Latest Research

  • Article |

    The Ribosolve pipeline combines single-particle cryo-EM, M2-seq biochemical analysis and Rosetta auto-DRRAFTER modeling to guide three-dimensional RNA structure determination.

    • Kalli Kappel
    • , Kaiming Zhang
    • , Zhaoming Su
    • , Andrew M. Watkins
    • , Wipapat Kladwang
    • , Shanshan Li
    • , Grigore Pintilie
    • , Ved V. Topkar
    • , Ramya Rangan
    • , Ivan N. Zheludev
    • , Joseph D. Yesselman
    • , Wah Chiu
    •  & Rhiju Das
  • Brief Communication |

    Hundred-fold-faster DNA-PAINT imaging is enabled by the introduction of concatenated, periodic DNA sequence motifs in the docking strand. Six orthogonal sequences are described for speed-optimized and highly multiplexed cellular imaging.

    • Sebastian Strauss
    •  & Ralf Jungmann
  • Article |

    Small vibrational tags (azide, 13C-edited carbonyl and deuterium-labeled probes) were introduced as metabolic probes for mid-infrared imaging. The tags allow unprecedented in situ visualization of metabolism in cells and animals with high information throughput.

    • Lixue Shi
    • , Xinwen Liu
    • , Lingyan Shi
    • , H. Ted Stinson
    • , Jeremy Rowlette
    • , Lisa J. Kahl
    • , Christopher R. Evans
    • , Chaogu Zheng
    • , Lars E. P. Dietrich
    •  & Wei Min
  • Article |

    PULSE is an optogenetic tool that consists of two modules with different wavelength sensitivities. Their interplay enables optogenetic access to gene expression in plants independently of ambient light.

    • Rocio Ochoa-Fernandez
    • , Nikolaj B. Abel
    • , Franz-Georg Wieland
    • , Jenia Schlegel
    • , Leonie-Alexa Koch
    • , J. Benjamin Miller
    • , Raphael Engesser
    • , Giovanni Giuriani
    • , Simon M. Brandl
    • , Jens Timmer
    • , Wilfried Weber
    • , Thomas Ott
    • , Rüdiger Simon
    •  & Matias D. Zurbriggen
  • Brief Communication |

    CARPID uses CRISPR technology to navigate biotin ligase to specific lncRNAs, which allows proximal labeling and thus the querying of RNA–protein interactions in living cells.

    • Wenkai Yi
    • , Jingyu Li
    • , Xiaoxuan Zhu
    • , Xi Wang
    • , Ligang Fan
    • , Wenju Sun
    • , Linbu Liao
    • , Jilin Zhang
    • , Xiaoyu Li
    • , Jing Ye
    • , Fulin Chen
    • , Jussi Taipale
    • , Kui Ming Chan
    • , Liang Zhang
    •  & Jian Yan
  • Article |

    Multifocal flat illumination for field-independent imaging (mfFIFI) enables patterned illumination over an extended field of view. Integration with instant structured illumination microscope allowed for high-speed, multicolor, volumetric super-resolution imaging over 100 × 100 µm2.

    • Dora Mahecic
    • , Davide Gambarotto
    • , Kyle M. Douglass
    • , Denis Fortun
    • , Niccoló Banterle
    • , Khalid A. Ibrahim
    • , Maeva Le Guennec
    • , Pierre Gönczy
    • , Virginie Hamel
    • , Paul Guichard
    •  & Suliana Manley
  • Brief Communication |

    Split-FISH leverages a split-probe design to achieve enhanced specificity in multiplexed fluorescence in situ hybridization. Split-FISH reduces background and false positives, enabling transcriptome profiling in uncleared tissues.

