform are discussed.

    • Pieter Mestdagh
    • , Nicole Hartmann
    • , Lukas Baeriswyl
    • , Ditte Andreasen
    • , Nathalie Bernard
    • , Caifu Chen
    • , David Cheo
    • , Petula D'Andrade
    • , Mike DeMayo
    • , Lucas Dennis
    • , Stefaan Derveaux
    • , Yun Feng
    • , Stephanie Fulmer-Smentek
    • , Bernhard Gerstmayer
    • , Julia Gouffon
    • , Chris Grimley
    • , Eric Lader
    • , Kathy Y Lee
    • , Shujun Luo
    • , Peter Mouritzen
    • , Aishwarya Narayanan
    • , Sunali Patel
    • , Sabine Peiffer
    • , Silvia Rüberg
    • , Gary Schroth
    • , Dave Schuster
    • , Jonathan M Shaffer
    • , Elliot J Shelton
    • , Scott Silveria
    • , Umberto Ulmanella
    • , Vamsi Veeramachaneni
    • , Frank Staedtler
    • , Thomas Peters
    • , Toumy Guettouche
    • , Linda Wong
    •  & Jo Vandesompele
  • Analysis |

    This Analysis compares four commonly used assays to measure food intake in flies and identifies radioisotope-labeling and the capillary feeder (CAFE) as the most reproducible and sensitive.

    • Sonali A Deshpande
    • , Gil B Carvalho
    • , Ariadna Amador
    • , Angela M Phillips
    • , Sany Hoxha
    • , Keith J Lizotte
    •  & William W Ja
  • Analysis |

    A comparative analysis of methods for scoring human sleep data, in particular sleep spindles, from encephalographic recordings is reported. The authors develop methods for crowdsourcing the identification of sleep spindles and compare the detection performance of experts, non-experts and automated algorithms.

    • Simon C Warby
    • , Sabrina L Wendt
    • , Peter Welinder
    • , Emil G S Munk
    • , Oscar Carrillo
    • , Helge B D Sorensen
    • , Poul Jennum
    • , Paul E Peppard
    • , Pietro Perona
    •  & Emmanuel Mignot
  • Analysis | | open

    The first community competition designed to objectively compare the performance of particle tracking algorithms provides valuable practical information for both users and developers.

    • Nicolas Chenouard
    • , Ihor Smal
    • , Fabrice de Chaumont
    • , Martin Maška
    • , Ivo F Sbalzarini
    • , Yuanhao Gong
    • , Janick Cardinale
    • , Craig Carthel
    • , Stefano Coraluppi
    • , Mark Winter
    • , Andrew R Cohen
    • , William J Godinez
    • , Karl Rohr
    • , Yannis Kalaidzidis
    • , Liang Liang
    • , James Duncan
    • , Hongying Shen
    • , Yingke Xu
    • , Klas E G Magnusson
    • , Joakim Jaldén
    • , Helen M Blau
    • , Perrine Paul-Gilloteaux
    • , Philippe Roudot
    • , Charles Kervrann
    • , François Waharte
    • , Jean-Yves Tinevez
    • , Spencer L Shorte
    • , Joost Willemse
    • , Katherine Celler
    • , Gilles P van Wezel
    • , Han-Wei Dan
    • , Yuh-Show Tsai
    • , Carlos Ortiz de Solórzano
    • , Jean-Christophe Olivo-Marin
    •  & Erik Meijering
  • Analysis |

    A system using the human glycine receptor expressed in Xenopus oocytes allows characterization of the photoactivation efficiency of photoactivatable and photoconvertible fluorescent proteins at the single-molecule level, providing crucial data for using these probes for quantitative super-resolution microscopy.

    • Nela Durisic
    • , Lara Laparra-Cuervo
    • , Ángel Sandoval-Álvarez
    • , Joseph Steven Borbely
    •  & Melike Lakadamyali
  • Analysis |

    This Analysis reports the development and assessment of 645 multiple reaction monitoring (MRM) mass spectrometry assays to quantify 319 targeted human breast cancer proteins. The results of this pilot project coordinated among three individual groups suggest that an organized international effort to generate MRM assays to the human proteome will be possible.

