Articles

  • Article |

    Segmental Duplication Assembler (SDA) uses long sequence reads to resolve segmental duplications that are collapsed in current genome assemblies. These assemblies correspond in total to the length of an average human chromosome.

    • Mitchell R. Vollger
    • , Philip C. Dishuck
    • , Melanie Sorensen
    • , AnneMarie E. Welch
    • , Vy Dang
    • , Max L. Dougherty
    • , Tina A. Graves-Lindsay
    • , Richard K. Wilson
    • , Mark J. P. Chaisson
    •  & Evan E. Eichler
  • Article |

    Deep learning enables cross-modality super-resolution imaging, including confocal-to-STED and TIRF-to-TIRF-SIM image transformation. Imaging of a larger FOV and greater depth of field is possible with higher resolution and SNR at lower light doses.

    • Hongda Wang
    • , Yair Rivenson
    • , Yiyin Jin
    • , Zhensong Wei
    • , Ronald Gao
    • , Harun Günaydın
    • , Laurent A. Bentolila
    • , Comert Kural
    •  & Aydogan Ozcan
  • Article |

    The DNA-based, ratiometric fluorescent reporter CalipHluor enables quantitative imaging of pH and calcium in acidic organelles with single-organelle resolution. The probe was used to identify a lysosome-specific Ca2+ importer in animals.

    • Nagarjun Narayanaswamy
    • , Kasturi Chakraborty
    • , Anand Saminathan
    • , Elizabeth Zeichner
    • , KaHo Leung
    • , John Devany
    •  & Yamuna Krishnan
  • Article |

    fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.

    • Oscar Esteban
    • , Christopher J. Markiewicz
    • , Ross W. Blair
    • , Craig A. Moodie
    • , A. Ilkay Isik
    • , Asier Erramuzpe
    • , James D. Kent
    • , Mathias Goncalves
    • , Elizabeth DuPre
    • , Madeleine Snyder
    • , Hiroyuki Oya
    • , Satrajit S. Ghosh
    • , Jessey Wright
    • , Joke Durnez
    • , Russell A. Poldrack
    •  & Krzysztof J. Gorgolewski
  • Article |

    An ex vivo 3D culture model of mycobacterial granulomas recapitulates the in vivo physiology of these structures and enables longitudinal imaging studies. The platform allows genetic and pharmacological manipulation of this key structure.

    • Mark R. Cronan
    • , Molly A. Matty
    • , Allison F. Rosenberg
    • , Landry Blanc
    • , Charlie J. Pyle
    • , Scott T. Espenschied
    • , John F. Rawls
    • , Véronique Dartois
    •  & David M. Tobin
  • Article |

    Imaging of neuronal activity across the whole zebrafish brain in combination with online analysis allows for manipulating neuronal activity according to function. This approach is used to ablate or activate neurons in fictively swimming zebrafish larvae.

    • Nikita Vladimirov
    • , Chen Wang
    • , Burkhard Höckendorf
    • , Avinash Pujala
    • , Masashi Tanimoto
    • , Yu Mu
    • , Chao-Tsung Yang
    • , Jason D. Wittenbach
    • , Jeremy Freeman
    • , Stephan Preibisch
    • , Minoru Koyama
    • , Philipp J. Keller
    •  & Misha B. Ahrens
  • Article |

    A particle-filter algorithm for single-particle cryo-electron microscopy, implemented in a tool called THUNDER, provides high-dimensional parameter estimation, improving the obtainable resolution for several protein structures.

    • Mingxu Hu
    • , Hongkun Yu
    • , Kai Gu
    • , Zhao Wang
    • , Huabin Ruan
    • , Kunpeng Wang
    • , Siyuan Ren
    • , Bing Li
    • , Lin Gan
    • , Shizhen Xu
    • , Guangwen Yang
    • , Yuan Shen
    •  & Xueming Li
  • Article |

    scVI is a ready-to-use generative deep learning tool for large-scale single-cell RNA-seq data that enables raw data processing and a wide range of rapid and accurate downstream analyses.

    • Romain Lopez
    • , Jeffrey Regier
    • , Michael B. Cole
    • , Michael I. Jordan
    •  & Nir Yosef
  • Article |

    YETI puts individual -omics experiments in the context of public genomics data by creating an integrated dataset-specific functional network, thus allowing more thorough interpretation of the data.