    • Jolene Jie Lin Goh
    • , Nigel Chou
    • , Wan Yi Seow
    • , Norbert Ha
    • , Chung Pui Paul Cheng
    • , Yun-Ching Chang
    • , Ziqing Winston Zhao
    •  & Kok Hao Chen
  • Article |

    DeepSTORM3D uses deep learning for accurate localization of point emitters in densely labeled samples in three dimensions for volumetric localization microscopy with high temporal resolution, as well as for optimal point-spread function design.

    • Elias Nehme
    • , Daniel Freedman
    • , Racheli Gordon
    • , Boris Ferdman
    • , Lucien E. Weiss
    • , Onit Alalouf
    • , Tal Naor
    • , Reut Orange
    • , Tomer Michaeli
    •  & Yoav Shechtman
  • Perspective |

    This Perspective highlights recently developed computational models for studying chromosome organization, with a focus on how mechanistic modeling helps biologists to interpret the biological function behind the genome structures.

    • Chris A. Brackey
    • , Davide Marenduzzo
    •  & Nick Gilbert
  • Article |

    Guide RNA selection plays an essential role in CRISPR screens, the Vienna Bioactivity CRISPR (VBC) scoring system provides an improved selection for sgRNAs that generate loss-of-function alleles.

    • Georg Michlits
    • , Julian Jude
    • , Matthias Hinterndorfer
    • , Melanie de Almeida
    • , Gintautas Vainorius
    • , Maria Hubmann
    • , Tobias Neumann
    • , Alexander Schleiffer
    • , Thomas Rainer Burkard
    • , Michaela Fellner
    • , Max Gijsbertsen
    • , Anna Traunbauer
    • , Johannes Zuber
    •  & Ulrich Elling
  • Perspective |

    This Perspective reviews tools developed over the past five years in the macromolecular modeling, docking and design software Rosetta.

    • Julia Koehler Leman
    • , Brian D. Weitzner
    • , Steven M. Lewis
    • , Jared Adolf-Bryfogle
    • , Nawsad Alam
    • , Rebecca F. Alford
    • , Melanie Aprahamian
    • , David Baker
    • , Kyle A. Barlow
    • , Patrick Barth
    • , Benjamin Basanta
    • , Brian J. Bender
    • , Kristin Blacklock
    • , Jaume Bonet
    • , Scott E. Boyken
    • , Phil Bradley
    • , Chris Bystroff
    • , Patrick Conway
    • , Seth Cooper
    • , Bruno E. Correia
    • , Brian Coventry
    • , Rhiju Das
    • , René M. De Jong
    • , Frank DiMaio
    • , Lorna Dsilva
    • , Roland Dunbrack
    • , Alexander S. Ford
    • , Brandon Frenz
    • , Darwin Y. Fu
    • , Caleb Geniesse
    • , Lukasz Goldschmidt
    • , Ragul Gowthaman
    • , Jeffrey J. Gray
    • , Dominik Gront
    • , Sharon Guffy
    • , Scott Horowitz
    • , Po-Ssu Huang
    • , Thomas Huber
    • , Tim M. Jacobs
    • , Jeliazko R. Jeliazkov
    • , David K. Johnson
    • , Kalli Kappel
    • , John Karanicolas
    • , Hamed Khakzad
    • , Karen R. Khar
    • , Sagar D. Khare
    • , Firas Khatib
    • , Alisa Khramushin
    • , Indigo C. King
    • , Robert Kleffner
    • , Brian Koepnick
    • , Tanja Kortemme
    • , Georg Kuenze
    • , Brian Kuhlman
    • , Daisuke Kuroda
    • , Jason W. Labonte
    • , Jason K. Lai
    • , Gideon Lapidoth
    • , Andrew Leaver-Fay
    • , Steffen Lindert
    • , Thomas Linsky
    • , Nir London
    • , Joseph H. Lubin
    • , Sergey Lyskov
    • , Jack Maguire
    • , Lars Malmström
    • , Enrique Marcos
    • , Orly Marcu
    • , Nicholas A. Marze
    • , Jens Meiler
    • , Rocco Moretti
    • , Vikram Khipple Mulligan
    • , Santrupti Nerli
    • , Christoffer Norn
    • , Shane Ó’Conchúir
    • , Noah Ollikainen
    • , Sergey Ovchinnikov
    • , Michael S. Pacella
    • , Xingjie Pan
    • , Hahnbeom Park
    • , Ryan E. Pavlovicz
    • , Manasi Pethe
    • , Brian G. Pierce
    • , Kala Bharath Pilla
    • , Barak Raveh
    • , P. Douglas Renfrew
    • , Shourya S. Roy Burman
    • , Aliza Rubenstein
    • , Marion F. Sauer
    • , Andreas Scheck
    • , William Schief
    • , Ora Schueler-Furman
    • , Yuval Sedan
    • , Alexander M. Sevy
    • , Nikolaos G. Sgourakis
    • , Lei Shi
    • , Justin B. Siegel
    • , Daniel-Adriano Silva
    • , Shannon Smith
    • , Yifan Song
    • , Amelie Stein
    • , Maria Szegedy
    • , Frank D. Teets
    • , Summer B. Thyme
    • , Ray Yu-Ruei Wang
    • , Andrew Watkins
    • , Lior Zimmerman
    •  & Richard Bonneau
  • Article |