    • Jacob J Kennedy
    • , Susan E Abbatiello
    • , Kyunggon Kim
    • , Ping Yan
    • , Jeffrey R Whiteaker
    • , Chenwei Lin
    • , Jun Seok Kim
    • , Yuzheng Zhang
    • , Xianlong Wang
    • , Richard G Ivey
    • , Lei Zhao
    • , Hophil Min
    • , Youngju Lee
    • , Myeong-Hee Yu
    • , Eun Gyeong Yang
    • , Cheolju Lee
    • , Pei Wang
    • , Henry Rodriguez
    • , Youngsoo Kim
    • , Steven A Carr
    •  & Amanda G Paulovich
  • Analysis | | open

    The RGASP consortium compared 25 RNA-seq analysis programs in their ability to identify exons, reconstruct transcripts and quantify expression levels. Assembly of isoforms and their expression levels in higher eukaryotes remains a challenge.

    • Tamara Steijger
    • , Josep F Abril
    • , Pär G Engström
    • , Felix Kokocinski
    • , The RGASP Consortium
    • , Josep F Abril
    • , Martin Akerman
    • , Tyler Alioto
    • , Giovanna Ambrosini
    • , Stylianos E Antonarakis
    • , Jonas Behr
    • , Paul Bertone
    • , Regina Bohnert
    • , Philipp Bucher
    • , Nicole Cloonan
    • , Thomas Derrien
    • , Sarah Djebali
    • , Jiang Du
    • , Sandrine Dudoit
    • , Pär G Engström
    • , Mark Gerstein
    • , Thomas R Gingeras
    • , David Gonzalez
    • , Sean M Grimmond
    • , Roderic Guigó
    • , Lukas Habegger
    • , Jennifer Harrow
    • , Tim J Hubbard
    • , Christian Iseli
    • , Géraldine Jean
    • , André Kahles
    • , Felix Kokocinski
    • , Julien Lagarde
    • , Jing Leng
    • , Gregory Lefebvre
    • , Suzanna Lewis
    • , Ali Mortazavi
    • , Peter Niermann
    • , Gunnar Rätsch
    • , Alexandre Reymond
    • , Paolo Ribeca
    • , Hugues Richard
    • , Jacques Rougemont
    • , Joel Rozowsky
    • , Michael Sammeth
    • , Andrea Sboner
    • , Marcel H Schulz
    • , Steven M J Searle
    • , Naryttza Diaz Solorzano
    • , Victor Solovyev
    • , Mario Stanke
    • , Tamara Steijger
    • , Brian J Stevenson
    • , Heinz Stockinger
    • , Armand Valsesia
    • , David Weese
    • , Simon White
    • , Barbara J Wold
    • , Jie Wu
    • , Thomas D Wu
    • , Georg Zeller
    • , Daniel Zerbino
    • , Michael Q Zhang
    • , Tim J Hubbard
    • , Roderic Guigó
    • , Jennifer Harrow
    •  & Paul Bertone
  • Analysis | | open

    Authors compare RNA-seq aligners on mouse and human data sets using benchmarks such as alignment yield, splice junction accuracy and suitability for transcript reconstruction. The work highlights the strength of each program and discusses outstanding needs in RNA-seq analysis.

