Latest Research

  • Brief Communication |

    Enrichment of biotinylated peptides using an anti-biotin antibody results in substantially improved biotinylation site identifications by mass spectrometry compared to traditional streptavidin-based biotinylated protein enrichment.

    • Namrata D Udeshi
    • , Kayvon Pedram
    • , Tanya Svinkina
    • , Shaunt Fereshetian
    • , Samuel A Myers
    • , Ozan Aygun
    • , Karsten Krug
    • , Karl Clauser
    • , Dominic Ryan
    • , Tslil Ast
    • , Vamsi K Mootha
    • , Alice Y Ting
    •  & Steven A Carr
  • Brief Communication |

    A rescanning microscopy approach enables two-photon image-scanning microscopy that doubles resolution relative to that of conventional two-photon microscopy at high frame rates and with high sensitivity for improved super-resolution imaging of living specimens.

    • Ingo Gregor
    • , Martin Spiecker
    • , Roman Petrovsky
    • , Jörg Großhans
    • , Robert Ros
    •  & Jörg Enderlein
  • Article |

    A reverse two-hybrid approach combined with massively parallel programmed mutagenesis and sequencing allows profiling protein interaction determinants at amino-acid resolution, as demonstrated by identifying interaction-disrupting mutations in a cilia protein complex associated with Bardet–Biedl syndrome.

    • Jonathan Woodsmith
    • , Luise Apelt
    • , Victoria Casado-Medrano
    • , Ziya Özkan
    • , Bernd Timmermann
    •  & Ulrich Stelzl
  • Article |

    Combining each sgRNA with a unique molecular identifier in a genome-wide screen increases sensitivity and robustness in both positive and negative selection.

    • Georg Michlits
    • , Maria Hubmann
    • , Szu-Hsien Wu
    • , Gintautas Vainorius
    • , Elena Budusan
    • , Sergei Zhuk
    • , Thomas R Burkard
    • , Maria Novatchkova
    • , Martin Aichinger
    • , Yiqing Lu
    • , John Reece-Hoyes
    • , Roberto Nitsch
    • , Daniel Schramek
    • , Dominic Hoepfner
    •  & Ulrich Elling
  • Brief Communication |

    SCENIC enables simultaneous regulatory network inference and robust cell clustering from single-cell RNA-seq data.

    • Sara Aibar
    • , Carmen Bravo González-Blas
    • , Thomas Moerman
    • , Vân Anh Huynh-Thu
    • , Hana Imrichova
    • , Gert Hulselmans
    • , Florian Rambow
    • , Jean-Christophe Marine
    • , Pierre Geurts
    • , Jan Aerts
    • , Joost van den Oord
    • , Zeynep Kalender Atak
    • , Jasper Wouters
    •  & Stein Aerts
  • Brief Communication |

    NeuBtracker is an open-source platform that enables simultaneous imaging of behavior and neural activity in freely behaving zebrafish larvae. Its performance is demonstrated during several spontaneous or stimulus-induced behaviors.

    • Panagiotis Symvoulidis
    • , Antonella Lauri
    • , Anca Stefanoiu
    • , Michele Cappetta
    • , Steffen Schneider
    • , Hongbo Jia
    • , Anja Stelzl
    • , Maximilian Koch
    • , Carlos Cruz Perez
    • , Ahne Myklatun
    • , Sabine Renninger
    • , Andriy Chmyrov
    • , Tobias Lasser
    • , Wolfgang Wurst
    • , Vasilis Ntziachristos
    •  & Gil G Westmeyer
  • Article |

    This paper reports the efficient generation of human alveolar cells from induced pluripotent stem cells and their expansion in 3D culture.

    • Yuki Yamamoto
    • , Shimpei Gotoh
    • , Yohei Korogi
    • , Masahide Seki
    • , Satoshi Konishi
    • , Satoshi Ikeo
    • , Naoyuki Sone
    • , Tadao Nagasaki
    • , Hisako Matsumoto
    • , Shigeo Muro
    • , Isao Ito
    • , Toyohiro Hirai
    • , Takashi Kohno
    • , Yutaka Suzuki
    •  & Michiaki Mishima
  • Analysis |

    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
  • Article |

    SLAM seq detects s4U incorporation into RNA and, combined with 3′-end RNA-seq, provides insight into RNA turnover.

    • Veronika A Herzog
    • , Brian Reichholf
    • , Tobias Neumann
    • , Philipp Rescheneder
    • , Pooja Bhat
    • , Thomas R Burkard
    • , Wiebke Wlotzka
    • , Arndt von Haeseler
    • , Johannes Zuber
    •  & Stefan L Ameres
  • Article |

    A genetically encoded tension sensor module for measuring molecular forces at 3–5 pN along with tools for multiplexed tension sensing and data analysis reveal an intramolecular tension gradient across talin-1 during cell adhesion.