    Targeted sequencing of perturbation effects offers a sensitive approach to capture genes of interest in CRISPR-mediated screens, enabling genome-scale screens at higher scale and lower cost than whole-transcriptome Perturb-seq.

    • Daniel Schraivogel
    • , Andreas R. Gschwind
    • , Jennifer H. Milbank
    • , Daniel R. Leonce
    • , Petra Jakob
    • , Lukas Mathur
    • , Jan O. Korbel
    • , Christoph A. Merten
    • , Lars Velten
    •  & Lars M. Steinmetz
  • Article |

    Real-time 3D movement correction by tracking a fluorescent bead in the field of view enables functional imaging with 3D two-photon random-access microscopy in behaving mice and zebrafish.

    • Victoria A. Griffiths
    • , Antoine M. Valera
    • , Joanna YN. Lau
    • , Hana Roš
    • , Thomas J. Younts
    • , Bóris Marin
    • , Chiara Baragli
    • , Diccon Coyle
    • , Geoffrey J. Evans
    • , George Konstantinou
    • , Theo Koimtzis
    • , K. M. Naga Srinivas Nadella
    • , Sameer A. Punde
    • , Paul A. Kirkby
    • , Isaac H. Bianco
    •  & R. Angus Silver
  • Brief Communication |

    Sorting RT-FDC combines real-time fluorescence and deformability cytometry with sorting based on standing surface acoustic waves to transfer molecular specificity to label-free, image-based cell sorting using an efficient deep neural network.

    • Ahmad Ahsan Nawaz
    • , Marta Urbanska
    • , Maik Herbig
    • , Martin Nötzel
    • , Martin Kräter
    • , Philipp Rosendahl
    • , Christoph Herold
    • , Nicole Toepfner
    • , Markéta Kubánková
    • , Ruchi Goswami
    • , Shada Abuhattum
    • , Felix Reichel
    • , Paul Müller
    • , Anna Taubenberger
    • , Salvatore Girardo
    • , Angela Jacobi
    •  & Jochen Guck
  • Brief Communication |

    Theoretical and experimental guidelines to determine laser intensity for single-photon excitation in microcrystals for ultrafast pump–probe experiments by serial femtosecond crystallography.

    • Marie Luise Grünbein
    • , Miriam Stricker
    • , Gabriela Nass Kovacs
    • , Marco Kloos
    • , R. Bruce Doak
    • , Robert L. Shoeman
    • , Jochen Reinstein
    • , Sylvain Lecler
    • , Stefan Haacke
    •  & Ilme Schlichting
  • Brief Communication |

    jYCaMP1, a yellow variant of the calcium indicator jGCaMP7, enables fast multicolor two-photon imaging at excitation wavelengths above 1,000 nm for use with popular ytterbium-doped fiber and modelocked semiconductor lasers.