    • Pär G Engström
    • , Tamara Steijger
    • , Botond Sipos
    • , Gregory R Grant
    • , André Kahles
    • , The RGASP Consortium
    • , Tyler Alioto
    • , Jonas Behr
    • , Paul Bertone
    • , Regina Bohnert
    • , Davide Campagna
    • , Carrie A Davis
    • , Alexander Dobin
    • , Pär G Engström
    • , Thomas R Gingeras
    • , Nick Goldman
    • , Gregory R Grant
    • , Roderic Guigó
    • , Jennifer Harrow
    • , Tim J Hubbard
    • , Géraldine Jean
    • , André Kahles
    • , Peter Kosarev
    • , Sheng Li
    • , Jinze Liu
    • , Christopher E Mason
    • , Vladimir Molodtsov
    • , Zemin Ning
    • , Hannes Ponstingl
    • , Jan F Prins
    • , Gunnar Rätsch
    • , Paolo Ribeca
    • , Igor Seledtsov
    • , Botond Sipos
    • , Victor Solovyev
    • , Tamara Steijger
    • , Giorgio Valle
    • , Nicola Vitulo
    • , Kai Wang
    • , Thomas D Wu
    • , Georg Zeller
    • , Gunnar Rätsch
    • , Nick Goldman
    • , Tim J Hubbard
    • , Jennifer Harrow
    • , Roderic Guigó
    •  & Paul Bertone
  • Analysis |

    A systematic evaluation of various single-cell RNA-seq approaches reports their sensitivity, accuracy and reproducibility and establishes the high performance of a high-throughput microfluidic method.

    • Angela R Wu
    • , Norma F Neff
    • , Tomer Kalisky
    • , Piero Dalerba
    • , Barbara Treutlein
    • , Michael E Rothenberg
    • , Francis M Mburu
    • , Gary L Mantalas
    • , Sopheak Sim
    • , Michael F Clarke
    •  & Stephen R Quake
  • Analysis |

    This comparison of five RNA-seq library preparation methods highlights metrics for assessing the suitability of the methods for samples with low amounts of RNA and/or those with low-quality RNA.

    • Xian Adiconis
    • , Diego Borges-Rivera
    • , Rahul Satija
    • , David S DeLuca
    • , Michele A Busby
    • , Aaron M Berlin
    • , Andrey Sivachenko
    • , Dawn Anne Thompson
    • , Alec Wysoker
    • , Timothy Fennell
    • , Andreas Gnirke
    • , Nathalie Pochet
    • , Aviv Regev
    •  & Joshua Z Levin
  • Analysis |

    A systematic study of the intra- and interlaboratory reproducibility of a standardized affinity purification–mass spectrometry protocol demonstrates the high reproducibility of this technique and hints at the feasibility of a large-scale human interactome project through interlaboratory efforts.

    • Markku Varjosalo
    • , Roberto Sacco
    • , Alexey Stukalov
    • , Audrey van Drogen
    • , Melanie Planyavsky
    • , Simon Hauri
    • , Ruedi Aebersold
    • , Keiryn L Bennett
    • , Jacques Colinge
    • , Matthias Gstaiger
    •  & Giulio Superti-Furga
  • Analysis |

    In this analysis, the authors directly compared immunofluorescence and fluorescent-protein tagging of 506 human proteins and studied their subcellular localization. They conclude that the two methodologies are highly complementary and propose an integrative strategy for the characterization of newly identified proteins.

    • Charlotte Stadler
    • , Elton Rexhepaj
    • , Vasanth R Singan
    • , Robert F Murphy
    • , Rainer Pepperkok
    • , Mathias Uhlén
    • , Jeremy C Simpson
    •  & Emma Lundberg
  • Analysis | | open

    In this analysis, the authors directly compared the performance of flow cytometry data processing algorithms to manual gating approaches. The results offer information of practical utility about the performance of the algorithms as applied to different data sets and challenges.

    • Nima Aghaeepour
    • , Greg Finak
    • , The FlowCAP Consortium
    • , The DREAM Consortium
    • , Holger Hoos
    • , Tim R Mosmann
    • , Ryan Brinkman
    • , Raphael Gottardo
    •  & Richard H Scheuermann
  • Analysis | | open

    A report on the results of the first large-scale community-based critical assessment of protein function annotation (CAFA) experiment.

