Nat. Methods

ISSN	1548-7105
ISSN-L	1548-7091
IUID	37b36f43c66949f2befe0de14debbf3e
Modified	2020-11-27T13:12:55.458Z
Created	2018-12-03T14:52:00.191Z

Nat. Methods 22 (12) 2500-2502 [2025-12-00; online 2025-11-25]

PubMed DOI Crossref

Translon: a single term for translated regions.

Świrski MI, Tierney JAS, Albà MM, ..., Valen E, Baranov PV

Nat. Methods 22 (10) 2002-2006 [2025-10-00; online 2025-09-02]

PubMed DOI Crossref

Author Correction: A universal language for finding mass spectrometry data patterns.

Damiani T, Jarmusch AK, Aron AT, ..., Dorrestein PC, Wang M

Nat. Methods 22 (9) 1995 [2025-09-00; online 2025-08-09]

PubMed DOI Crossref

A universal language for finding mass spectrometry data patterns.

Damiani T, Jarmusch AK, Aron AT, ..., Dorrestein PC, Wang M

Nat. Methods 22 (6) 1247-1254 [2025-06-00; online 2025-05-12]

PubMed DOI Crossref

Enabling global image data sharing in the life sciences.

Bajcsy P, Bhattiprolu S, Börner K, ..., Taylor A, Keppler A

Nat. Methods 22 (4) 672-676 [2025-04-00; online 2025-03-28]

PubMed DOI Crossref

The need to implement FAIR principles in biomolecular simulations.

Amaro RE, Åqvist J, Bahar I, ..., Zacharias M, Orozco M

Nat. Methods 22 (4) 641-645 [2025-04-00; online 2025-04-03]

PubMed DOI Crossref

Author Correction: Cell Painting: a decade of discovery and innovation in cellular imaging.

Seal S, Trapotsi MA, Spjuth O, ..., Bender A, Carpenter AE

Nat. Methods 22 (2) 447 [2025-02-00; online 2024-12-13]

PubMed DOI Crossref

ProHap enables human proteomic database generation accounting for population diversity.

Vašíček J, Kuznetsova KG, Skiadopoulou D, ..., Käll L, Vaudel M

Nat. Methods 22 (2) 273-277 [2025-02-00; online 2024-12-09]

PubMed DOI Crossref

Cell Painting: a decade of discovery and innovation in cellular imaging.

Seal S, Trapotsi MA, Spjuth O, ..., Bender A, Carpenter AE

Nat. Methods 22 (2) 254-268 [2025-02-00; online 2024-12-05]

PubMed DOI Crossref

Efficiently accelerated bioimage analysis with NanoPyx, a Liquid Engine-powered Python framework.

Saraiva BM, Cunha I, Brito AD, ..., Jacquemet G, Henriques R

Nat. Methods 22 (2) 283-286 [2025-02-00; online 2025-01-02]

PubMed DOI Crossref

Probe set selection for targeted spatial transcriptomics.

Kuemmerle LB, Luecken MD, Firsova AB, ..., Samakovlis C, Theis FJ

Nat. Methods 21 (12) 2260-2270 [2024-12-00; online 2024-11-18]

PubMed DOI Crossref

Building pangenome graphs.

Garrison E, Guarracino A, Heumos S, ..., Williams RW, Prins P

Nat. Methods 21 (11) 2008-2012 [2024-11-00; online 2024-10-21]

DDLS Fellow Kaisa Thorell

PubMed DOI Crossref

Serial Lift-Out: sampling the molecular anatomy of whole organisms.

Schiøtz OH, Kaiser CJO, Klumpe S, ..., Thompson C, Plitzko JM

Nat. Methods 21 (9) 1684-1692 [2024-09-00; online 2023-12-18]

PubMed DOI Crossref

quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data.