    • Manuel Alexander Mohr
    • , Daniel Bushey
    • , Abhi Aggarwal
    • , Jonathan S. Marvin
    • , Jeong Jun Kim
    • , Emiliano Jimenez Marquez
    • , Yajie Liang
    • , Ronak Patel
    • , John J. Macklin
    • , Chi-Yu Lee
    • , Arthur Tsang
    • , Getahun Tsegaye
    • , Allison M. Ahrens
    • , Jerry L. Chen
    • , Douglas S. Kim
    • , Allan M. Wong
    • , Loren L. Looger
    • , Eric R. Schreiter
    •  & Kaspar Podgorski
  • Article |

    CRISPR-based microraft followed by guide RNA identification (CRaft-ID) combines microraft arrays, microscopy and CRISPR–Cas9 technology for high-content image-based phenotyping. CRaft-ID was used to identify proteins involved in stress granule formation.

    • Emily C. Wheeler
    • , Anthony Q. Vu
    • , Jaclyn M. Einstein
    • , Matthew DiSalvo
    • , Noorsher Ahmed
    • , Eric L. Van Nostrand
    • , Alexander A. Shishkin
    • , Wenhao Jin
    • , Nancy L. Allbritton
    •  & Gene W. Yeo
  • Brief Communication |

    A head-mounted three-photon microscope based on a custom-designed optical fiber and dispersion compensation enables imaging of activity from neuronal populations deep in the cortex of freely moving rats.

    • Alexandr Klioutchnikov
    • , Damian J. Wallace
    • , Michael H. Frosz
    • , Richard Zeltner
    • , Juergen Sawinski
    • , Verena Pawlak
    • , Kay-Michael Voit
    • , Philip St. J. Russell
    •  & Jason N. D. Kerr
  • Article |

    In situ point spread function (PSF) retrieval (INSPR) enables precise single-molecule localization in 3D single-molecule localization microscopy of whole cells and tissues. It directly determines PSF from a single-molecule blinking dataset, removing errors associated with sample-induced aberrations.

    • Fan Xu
    • , Donghan Ma
    • , Kathryn P. MacPherson
    • , Sheng Liu
    • , Ye Bu
    • , Yu Wang
    • , Yu Tang
    • , Cheng Bi
    • , Tim Kwok
    • , Alexander A. Chubykin
    • , Peng Yin
    • , Sarah Calve
    • , Gary E. Landreth
    •  & Fang Huang
  • Brief Communication |

    ‘Nativeomics’ enables identification of ligands bound to membrane proteins through detection of intact protein–ligand assemblies followed by dissociation and identification of individual ligands within the same mass spectrometry experiment.

    • Joseph Gault
    • , Idlir Liko
    • , Michael Landreh
    • , Denis Shutin
    • , Jani Reddy Bolla
    • , Damien Jefferies
    • , Mark Agasid
    • , Hsin-Yung Yen
    • , Marcus J. G. W. Ladds
    • , David P. Lane
    • , Syma Khalid
    • , Christopher Mullen
    • , Philip M. Remes
    • , Romain Huguet
    • , Graeme McAlister
    • , Michael Goodwin
    • , Rosa Viner
    • , John E.P. Syka
    •  & Carol V. Robinson
  • Brief Communication |

    Three-photon microscopy provides access to most of the adult zebrafish brain for both structural and functional imaging, as well as to the Danionella dracula brain.

    • Dawnis M. Chow
    • , David Sinefeld
    • , Kristine E. Kolkman
    • , Dimitre G. Ouzounov
    • , Najva Akbari
    • , Rose Tatarsky
    • , Andrew Bass
    • , Chris Xu
    •  & Joseph R. Fetcho
  • Article |

    M-CREATE is an in vivo screening strategy for identifying recombinant AAVs with desired tropism. The approach involves both positive and negative selection and yields vectors with diversified cell-type tropism that can cross the blood–brain barrier in adult mice across strains when delivered intravenously.