    • Predrag Radivojac
    • , Wyatt T Clark
    • , Tal Ronnen Oron
    • , Alexandra M Schnoes
    • , Tobias Wittkop
    • , Artem Sokolov
    • , Kiley Graim
    • , Christopher Funk
    • , Karin Verspoor
    • , Asa Ben-Hur
    • , Gaurav Pandey
    • , Jeffrey M Yunes
    • , Ameet S Talwalkar
    • , Susanna Repo
    • , Michael L Souza
    • , Damiano Piovesan
    • , Rita Casadio
    • , Zheng Wang
    • , Jianlin Cheng
    • , Hai Fang
    • , Julian Gough
    • , Patrik Koskinen
    • , Petri Törönen
    • , Jussi Nokso-Koivisto
    • , Liisa Holm
    • , Domenico Cozzetto
    • , Daniel W A Buchan
    • , Kevin Bryson
    • , David T Jones
    • , Bhakti Limaye
    • , Harshal Inamdar
    • , Avik Datta
    • , Sunitha K Manjari
    • , Rajendra Joshi
    • , Meghana Chitale
    • , Daisuke Kihara
    • , Andreas M Lisewski
    • , Serkan Erdin
    • , Eric Venner
    • , Olivier Lichtarge
    • , Robert Rentzsch
    • , Haixuan Yang
    • , Alfonso E Romero
    • , Prajwal Bhat
    • , Alberto Paccanaro
    • , Tobias Hamp
    • , Rebecca Kaßner
    • , Stefan Seemayer
    • , Esmeralda Vicedo
    • , Christian Schaefer
    • , Dominik Achten
    • , Florian Auer
    • , Ariane Boehm
    • , Tatjana Braun
    • , Maximilian Hecht
    • , Mark Heron
    • , Peter Hönigschmid
    • , Thomas A Hopf
    • , Stefanie Kaufmann
    • , Michael Kiening
    • , Denis Krompass
    • , Cedric Landerer
    • , Yannick Mahlich
    • , Manfred Roos
    • , Jari Björne
    • , Tapio Salakoski
    • , Andrew Wong
    • , Hagit Shatkay
    • , Fanny Gatzmann
    • , Ingolf Sommer
    • , Mark N Wass
    • , Michael J E Sternberg
    • , Nives Škunca
    • , Fran Supek
    • , Matko Bošnjak
    • , Panče Panov
    • , Sašo Džeroski
    • , Tomislav Šmuc
    • , Yiannis A I Kourmpetis
    • , Aalt D J van Dijk
    • , Cajo J F ter Braak
    • , Yuanpeng Zhou
    • , Qingtian Gong
    • , Xinran Dong
    • , Weidong Tian
    • , Marco Falda
    • , Paolo Fontana
    • , Enrico Lavezzo
    • , Barbara Di Camillo
    • , Stefano Toppo
    • , Liang Lan
    • , Nemanja Djuric
    • , Yuhong Guo
    • , Slobodan Vucetic
    • , Amos Bairoch
    • , Michal Linial
    • , Patricia C Babbitt
    • , Steven E Brenner
    • , Christine Orengo
    • , Burkhard Rost
    • , Sean D Mooney
    •  & Iddo Friedberg
  • Analysis |

    This analysis comprehensively compares methods for gene regulatory network inference submitted through the DREAM5 challenge. It demonstrates that integration of predictions from multiple methods shows the most robust performance across data sets.