Dai C, Pfeuffer J, Wang H, ..., Kohlbacher O, Perez-Riverol Y

Nat. Methods 21 (9) 1603-1607 [2024-09-00; online 2024-07-04]

PubMed DOI Crossref

Microsecond time-resolved X-ray scattering by utilizing MHz repetition rate at second-generation XFELs.

Konold PE, Monrroy L, Bellisario A, ..., Maia F, Westenhoff S

Nat. Methods 21 (9) 1608-1611 [2024-09-00; online 2024-07-05]

PubMed DOI Crossref

BioImage.IO Chatbot: a community-driven AI assistant for integrative computational bioimaging.

Lei W, Fuster-Barceló C, Reder G, Muñoz-Barrutia A, Ouyang W

Nat. Methods 21 (8) 1368-1370 [2024-08-00; online 2024-08-10]

DDLS Fellow Wei Ouyang

PubMed DOI Crossref

Effects and avoidance of photoconversion-induced artifacts in confocal and STED microscopy.

Dasgupta A, Koerfer A, Kokot B, ..., Eggeling C, Carravilla P

Nat. Methods 21 (7) 1171-1174 [2024-07-00; online 2024-06-04]

PubMed DOI Crossref

DL4MicEverywhere: deep learning for microscopy made flexible, shareable and reproducible.

Hidalgo-Cenalmor I, Pylvänäinen JW, G Ferreira M, ..., Henriques R, Gómez-de-Mariscal E

Nat. Methods 21 (6) 925-927 [2024-06-00; online 2024-05-18]

PubMed DOI Crossref

Super-sectioning with multi-sheet reversible saturable optical fluorescence transitions (RESOLFT) microscopy.

Bodén A, Ollech D, York AG, Millett-Sikking A, Testa I

Nat. Methods 21 (5) 882-888 [2024-05-00; online 2024-02-23]

PubMed DOI Crossref

Spatial landmark detection and tissue registration with deep learning.

Ekvall M, Bergenstråhle L, Andersson A, ..., Käll L, Lundeberg J

Nat. Methods 21 (4) 673-679 [2024-04-00; online 2024-03-04]

PubMed DOI Crossref

DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes.

Frommelt F, Fossati A, Uliana F, ..., Ciuffa R, Gstaiger M

Nat. Methods 21 (4) 635-647 [2024-04-00; online 2024-03-26]

Andrea Fossati DDLS Fellow

PubMed DOI Crossref

JDLL: a library to run deep learning models on Java bioimage informatics platforms.

García López de Haro C, Dallongeville S, Musset T, ..., Tinevez JY, Olivo-Marin JC

Nat. Methods 21 (1) 7-8 [2024-01-00; online 2024-01-09]

PubMed DOI Crossref

Expansion spatial transcriptomics.

Fan Y, Andrusivová Ž, Wu Y, ..., Lundeberg J, Wang B

Nat. Methods 20 (8) 1179-1182 [2023-08-00; online 2023-06-22]

PubMed DOI Crossref

Organ Mapping Antibody Panels: a community resource for standardized multiplexed tissue imaging.

Quardokus EM, Saunders DC, McDonough E, ..., Börner K, Radtke AJ

Nat. Methods 20 (8) 1174-1178 [2023-08-00; online 2023-07-19]

PubMed DOI Crossref

Discovering CRISPR-Cas off-target breaks.

Jiménez C, Crosetto N

Nat. Methods 20 (5) 641-642 [2023-05-00; online 2023-04-07]

PubMed DOI Crossref

In silico tissue generation and power analysis for spatial omics.

Baker EAG, Schapiro D, Dumitrascu B, Vickovic S, Regev A

Nat. Methods 20 (3) 424-431 [2023-03-00; online 2023-03-02]

Sanja Vickovic SciLifeLab Fellow

PubMed DOI Crossref

ShareLoc - an open platform for sharing localization microscopy data.