    • Sripriya Ravindra Kumar
    • , Timothy F. Miles
    • , Xinhong Chen
    • , David Brown
    • , Tatyana Dobreva
    • , Qin Huang
    • , Xiaozhe Ding
    • , Yicheng Luo
    • , Pétur H. Einarsson
    • , Alon Greenbaum
    • , Min J. Jang
    • , Benjamin E. Deverman
    •  & Viviana Gradinaru
  • Publisher Correction
    | Open Access

    • Drahomíra Faktorová
    • , R. Ellen R. Nisbet
    • , José A. Fernández Robledo
    • , Elena Casacuberta
    • , Lisa Sudek
    • , Andrew E. Allen
    • , Manuel Ares Jr
    • , Cristina Aresté
    • , Cecilia Balestreri
    • , Adrian C. Barbrook
    • , Patrick Beardslee
    • , Sara Bender
    • , David S. Booth
    • , François-Yves Bouget
    • , Chris Bowler
    • , Susana A. Breglia
    • , Colin Brownlee
    • , Gertraud Burger
    • , Heriberto Cerutti
    • , Rachele Cesaroni
    • , Miguel A. Chiurillo
    • , Thomas Clemente
    • , Duncan B. Coles
    • , Jackie L. Collier
    • , Elizabeth C. Cooney
    • , Kathryn Coyne
    • , Roberto Docampo
    • , Christopher L. Dupont
    • , Virginia Edgcomb
    • , Elin Einarsson
    • , Pía A. Elustondo
    • , Fernan Federici
    • , Veronica Freire-Beneitez
    • , Nastasia J. Freyria
    • , Kodai Fukuda
    • , Paulo A. García
    • , Peter R. Girguis
    • , Fatma Gomaa
    • , Sebastian G. Gornik
    • , Jian Guo
    • , Vladimír Hampl
    • , Yutaka Hanawa
    • , Esteban R. Haro-Contreras
    • , Elisabeth Hehenberger
    • , Andrea Highfield
    • , Yoshihisa Hirakawa
    • , Amanda Hopes
    • , Christopher J. Howe
    • , Ian Hu
    • , Jorge Ibañez
    • , Nicholas A. T. Irwin
    • , Yuu Ishii
    • , Natalia Ewa Janowicz
    • , Adam C. Jones
    • , Ambar Kachale
    • , Konomi Fujimura-Kamada
    • , Binnypreet Kaur
    • , Jonathan Z. Kaye
    • , Eleanna Kazana
    • , Patrick J. Keeling
    • , Nicole King
    • , Lawrence A. Klobutcher
    • , Noelia Lander
    • , Imen Lassadi
    • , Zhuhong Li
    • , Senjie Lin
    • , Jean-Claude Lozano
    • , Fulei Luan
    • , Shinichiro Maruyama
    • , Tamara Matute
    • , Cristina Miceli
    • , Jun Minagawa
    • , Mark Moosburner
    • , Sebastián R. Najle
    • , Deepak Nanjappa
    • , Isabel C. Nimmo
    • , Luke Noble
    • , Anna M. G. Novák Vanclová
    • , Mariusz Nowacki
    • , Isaac Nuñez
    • , Arnab Pain
    • , Angela Piersanti
    • , Sandra Pucciarelli
    • , Jan Pyrih
    • , Joshua S. Rest
    • , Mariana Rius
    • , Deborah Robertson
    • , Albane Ruaud
    • , Iñaki Ruiz-Trillo
    • , Monika A. Sigg
    • , Pamela A. Silver
    • , Claudio H. Slamovits
    • , G. Jason Smith
    • , Brittany N. Sprecher
    • , Rowena Stern
    • , Estienne C. Swart
    • , Anastasios D. Tsaousis
    • , Lev Tsypin
    • , Aaron Turkewitz
    • , Jernej Turnšek
    • , Matus Valach
    • , Valérie Vergé
    • , Peter von Dassow
    • , Tobias von der Haar
    • , Ross F. Waller
    • , Lu Wang
    • , Xiaoxue Wen
    • , Glen Wheeler
    • , April Woods
    • , Huan Zhang
    • , Thomas Mock
    • , Alexandra Z. Worden
    •  & Julius Lukeš
  • Review Article |