    • Daniel Marbach
    • , James C Costello
    • , Robert Küffner
    • , Nicole M Vega
    • , Robert J Prill
    • , Diogo M Camacho
    • , Kyle R Allison
    • , The DREAM5 Consortium
    • , Andrej Aderhold
    • , Kyle R Allison
    • , Richard Bonneau
    • , Diogo M Camacho
    • , Yukun Chen
    • , James J Collins
    • , Francesca Cordero
    • , James C Costello
    • , Martin Crane
    • , Frank Dondelinger
    • , Mathias Drton
    • , Roberto Esposito
    • , Rina Foygel
    • , Alberto de la Fuente
    • , Jan Gertheiss
    • , Pierre Geurts
    • , Alex Greenfield
    • , Marco Grzegorczyk
    • , Anne-Claire Haury
    • , Benjamin Holmes
    • , Torsten Hothorn
    • , Dirk Husmeier
    • , Vân Anh Huynh-Thu
    • , Alexandre Irrthum
    • , Manolis Kellis
    • , Guy Karlebach
    • , Robert Küffner
    • , Sophie Lèbre
    • , Vincenzo De Leo
    • , Aviv Madar
    • , Subramani Mani
    • , Daniel Marbach
    • , Fantine Mordelet
    • , Harry Ostrer
    • , Zhengyu Ouyang
    • , Ravi Pandya
    • , Tobias Petri
    • , Andrea Pinna
    • , Christopher S Poultney
    • , Robert J Prill
    • , Serena Rezny
    • , Heather J Ruskin
    • , Yvan Saeys
    • , Ron Shamir
    • , Alina Sîrbu
    • , Mingzhou Song
    • , Nicola Soranzo
    • , Alexander Statnikov
    • , Gustavo Stolovitzky
    • , Nicci Vega
    • , Paola Vera-Licona
    • , Jean-Philippe Vert
    • , Alessia Visconti
    • , Haizhou Wang
    • , Louis Wehenkel
    • , Lukas Windhager
    • , Yang Zhang
    • , Ralf Zimmer
    • , Manolis Kellis
    • , James J Collins
    •  & Gustavo Stolovitzky
  • Analysis |

    Algorithms that integrate genome-wide copy number and gene expression data offer a promising way to uncover genes that drive the progression of cancers. The performance of ten software tools on simulated and real cancer datasets of different sizes is directly compared in this Analysis.

    • Riku Louhimo
    • , Tatiana Lepikhova
    • , Outi Monni
    •  & Sampsa Hautaniemi
  • Analysis |

    In this Analysis, the authors directly experimentally compare microbial opsins used for the control of neural activity. They extract essential principles and key parameters that can help end users with the design and interpretation of optogenetic experiments and guide tool developers in the characterization of future tools.

    • Joanna Mattis
    • , Kay M Tye
    • , Emily A Ferenczi
    • , Charu Ramakrishnan
    • , Daniel J O'Shea
    • , Rohit Prakash
    • , Lisa A Gunaydin
    • , Minsuk Hyun
    • , Lief E Fenno
    • , Viviana Gradinaru
    • , Ofer Yizhar
    •  & Karl Deisseroth
  • Analysis |

    The comparison of cross-linking and immunoprecipitation (CLIP) and photoactivatable ribonucleoside–enhanced CLIP (PAR-CLIP) protocols shows specific biases of each method in enriching subsets of binding sites of RNA-binding proteins and shows ways around these biases.

    • Shivendra Kishore
    • , Lukasz Jaskiewicz
    • , Lukas Burger
    • , Jean Hausser
    • , Mohsen Khorshid
    •  & Mihaela Zavolan
  • Analysis |

    A multilaboratory pilot project demonstrates that hybridoma and phage display technologies can be applied to produce high-affinity, high-specificity renewable antibodies to a set of 20 human SH2 domain proteins in a reasonable time frame, suggesting that a systematic, large-scale effort to generate renewable protein binders will be feasible.

    • Karen Colwill
    • , Renewable Protein Binder Working Group
    •  & Susanne Gräslund
  • Analysis |

    Compared in this Analysis are two widely used procedures for ribosomal RNA removal in metatranscriptomic samples, and the authors present recommendations to prevent misleading analyses of microbial communities.

    • Shaomei He
    • , Omri Wurtzel
    • , Kanwar Singh
    • , Jeff L Froula
    • , Suzan Yilmaz
    • , Susannah G Tringe
    • , Zhong Wang
    • , Feng Chen
    • , Erika A Lindquist
    • , Rotem Sorek
    •  & Philip Hugenholtz
  • Analysis |

    The authors compare quality metrics of libraries from seven strand-specific RNA-seq methods in terms of complexity, strand specificity, evenness and continuity of coverage, and expression profiling. They provide a computational pipeline to compare these metrics from any RNA-seq protocol.