    • Young-suk Lee
    • , Aaron K. Wong
    • , Alicja Tadych
    • , Boris M. Hartmann
    • , Christopher Y. Park
    • , Veronica A. DeJesus
    • , Irene Ramos
    • , Elena Zaslavsky
    • , Stuart C. Sealfon
    •  & Olga G. Troyanskaya
  • Article |

    Content-aware image restoration (CARE) uses deep learning to improve microscopy images. CARE bypasses the trade-offs between imaging speed, resolution, and maximal light exposure that limit fluorescence imaging to enable discovery.

    • Martin Weigert
    • , Uwe Schmidt
    • , Tobias Boothe
    • , Andreas Müller
    • , Alexandr Dibrov
    • , Akanksha Jain
    • , Benjamin Wilhelm
    • , Deborah Schmidt
    • , Coleman Broaddus
    • , Siân Culley
    • , Mauricio Rocha-Martins
    • , Fabián Segovia-Miranda
    • , Caren Norden
    • , Ricardo Henriques
    • , Marino Zerial
    • , Michele Solimena
    • , Jochen Rink
    • , Pavel Tomancak
    • , Loic Royer
    • , Florian Jug
    •  & Eugene W. Myers
  • Article |

    The machine learning approach FIT leverages public mouse and human expression data to improve the translation of mouse model results to analogous human disease.

    • Rachelly Normand
    • , Wenfei Du
    • , Mayan Briller
    • , Renaud Gaujoux
    • , Elina Starosvetsky
    • , Amit Ziv-Kenet
    • , Gali Shalev-Malul
    • , Robert J. Tibshirani
    •  & Shai S. Shen-Orr
  • Article |

    VARNAM is a red-shifted genetically encoded voltage sensor based on the Ace opsin. It is applied in Drosophila, mouse brain slices and behaving mice. It can be readily combined with blue-light-sensitive tools for dual-color applications.

    • Madhuvanthi Kannan
    • , Ganesh Vasan
    • , Cheng Huang
    • , Simon Haziza
    • , Jin Zhong Li
    • , Hakan Inan
    • , Mark J. Schnitzer
    •  & Vincent A. Pieribone
  • Article |

    BLINK2 is a light-activated potassium channel for optogenetic inhibition of neuronal activity. Alberio et al. apply the tool in systems as diverse as cultured rat neurons, mouse brain slices, behaving zebrafish and a rat model of neuropathic pain.

    • Laura Alberio
    • , Andrea Locarno
    • , Andrea Saponaro
    • , Edoardo Romano
    • , Valérie Bercier
    • , Shahad Albadri
    • , Federica Simeoni
    • , Silvia Moleri
    • , Silvia Pelucchi
    • , Alessandro Porro
    • , Elena Marcello
    • , Noemi Barsotti
    • , Kerri Kukovetz
    • , Arjen J. Boender
    • , Andrea Contestabile
    • , Shizhen Luo
    • , Aubin Moutal
    • , Yingshi Ji
    • , Giulia Romani
    • , Monica Beltrame
    • , Filippo Del Bene
    • , Monica Di Luca
    • , Rajesh Khanna
    • , Henry M. Colecraft
    • , Massimo Pasqualetti
    • , Gerhard Thiel
    • , Raffaella Tonini
    •  & Anna Moroni
  • Article |

    HUMAnN2 uses a tiered sequence search to provide rapid and accurate species-level functional profiles of microbial communities from metagenomic and metatranscriptomic data.

    • Eric A. Franzosa
    • , Lauren J. McIver
    • , Gholamali Rahnavard
    • , Luke R. Thompson
    • , Melanie Schirmer
    • , George Weingart
    • , Karen Schwarzberg Lipson
    • , Rob Knight
    • , J. Gregory Caporaso
    • , Nicola Segata
    •  & Curtis Huttenhower
  • Article |

    The combination of transparency, small brain size and genetic access positions Danionella translucida as a promising model organism for functional imaging of neuronal circuits, especially during complex behaviors in adults.

    • Lisanne Schulze
    • , Jörg Henninger
    • , Mykola Kadobianskyi
    • , Thomas Chaigne
    • , Ana Isabel Faustino
    • , Nahid Hakiy
    • , Shahad Albadri
    • , Markus Schuelke
    • , Leonard Maler
    • , Filippo Del Bene
    •  & Benjamin Judkewitz
  • Article |

    Guide Swap challenges the hypothesis that Cas9–sgRNA binding is irreversible. The authors find that instead, nontargeting sgRNAs are swapped for targeting sgRNAs in the Cas9 complex. The method allows genome-scale functional screens in primary cells

    • Pamela Y. Ting
    • , Albert E. Parker
    • , J. Scott Lee
    • , Chris Trussell
    • , Orzala Sharif
    • , Fabio Luna
    • , Glenn Federe
    • , S. Whitney Barnes
    • , John R. Walker
    • , Julie Vance
    • , Mu-Yun Gao
    • , Heath E. Klock
    • , Scott Clarkson
    • , Carsten Russ
    • , Loren J. Miraglia
    • , Michael P. Cooke
    • , Anthony E. Boitano
    • , Peter McNamara
    • , John Lamb
    • , Christian Schmedt
    •  & Jennifer L. Snead
  • Article |

    A charge-integrating pixel-array detector called JUNGFRAU enables the collection of highly accurate X-ray crystallography data at synchrotron sources at unprecedented speeds.