    This Review discusses temporal focusing microscopy and its applications in neuroscience for imaging and optogenetic activation.

    • Eirini Papagiakoumou
    • , Emiliano Ronzitti
    •  & Valentina Emiliani
  • Resource |

    The meltome atlas compiles the thermal stability of 48,000 proteins across 13 species ranging from archaea to humans, providing a resource for analyzing protein stability in the context of function and interactions.

    • Anna Jarzab
    • , Nils Kurzawa
    • , Thomas Hopf
    • , Matthias Moerch
    • , Jana Zecha
    • , Niels Leijten
    • , Yangyang Bian
    • , Eva Musiol
    • , Melanie Maschberger
    • , Gabriele Stoehr
    • , Isabelle Becher
    • , Charlotte Daly
    • , Patroklos Samaras
    • , Julia Mergner
    • , Britta Spanier
    • , Angel Angelov
    • , Thilo Werner
    • , Marcus Bantscheff
    • , Mathias Wilhelm
    • , Martin Klingenspor
    • , Simone Lemeer
    • , Wolfgang Liebl
    • , Hannes Hahne
    • , Mikhail M. Savitski
    •  & Bernhard Kuster
  • Resource
    | Open Access

    This Resource describes genetic tools for microbial eukaryotes, providing a roadmap for developing genetically tractable organisms.

    • Drahomíra Faktorová
    • , R. Ellen R. Nisbet
    • , José A. Fernández Robledo
    • , Elena Casacuberta
    • , Lisa Sudek
    • , Andrew E. Allen
    • , Manuel Ares Jr
    • , Cristina Aresté
    • , Cecilia Balestreri
    • , Adrian C. Barbrook
    • , Patrick Beardslee
    • , Sara Bender
    • , David S. Booth
    • , François-Yves Bouget
    • , Chris Bowler
    • , Susana A. Breglia
    • , Colin Brownlee
    • , Gertraud Burger
    • , Heriberto Cerutti
    • , Rachele Cesaroni
    • , Miguel A. Chiurillo
    • , Thomas Clemente
    • , Duncan B. Coles
    • , Jackie L. Collier
    • , Elizabeth C. Cooney
    • , Kathryn Coyne
    • , Roberto Docampo
    • , Christopher L. Dupont
    • , Virginia Edgcomb
    • , Elin Einarsson
    • , Pía A. Elustondo
    • , Fernan Federici
    • , Veronica Freire-Beneitez
    • , Nastasia J. Freyria
    • , Kodai Fukuda
    • , Paulo A. García
    • , Peter R. Girguis
    • , Fatma Gomaa
    • , Sebastian G. Gornik
    • , Jian Guo
    • , Vladimír Hampl
    • , Yutaka Hanawa
    • , Esteban R. Haro-Contreras
    • , Elisabeth Hehenberger
    • , Andrea Highfield
    • , Yoshihisa Hirakawa
    • , Amanda Hopes
    • , Christopher J. Howe
    • , Ian Hu
    • , Jorge Ibañez
    • , Nicholas A. T. Irwin
    • , Yuu Ishii
    • , Natalia Ewa Janowicz
    • , Adam C. Jones
    • , Ambar Kachale
    • , Konomi Fujimura-Kamada
    • , Binnypreet Kaur
    • , Jonathan Z. Kaye
    • , Eleanna Kazana
    • , Patrick J. Keeling
    • , Nicole King
    • , Lawrence A. Klobutcher
    • , Noelia Lander
    • , Imen Lassadi
    • , Zhuhong Li
    • , Senjie Lin
    • , Jean-Claude Lozano
    • , Fulei Luan
    • , Shinichiro Maruyama
    • , Tamara Matute
    • , Cristina Miceli
    • , Jun Minagawa
    • , Mark Moosburner
    • , Sebastián R. Najle
    • , Deepak Nanjappa
    • , Isabel C. Nimmo
    • , Luke Noble
    • , Anna M. G. Novák Vanclová
    • , Mariusz Nowacki
    • , Isaac Nuñez
    • , Arnab Pain
    • , Angela Piersanti
    • , Sandra Pucciarelli
    • , Jan Pyrih
    • , Joshua S. Rest
    • , Mariana Rius
    • , Deborah Robertson
    • , Albane Ruaud
    • , Iñaki Ruiz-Trillo
    • , Monika A. Sigg
    • , Pamela A. Silver
    • , Claudio H. Slamovits
    • , G. Jason Smith
    • , Brittany N. Sprecher
    • , Rowena Stern
    • , Estienne C. Swart
    • , Anastasios D. Tsaousis
    • , Lev Tsypin
    • , Aaron Turkewitz
    • , Jernej Turnšek
    • , Matus Valach
    • , Valérie Vergé
    • , Peter von Dassow
    • , Tobias von der Haar
    • , Ross F. Waller
    • , Lu Wang
    • , Xiaoxue Wen
    • , Glen Wheeler
    • , April Woods
    • , Huan Zhang
    • , Thomas Mock
    • , Alexandra Z. Worden
    •  & Julius Lukeš
  • Article |