Ouyang W, Bai J, Singh MK, ..., Lelandais B, Zimmer C

Nat. Methods 19 (11) 1331-1333 [2022-11-00; online 2022-10-22]

PubMed DOI Crossref

Event-triggered STED imaging.

Alvelid J, Damenti M, Sgattoni C, Testa I

Nat. Methods 19 (10) 1268-1275 [2022-10-00; online 2022-09-08]

Ilaria Testa SciLifeLab Fellow

PubMed DOI Crossref

Analysis of the Human Protein Atlas Weakly Supervised Single-Cell Classification competition.

Le T, Winsnes CF, Axelsson U, ..., Ouyang W, Lundberg E

Nat. Methods 19 (10) 1221-1229 [2022-10-00; online 2022-09-29]

PubMed DOI Crossref

Understudied proteins: opportunities and challenges for functional proteomics.

Kustatscher G, Collins T, Gingras AC, ..., Ralser M, Rappsilber J

Nat. Methods 19 (7) 774-779 [2022-07-00; online 2022-05-10]

PubMed DOI Crossref

Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram.

Biancalani T, Scalia G, Buffoni L, ..., Macosko EZ, Regev A

Nat. Methods 18 (11) 1352-1362 [2021-11-00; online 2021-10-28]

Sanja Vickovic SciLifeLab Fellow

PubMed DOI Crossref

DeepImageJ: A user-friendly environment to run deep learning models in ImageJ.

Gómez-de-Mariscal E, García-López-de-Haro C, Ouyang W, ..., Muñoz-Barrutia A, Sage D

Nat. Methods 18 (10) 1192-1195 [2021-10-00; online 2021-09-30]

PubMed DOI Crossref

Diversity in immunogenomics: the value and the challenge.

Peng K, Safonova Y, Shugay M, ..., Karlsson Hedestam GB, Mangul S

Nat. Methods 18 (6) 588-591 [2021-06-00; online 2021-05-19]

PubMed DOI Crossref

Critical assessment of protein intrinsic disorder prediction.

Necci M, Piovesan D, CAID Predictors , DisProt Curators , Tosatto SCE

Nat. Methods 18 (5) 472-481 [2021-05-00; online 2021-04-19]

PubMed DOI Crossref

Imaging-based screens of pool-synthesized cell libraries.

Lawson M, Elf J

Nat. Methods 18 (4) 358-365 [2021-04-00; online 2021-02-15]

PubMed DOI Crossref

Pycro-Manager: open-source software for customized and reproducible microscope control.

Pinkard H, Stuurman N, Ivanov IE, ..., Mehta SB, Waller L

Nat. Methods 18 (3) 226-228 [2021-03-00; online 2021-03-07]

PubMed DOI Crossref

Spatially resolved transcriptomics adds a new dimension to genomics.

Larsson L, Frisén J, Lundeberg J

Nat. Methods 18 (1) 15-18 [2021-01-00; online 2021-01-08]

PubMed DOI Crossref

Author Correction: Analysis of the Human Protein Atlas Image Classification competition.

Ouyang W, Winsnes CF, Hjelmare M, ..., Kappel C, Lundberg E

Nat. Methods 17 (9) 948 [2020-09-00; online 2020-08-08]

PubMed DOI Crossref

GPCRmd uncovers the dynamics of the 3D-GPCRome.

Rodríguez-Espigares I, Torrens-Fontanals M, Tiemann JKS, ..., Guixà-González R, Selent J

Nat. Methods 17 (8) 777-787 [2020-08-00; online 2020-07-13]

Jens Carlsson SciLifeLab Fellow

PubMed DOI Crossref

Publisher Correction: GPCRmd uncovers the dynamics of the 3D-GPCRome.

Rodríguez-Espigares I, Torrens-Fontanals M, Tiemann JKS, ..., Guixà-González R, Selent J

Nat. Methods 17 (8) 861-862 [2020-08-00; online 2020-07-25]

PubMed DOI Crossref

Publisher Correction: Analysis of the Human Protein Atlas Image Classification competition.