    • Filip Leonarski
    • , Sophie Redford
    • , Aldo Mozzanica
    • , Carlos Lopez-Cuenca
    • , Ezequiel Panepucci
    • , Karol Nass
    • , Dmitry Ozerov
    • , Laura Vera
    • , Vincent Olieric
    • , Dominik Buntschu
    • , Roman Schneider
    • , Gemma Tinti
    • , Erik Froejdh
    • , Kay Diederichs
    • , Oliver Bunk
    • , Bernd Schmitt
    •  & Meitian Wang
  • Article |

    LFADS, a deep learning method for analyzing neural population activity, can extract neural dynamics from single-trial recordings, stitch separate datasets into a single model, and infer perturbations, for example, from behavioral choices to these dynamics.

    • Chethan Pandarinath
    • , Daniel J. O’Shea
    • , Jasmine Collins
    • , Rafal Jozefowicz
    • , Sergey D. Stavisky
    • , Jonathan C. Kao
    • , Eric M. Trautmann
    • , Matthew T. Kaufman
    • , Stephen I. Ryu
    • , Leigh R. Hochberg
    • , Jaimie M. Henderson
    • , Krishna V. Shenoy
    • , L. F. Abbott
    •  & David Sussillo
  • Article |

    REVOLVER uses transfer learning on multi-region tumor sequencing data to jointly infer tumor evolution models in multiple individuals and to detect repeated evolutionary trajectories. Repeated evolution can be used to stratify the cohort.

    • Giulio Caravagna
    • , Ylenia Giarratano
    • , Daniele Ramazzotti
    • , Ian Tomlinson
    • , Trevor A. Graham
    • , Guido Sanguinetti
    •  & Andrea Sottoriva
  • Article |

    Insertion of a bivalent linker between two regions of interest allows chromatin contacts to be probed without proximity ligation.

    • Binbin Lai
    • , Qingsong Tang
    • , Wenfei Jin
    • , Gangqing Hu
    • , Darawalee Wangsa
    • , Kairong Cui
    • , Benjamin Z. Stanton
    • , Gang Ren
    • , Yi Ding
    • , Ming Zhao
    • , Shuai Liu
    • , Jiuzhou Song
    • , Thomas Ried
    •  & Keji Zhao
  • Article |

    This paper describes modifications to standard culture conditions that permit the growth of naive human pluripotent stem cells with reduced genomic instability.

    • Bruno Di Stefano
    • , Mai Ueda
    • , Shan Sabri
    • , Justin Brumbaugh
    • , Aaron J. Huebner
    • , Anna Sahakyan
    • , Kendell Clement
    • , Katie J. Clowers
    • , Alison R. Erickson
    • , Keiko Shioda
    • , Steven P. Gygi
    • , Hongcang Gu
    • , Toshi Shioda
    • , Alexander Meissner
    • , Yasuhiro Takashima
    • , Kathrin Plath
    •  & Konrad Hochedlinger
  • Article |

    Spinal cord neural stem cells are generated from human pluripotent stem cells via a chemically defined, xeno-free method, and exhibit efficient and functional engraftment in rat spinal cord lesions.

    • Hiromi Kumamaru
    • , Ken Kadoya
    • , Andrew F. Adler
    • , Yoshio Takashima
    • , Lori Graham
    • , Giovanni Coppola
    •  & Mark H. Tuszynski
  • Article |

    Humanized mouse models are useful for studies of human hematopoiesis and immunity. Li et al. report an improved model that harbors lymph nodes and therefore permits investigation of local human adaptive immune processes in secondary lymphoid tissue.

    • Yan Li
    • , Guillemette Masse-Ranson
    • , Zacarias Garcia
    • , Timothée Bruel
    • , Ayrin Kök
    • , Helene Strick-Marchand
    • , Gregory Jouvion
    • , Nicolas Serafini
    • , Ai Ing Lim
    • , Mathilde Dusseaux
    • , Thierry Hieu
    • , Franck Bourgade
    • , Antoine Toubert
    • , Daniela Finke
    • , Olivier Schwartz
    • , Philippe Bousso
    • , Hugo Mouquet
    •  & James P. Di Santo
  • Article |

    A method for generating cortical spheroids from human pluripotent stem cells produces maturing oligodendrocytes that can myelinate axons and model myelin disease and drug effects.