    Light-dependent variants of Cre, Dre and Flp enable targeted sparse or single-cell labeling in mouse and zebrafish.

    • Shenqin Yao
    • , Peng Yuan
    • , Ben Ouellette
    • , Thomas Zhou
    • , Marty Mortrud
    • , Pooja Balaram
    • , Soumya Chatterjee
    • , Yun Wang
    • , Tanya L. Daigle
    • , Bosiljka Tasic
    • , Xiuli Kuang
    • , Hui Gong
    • , Qingming Luo
    • , Shaoqun Zeng
    • , Andrew Curtright
    • , Ajay Dhaka
    • , Anat Kahan
    • , Viviana Gradinaru
    • , Radosław Chrapkiewicz
    • , Mark Schnitzer
    • , Hongkui Zeng
    •  & Ali Cetin
  • Article |

    A set of isobaric labeling reagents called TMTpro enables deep quantitative comparisons of proteome measurements across 16 samples.

    • Jiaming Li
    • , Jonathan G. Van Vranken
    • , Laura Pontano Vaites
    • , Devin K. Schweppe
    • , Edward L. Huttlin
    • , Chris Etienne
    • , Premchendar Nandhikonda
    • , Rosa Viner
    • , Aaron M. Robitaille
    • , Andrew H. Thompson
    • , Karsten Kuhn
    • , Ian Pike
    • , Ryan D. Bomgarden
    • , John C. Rogers
    • , Steven P. Gygi
    •  & Joao A. Paulo
  • Article |

    3D ATAC-PALM integrates ATAC with super-resolution imaging for nanoscale views of the accessible genome. When combined with FISH, protein fluorescence and genetic perturbation, the method enables investigation of accessible chromatin in situ.

    • Liangqi Xie
    • , Peng Dong
    • , Xingqi Chen
    • , Tsung-Han S. Hsieh
    • , Sambashiva Banala
    • , Margherita De Marzio
    • , Brian P. English
    • , Yifeng Qi
    • , Seol Kyoung Jung
    • , Kyong-Rim Kieffer-Kwon
    • , Wesley R. Legant
    • , Anders S. Hansen
    • , Anton Schulmann
    • , Rafael Casellas
    • , Bin Zhang
    • , Eric Betzig
    • , Luke D. Lavis
    • , Howard Y. Chang
    • , Robert Tjian
    •  & Zhe Liu
  • Article |

    DNA-based FluoroCubes are ~6 nm small, monovalent probes that contain six organic dyes, which confer dramatic photostability relative to single dyes and offer more uniform signal compared to quantum dots for extended biological imaging.