Ouyang W, Winsnes CF, Hjelmare M, ..., Kappel C, Lundberg E

Nat. Methods 17 (2) 241 [2020-02-00; online 2020-01-24]

PubMed DOI Crossref

Publisher Correction: Analysis of the Human Protein Atlas Image Classification competition.

Ouyang W, Winsnes CF, Hjelmare M, ..., Kappel C, Lundberg E

Nat. Methods 17 (1) 115 [2020-01-00; online 2019-12-12]

PubMed DOI Crossref

Time-resolved imaging-based CRISPRi screening.

Camsund D, Lawson MJ, Larsson J, ..., Fange D, Elf J

Nat. Methods 17 (1) 86-92 [2020-01-00; online 2019-11-18]

PubMed DOI Crossref

Analysis of the Human Protein Atlas Image Classification competition.

Ouyang W, Winsnes CF, Hjelmare M, ..., Kappel C, Lundberg E

Nat. Methods 16 (12) 1254-1261 [2019-12-00; online 2019-11-28]

PubMed DOI Crossref

ImJoy: an open-source computational platform for the deep learning era.

Ouyang W, Mueller F, Hjelmare M, Lundberg E, Zimmer C

Nat. Methods 16 (12) 1199-1200 [2019-12-00; online 2019-11-30]

PubMed DOI Crossref

High-definition spatial transcriptomics for in situ tissue profiling.

Vickovic S, Eraslan G, Salmén F, ..., Regev A, Ståhl PL

Nat. Methods 16 (10) 987-990 [2019-10-00; online 2019-09-09]

Sanja Vickovic SciLifeLab Fellow

PubMed DOI Crossref

Voices in methods development.

Anikeeva P, Boyden E, Brangwynne C, ..., Zernicka-Goetz M, Zhuang X

Nat. Methods 16 (10) 945-951 [2019-10-00; online 2019-09-29]

PubMed DOI Crossref

Comprehensive mapping of neurotransmitter networks by MALDI-MS imaging.

Shariatgorji M, Nilsson A, Fridjonsdottir E, ..., Odell LR, Andrén PE

Nat. Methods 16 (10) 1021-1028 [2019-10-00; online 2019-09-23]

PubMed DOI Crossref

Spatial organization of the somatosensory cortex revealed by osmFISH.

Codeluppi S, Borm LE, Zeisel A, ..., Svensson CI, Linnarsson S

Nat. Methods 15 (11) 932-935 [2018-11-00; online 2018-10-30]

PubMed DOI Crossref

Fast reversibly photoswitching red fluorescent proteins for live-cell RESOLFT nanoscopy.

Pennacchietti F, Serebrovskaya EO, Faro AR, ..., Mishin AS, Testa I

Nat. Methods 15 (8) 601-604 [2018-08-00; online 2018-07-09]

Affiliated researcher Ilaria Testa SciLifeLab Fellow

PubMed DOI Crossref

A reassessment of DNA-immunoprecipitation-based genomic profiling.

Lentini A, Lagerwall C, Vikingsson S, ..., Benson M, Nestor CE

Nat. Methods 15 (7) 499-504 [2018-07-00; online 2018-06-25]

Antonio Lentini DDLS Fellow

PubMed DOI Crossref

Response to: Should we ignore western blots when selecting antibodies for other applications?

Uhlen M

Nat. Methods 14 (3) 215-216 [2017-02-28; online 2017-03-01]

PubMed DOI Crossref

A proposal for validation of antibodies.

Uhlen M, Bandrowski A, Carr S, ..., Snyder M, Yamamoto T

Nat. Methods 13 (10) 823-827 [2016-10-00; online 2016-09-05]

PubMed DOI Crossref

The quest for multiplexed spatially resolved transcriptional profiling.

Wählby C

Nat. Methods 13 (8) 623-624 [2016-07-28; online 2016-07-29]

PubMed DOI Crossref

Standardized benchmarking in the quest for orthologs.