    • Mayur Madhavan
    • , Zachary S. Nevin
    • , H. Elizabeth Shick
    • , Eric Garrison
    • , Cheryl Clarkson-Paredes
    • , Molly Karl
    • , Benjamin L. L. Clayton
    • , Daniel C. Factor
    • , Kevin C. Allan
    • , Lilianne Barbar
    • , Tanya Jain
    • , Panagiotis Douvaras
    • , Valentina Fossati
    • , Robert H. Miller
    •  & Paul J. Tesar
  • Article |

    Cerebral organoids are developed into in vitro models of human brain cancer by CRISPR–Cas9- and/or transposon-mediated introduction of oncogenic mutations.

    • Shan Bian
    • , Marko Repic
    • , Zhenming Guo
    • , Anoop Kavirayani
    • , Thomas Burkard
    • , Joshua A. Bagley
    • , Christian Krauditsch
    •  & Jürgen A. Knoblich
  • Article |

    The fusion of dead Cas9 with KRAB and the transcriptional repressor domain of the chromatin modifier MeCP2 leads to an efficient transcriptional silencer that can be applied to genome-scale screens and genetic circuits.

    • Nan Cher Yeo
    • , Alejandro Chavez
    • , Alissa Lance-Byrne
    • , Yingleong Chan
    • , David Menn
    • , Denitsa Milanova
    • , Chih-Chung Kuo
    • , Xiaoge Guo
    • , Sumana Sharma
    • , Angela Tung
    • , Ryan J. Cecchi
    • , Marcelle Tuttle
    • , Swechchha Pradhan
    • , Elaine T. Lim
    • , Noah Davidsohn
    • , Mo R. Ebrahimkhani
    • , James J. Collins
    • , Nathan E. Lewis
    • , Samira Kiani
    •  & George M. Church
  • Article |

    Flood-filling networks are a deep-learning-based pipeline for reconstruction of neurons from electron microscopy datasets. The approach results in exceptionally low error rates, thereby reducing the need for extensive human proofreading.

    • Michał Januszewski
    • , Jörgen Kornfeld
    • , Peter H. Li
    • , Art Pope
    • , Tim Blakely
    • , Larry Lindsey
    • , Jeremy Maitin-Shepard
    • , Mike Tyka
    • , Winfried Denk
    •  & Viren Jain
  • Article |

    A genome-wide collection of N-terminally tagged yeast libraries allows easy swapping of tags and exploration of the yeast proteome.

    • Uri Weill
    • , Ido Yofe
    • , Ehud Sass
    • , Bram Stynen
    • , Dan Davidi
    • , Janani Natarajan
    • , Reut Ben-Menachem
    • , Zohar Avihou
    • , Omer Goldman
    • , Nofar Harpaz
    • , Silvia Chuartzman
    • , Kiril Kniazev
    • , Barbara Knoblach
    • , Janina Laborenz
    • , Felix Boos
    • , Jacqueline Kowarzyk
    • , Shifra Ben-Dor
    • , Einat Zalckvar
    • , Johannes M. Herrmann
    • , Richard A. Rachubinski
    • , Ophry Pines
    • , Doron Rapaport
    • , Stephen W. Michnick
    • , Emmanuel D. Levy
    •  & Maya Schuldiner
  • Article |

    The ProximID approach generates single-cell expression profiles and a network of enriched physical cellular interactions within a tissue.

    • Jean-Charles Boisset
    • , Judith Vivié
    • , Dominic Grün
    • , Mauro J. Muraro
    • , Anna Lyubimova
    •  & Alexander van Oudenaarden
  • Article |

    Several methods make it possible to obtain depth information in 3D super-resolution microscopy. Here the authors exploit a self-interference phenomenon to allow deep imaging within tissue samples, as well as isotropic imaging.

    • Pierre Bon
    • , Jeanne Linarès-Loyez
    • , Maxime Feyeux
    • , Kevin Alessandri
    • , Brahim Lounis
    • , Pierre Nassoy
    •  & Laurent Cognet
  • Article |

    Data-independent-acquisition-based mass spectrometry enables highly reproducible proteome analysis, but results interpretation is challenging owing to the complex nature of the spectral data. A software tool, Specter, effectively resolves spectra for highly similar peptides.