    • Pia Ringer
    • , Andreas Weißl
    • , Anna-Lena Cost
    • , Andrea Freikamp
    • , Benedikt Sabass
    • , Alexander Mehlich
    • , Marc Tramier
    • , Matthias Rief
    •  & Carsten Grashoff
  • Article |

    A tracking microscope for imaging neuronal activity at single-cell resolution in freely swimming zebrafish larvae is described. This technology allows functional imaging during behaviors that have previously been inaccessible to real-time analysis.

    • Dal Hyung Kim
    • , Jungsoo Kim
    • , João C Marques
    • , Abhinav Grama
    • , David G C Hildebrand
    • , Wenchao Gu
    • , Jennifer M Li
    •  & Drew N Robson
  • Article |

    Guidelines for fine-tuning spectral and chemical properties of fluorophore are introduced, resulting in four new Janelia Fluor dyes, JF503, JF525, JF585 and JF635, that span the visible region and align well with standard laser lines.

    • Jonathan B Grimm
    • , Anand K Muthusamy
    • , Yajie Liang
    • , Timothy A Brown
    • , William C Lemon
    • , Ronak Patel
    • , Rongwen Lu
    • , John J Macklin
    • , Philipp J Keller
    • , Na Ji
    •  & Luke D Lavis
  • Brief Communication |

    A data-driven strategy is used to estimate the sampling depth required to faithfully capture the true heterogeneity of cellular populations.

    • Satwik Rajaram
    • , Louise E Heinrich
    • , John D Gordan
    • , Jayant Avva
    • , Kathy M Bonness
    • , Agnieszka K Witkiewicz
    • , James S Malter
    • , Chloe E Atreya
    • , Robert S Warren
    • , Lani F Wu
    •  & Steven J Altschuler
  • Brief Communication |

    Red-shifted luciferins and corresponding mutants of NanoLuc enable brighter bioluminescence imaging in vitro, in cells, and in deep tissues of living mice alone and in the context of the newly developed Antares2 BRET reporter.

    • Hsien-Wei Yeh
    • , Omran Karmach
    • , Ao Ji
    • , David Carter
    • , Manuela M Martins-Green
    •  & Hui-wang Ai
  • Article |

    The genetically encoded GEVAL sensors allow ratiometric imaging of the spatiotemporal dynamics of cellular GTP levels in living cells.

    • Anna Bianchi-Smiraglia
    • , Mitra S Rana
    • , Colleen E Foley
    • , Leslie M Paul
    • , Brittany C Lipchick
    • , Sudha Moparthy
    • , Kalyana Moparthy
    • , Emily E Fink
    • , Archis Bagati
    • , Edward Hurley
    • , Hayley C Affronti
    • , Andrei V Bakin
    • , Eugene S Kandel
    • , Dominic J Smiraglia
    • , Maria Laura Feltri
    • , Rui Sousa
    •  & Mikhail A Nikiforov
  • Review | | open

    This Review covers the steps required to create high-quality image-based profiles from high-throughput microscopy images.

    • Juan C Caicedo
    • , Sam Cooper
    • , Florian Heigwer
    • , Scott Warchal
    • , Peng Qiu
    • , Csaba Molnar
    • , Aliaksei S Vasilevich
    • , Joseph D Barry
    • , Harmanjit Singh Bansal
    • , Oren Kraus
    • , Mathias Wawer
    • , Lassi Paavolainen
    • , Markus D Herrmann
    • , Mohammad Rohban
    • , Jane Hung
    • , Holger Hennig
    • , John Concannon
    • , Ian Smith
    • , Paul A Clemons
    • , Shantanu Singh
    • , Paul Rees
    • , Peter Horvath
    • , Roger G Linington
    •  & Anne E Carpenter
  • Brief Communication |

    The Omni-ATAC protocol improves the signal-to-background ratio in chromatin accessibility profiles and is suitable for a range of cell lines and primary cell types, as well as frozen tissue.

    • M Ryan Corces
    • , Alexandro E Trevino
    • , Emily G Hamilton
    • , Peyton G Greenside
    • , Nicholas A Sinnott-Armstrong
    • , Sam Vesuna
    • , Ansuman T Satpathy
    • , Adam J Rubin
    • , Kathleen S Montine
    • , Beijing Wu
    • , Arwa Kathiria
    • , Seung Woo Cho
    • , Maxwell R Mumbach
    • , Ava C Carter
    • , Maya Kasowski
    • , Lisa A Orloff
    • , Viviana I Risca
    • , Anshul Kundaje
    • , Paul A Khavari
    • , Thomas J Montine
    • , William J Greenleaf
    •  & Howard Y Chang