    • Stefan Niekamp
    • , Nico Stuurman
    •  & Ronald D. Vale
  • Article |

    Cardelino leverages variant information from single-cell RNA-seq data for inferring clonal tree configuration and mapping cells to their clone of origin.

    • Davis J. McCarthy
    • , Raghd Rostom
    • , Yuanhua Huang
    • , Daniel J. Kunz
    • , Petr Danecek
    • , Marc Jan Bonder
    • , Tzachi Hagai
    • , Ruqian Lyu
    • , Helena Kilpinen
    • , Angela Goncalves
    • , Andreas Leha
    • , Vackar Afzal
    • , Kaur Alasoo
    • , Sofie Ashford
    • , Sendu Bala
    • , Dalila Bensaddek
    • , Marc Jan Bonder
    • , Francesco Paolo Casale
    • , Oliver J. Culley
    • , Anna Cuomo
    • , Petr Danecek
    • , Adam Faulconbridge
    • , Peter W. Harrison
    • , Annie Kathuria
    • , Davis J. McCarthy
    • , Shane A. McCarthy
    • , Ruta Meleckyte
    • , Yasin Memari
    • , Bogdan Mirauta
    • , Nathalie Moens
    • , Filipa Soares
    • , Alice Mann
    • , Daniel Seaton
    • , Ian Streeter
    • , Chukwuma A. Agu
    • , Alex Alderton
    • , Rachel Nelson
    • , Sarah Harper
    • , Minal Patel
    • , Alistair White
    • , Sharad R. Patel
    • , Laura Clarke
    • , Reena Halai
    • , Christopher M. Kirton
    • , Anja KolbKokocinski
    • , Philip Beales
    • , Ewan Birney
    • , Davide Danovi
    • , Angus I. Lamond
    • , Willem H. Ouwehand
    • , Ludovic Vallier
    • , Fiona M. Watt
    • , Richard Durbin
    • , Oliver Stegle
    • , Daniel J. Gaffney
    • , Wenyi Wang
    • , Daniel J. Gaffney
    • , Benjamin D. Simons
    • , Oliver Stegle
    •  & Sarah A. Teichmann
  • Article |

    VesSAP is a tissue clearing- and deep learning-based pipeline for comprehensively analyzing mouse vasculature, from large vessels to small capillaries.

    • Mihail Ivilinov Todorov
    • , Johannes Christian Paetzold
    • , Oliver Schoppe
    • , Giles Tetteh
    • , Suprosanna Shit
    • , Velizar Efremov
    • , Katalin Todorov-Völgyi
    • , Marco Düring
    • , Martin Dichgans
    • , Marie Piraud
    • , Bjoern Menze
    •  & Ali Ertürk
  • Perspective |

    This Perspective discusses the challenges, progress and future of proteome profiling at specific chromatin loci for elucidating genome biology.

    • Mathilde Gauchier
    • , Guido van Mierlo
    • , Michiel Vermeulen
    •  & Jérôme Déjardin
  • Brief Communication |

    High-speed two-photon laser scanning microscopy using a passive laser scanner based on free-space angular-chirp-enhanced delay achieves frame rates suitable for voltage imaging in vivo in the mouse brain.

    • Jianglai Wu
    • , Yajie Liang
    • , Shuo Chen
    • , Ching-Lung Hsu
    • , Mariya Chavarha
    • , Stephen W. Evans
    • , Dongqing Shi
    • , Michael Z. Lin
    • , Kevin K. Tsia
    •  & Na Ji