    • Ryan Peckner
    • , Samuel A Myers
    • , Alvaro Sebastian Vaca Jacome
    • , Jarrett D Egertson
    • , Jennifer G Abelin
    • , Michael J MacCoss
    • , Steven A Carr
    •  & Jacob D Jaffe
  • Article |

    In this CRISPR-based feedback control system, sgRNA expression is triggered by the burden of protein overexpression, and the sgRNA directs repression of the exogenous gene promoter to reduce burdensome expression and restore growth of the cell.

    • Francesca Ceroni
    • , Alice Boo
    • , Simone Furini
    • , Thomas E Gorochowski
    • , Olivier Borkowski
    • , Yaseen N Ladak
    • , Ali R Awan
    • , Charlie Gilbert
    • , Guy-Bart Stan
    •  & Tom Ellis
  • Article |

    Embedding a deep-learning model in the known structure of cellular systems yields DCell, a ‘visible’ neural network that can be used to mechanistically interpret genotype–phenotype relationships.

    • Jianzhu Ma
    • , Michael Ku Yu
    • , Samson Fong
    • , Keiichiro Ono
    • , Eric Sage
    • , Barry Demchak
    • , Roded Sharan
    •  & Trey Ideker
  • Article |

    Mime-seq achieves cell-type specific, methylation-based, microRNA tagging and sequencing to uncover cell-specific microRNomes in C. elegans and Drosophila.

    • Chiara Alberti
    • , Raphael A Manzenreither
    • , Ivica Sowemimo
    • , Thomas R Burkard
    • , Jingkui Wang
    • , Katharina Mahofsky
    • , Stefan L Ameres
    •  & Luisa Cochella
  • Article |

    Labeling newly transcribed RNA with 5-ethynyluridine and adding biotin via click chemistry allows the analysis of the proteome bound to the various RNA species, including nascent RNA.

    • Xichen Bao
    • , Xiangpeng Guo
    • , Menghui Yin
    • , Muqddas Tariq
    • , Yiwei Lai
    • , Shahzina Kanwal
    • , Jiajian Zhou
    • , Na Li
    • , Yuan Lv
    • , Carlos Pulido-Quetglas
    • , Xiwei Wang
    • , Lu Ji
    • , Muhammad J Khan
    • , Xihua Zhu
    • , Zhiwei Luo
    • , Changwei Shao
    • , Do-Hwan Lim
    • , Xiao Liu
    • , Nan Li
    • , Wei Wang
    • , Minghui He
    • , Yu-Lin Liu
    • , Carl Ward
    • , Tong Wang
    • , Gong Zhang
    • , Dongye Wang
    • , Jianhua Yang
    • , Yiwen Chen
    • , Chaolin Zhang
    • , Ralf Jauch
    • , Yun-Gui Yang
    • , Yangming Wang
    • , Baoming Qin
    • , Minna-Liisa Anko
    • , Andrew P Hutchins
    • , Hao Sun
    • , Huating Wang
    • , Xiang-Dong Fu
    • , Biliang Zhang
    •  & Miguel A Esteban
  • Article |

    RaPID uses biotin ligases BirA* and the faster acting BASU to label proteins in the proximity of an RNA motif of interest in living cells.

    • Muthukumar Ramanathan
    • , Karim Majzoub
    • , Deepti S Rao
    • , Poornima H Neela
    • , Brian J Zarnegar
    • , Smarajit Mondal
    • , Julien G Roth
    • , Hui Gai
    • , Joanna R Kovalski
    • , Zurab Siprashvili
    • , Theo D Palmer
    • , Jan E Carette
    •  & Paul A Khavari
  • Article |

    Direct sequencing of RNA molecules in real time using nanopores allows for the detection of splice variants and hold promises for profiling RNA modifications.

    • Daniel R Garalde
    • , Elizabeth A Snell
    • , Daniel Jachimowicz
    • , Botond Sipos
    • , Joseph H Lloyd
    • , Mark Bruce
    • , Nadia Pantic
    • , Tigist Admassu
    • , Phillip James
    • , Anthony Warland
    • , Michael Jordan
    • , Jonah Ciccone
    • , Sabrina Serra
    • , Jemma Keenan
    • , Samuel Martin
    • , Luke McNeill
    • , E Jayne Wallace
    • , Lakmal Jayasinghe
    • , Chris Wright
    • , Javier Blasco
    • , Stephen Young
    • , Denise Brocklebank
    • , Sissel Juul
    • , James Clarke
    • , Andrew J Heron
    •  & Daniel J Turner