Analyses

  • 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