Altenhoff AM, Boeckmann B, Capella-Gutierrez S, ..., Sonnhammer E, Dessimoz C

Nat. Methods 13 (5) 425-430 [2016-05-00; online 2016-04-04]

PubMed DOI Crossref

Genetic code expansion in stable cell lines enables encoded chromatin modification.

Elsässer SJ, Ernst RJ, Walker OS, Chin JW

Nat. Methods 13 (2) 158-164 [2016-02-00; online 2016-01-04]

SciLifeLab Fellow Simon Elsässer

PubMed DOI Crossref

Binning metagenomic contigs by coverage and composition.

Alneberg J, Bjarnason BS, de Bruijn I, ..., Andersson AF, Quince C

Nat. Methods 11 (11) 1144-1146 [2014-11-00; online 2014-09-14]

PubMed DOI Crossref

Spatial control of membrane receptor function using ligand nanocalipers.

Shaw A, Lundin V, Petrova E, ..., Högberg B, Teixeira AI

Nat. Methods 11 (8) 841-846 [2014-08-00; online 2014-07-06]

Erik Benson SciLifeLab Fellow

PubMed DOI Crossref

HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics.

Branca RM, Orre LM, Johansson HJ, ..., Käll L, Lehtiö J

Nat. Methods 11 (1) 59-62 [2014-01-00; online 2013-11-17]

PubMed DOI Crossref

In situ sequencing for RNA analysis in preserved tissue and cells.

Ke R, Mignardi M, Pacureanu A, ..., Wählby C, Nilsson M

Nat. Methods 10 (9) 857-860 [2013-09-00; online 2013-07-14]

PubMed DOI Crossref

Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing.

Crosetto N, Mitra A, Silva MJ, ..., Rowicka M, Dikic I

Nat. Methods 10 (4) 361-365 [2013-04-00; online 2013-03-17]

Affiliated researcher Magda Bienko SciLifeLab Fellow

PubMed DOI Crossref

Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells.

Stadler C, Rexhepaj E, Singan VR, ..., Simpson JC, Lundberg E

Nat. Methods 10 (4) 315-323 [2013-04-00; online 2013-02-24]

PubMed DOI Crossref

Extracting intracellular diffusive states and transition rates from single-molecule tracking data.

Persson F, Lindén M, Unoson C, Elf J

Nat. Methods 10 (3) 265-269 [2013-03-00; online 2013-02-10]

PubMed DOI Crossref

Lost in presumption: stochastic reactions in spatial models.

Mahmutovic A, Fange D, Berg OG, Elf J

Nat. Methods 9 (12) 1163-1166 [2012-12-00; online 2012-12-12]

PubMed DOI Crossref

An image analysis toolbox for high-throughput C. elegans assays.

Wählby C, Kamentsky L, Liu ZH, ..., Ausubel FM, Carpenter AE

Nat. Methods 9 (7) 714-716 [2012-04-22; online 2012-04-22]

PubMed DOI Crossref

Counting absolute numbers of molecules using unique molecular identifiers.

Kivioja T, Vähärautio A, Karlsson K, ..., Linnarsson S, Taipale J

Nat. Methods 9 (1) 72-74 [2011-11-20; online 2011-11-20]

PubMed DOI Crossref

SignalP 4.0: discriminating signal peptides from transmembrane regions.

Petersen TN, Brunak S, von Heijne G, Nielsen H

Nat. Methods 8 (10) 785-786 [2011-09-29; online 2011-09-29]

PubMed DOI Crossref

Large-scale sorting of C. elegans embryos reveals the dynamics of small RNA expression.

Stoeckius M, Maaskola J, Colombo T, ..., Piano F, Rajewsky N

Nat. Methods 6 (10) 745-751 [2009-10-00; online 2009-09-06]

Marc Friedländer SciLifeLab Fellow

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