    • Joshua Z Levin
    • , Moran Yassour
    • , Xian Adiconis
    • , Chad Nusbaum
    • , Dawn Anne Thompson
    • , Nir Friedman
    • , Andreas Gnirke
    •  & Aviv Regev
  • Analysis |

    A multilaboratory analysis characterized the ability of 27 different labs to identify 20 proteins at equimolar concentrations in a highly purified test sample mixture using mass spectrometry. The results show that while the technology is reproducible, many common experimental problems arise, and improved search engines and databases are still needed.

    • Alexander W Bell
    • , Eric W Deutsch
    • , Catherine E Au
    • , Robert E Kearney
    • , Ron Beavis
    • , Salvatore Sechi
    • , Tommy Nilsson
    • , John J M Bergeron
    • , HUPO Test Sample Working Group
    • , Thomas A Beardslee
    • , Thomas Chappell
    • , Gavin Meredith
    • , Peter Sheffield
    • , Phillip Gray
    • , Mahbod Hajivandi
    • , Marshall Pope
    • , Paul Predki
    • , Majlinda Kullolli
    • , Marina Hincapie
    • , William S Hancock
    • , Wei Jia
    • , Lina Song
    • , Lei Li
    • , Junying Wei
    • , Bing Yang
    • , Jinglan Wang
    • , Wantao Ying
    • , Yangjun Zhang
    • , Yun Cai
    • , Xiaohong Qian
    • , Fuchu He
    • , Helmut E Meyer
    • , Christian Stephan
    • , Martin Eisenacher
    • , Katrin Marcus
    • , Elmar Langenfeld
    • , Caroline May
    • , Steven A Carr
    • , Rushdy Ahmad
    • , Wenhong Zhu
    • , Jeffrey W Smith
    • , Samir M Hanash
    • , Jason J Struthers
    • , Hong Wang
    • , Qing Zhang
    • , Yanming An
    • , Radoslav Goldman
    • , Elisabet Carlsohn
    • , Sjoerd van der Post
    • , Kenneth E Hung
    • , David A Sarracino
    • , Kenneth Parker
    • , Bryan Krastins
    • , Raju Kucherlapati
    • , Sylvie Bourassa
    • , Guy G Poirier
    • , Eugene Kapp
    • , Heather Patsiouras
    • , Robert Moritz
    • , Richard Simpson
    • , Benoit Houle
    • , Sylvie LaBoissiere
    • , Pavel Metalnikov
    • , Vivian Nguyen
    • , Tony Pawson
    • , Catherine C L Wong
    • , Daniel Cociorva
    • , John R Yates III
    • , Michael J Ellison
    • , Ana Lopez-Campistrous
    • , Paul Semchuk
    • , Yueju Wang
    • , Peipei Ping
    • , Giuliano Elia
    • , Michael J Dunn
    • , Kieran Wynne
    • , Angela K Walker
    • , John R Strahler
    • , Philip C Andrews
    • , Brian L Hood
    • , William L Bigbee
    • , Thomas P Conrads
    • , Derek Smith
    • , Christoph H Borchers
    • , Gilles A Lajoie
    • , Sean C Bendall
    • , Kaye D Speicher
    • , David W Speicher
    • , Masanori Fujimoto
    • , Kazuyuki Nakamura
    • , Young-Ki Paik
    • , Sang Yun Cho
    • , Min-Seok Kwon
    • , Hyoung-Joo Lee
    • , Seul-Ki Jeong
    • , An Sung Chung
    • , Christine A Miller
    • , Rudolf Grimm
    • , Katy Williams
    • , Craig Dorschel
    • , Jayson A Falkner
    • , Lennart Martens
    •  & Juan Antonio Vizcaíno
  • Analysis |

    Different experimental designs for protein interaction mapping are modeled to compare their efficiency in completing an interactome map. Testing of the strategy that minimized the final experimental cost in an ongoing Drosophila melanogaster interactome project found 450 high-confidence interactions using only 47 microtiter plates.

    • Ariel S Schwartz
    • , Jingkai Yu
    • , Kyle R Gardenour
    • , Russell L Finley Jr
    •  & Trey Ideker