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ArticlesPeer ReviewedFull Text
Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning
Author / Creator:Greenwald, Noah F. ; Miller, Geneva ; Moen, Erick ; Kong, Alex ; Kagel, Adam ; Dougherty, Thomas ; Fullaway, Christine Camacho ; McIntosh, Brianna J. ; Leow, Ke Xuan ; Schwartz, Morgan Sarah ; Pavelchek, Cole ; Cui, Sunny ; Camplisson, Isabella ; Bar-Tal, Omer ; Singh, Jaiveer ; Fong, Mara ; Chaudhry, Gautam ; Abraham, Zion ; Moseley, Jackson ; Warshawsky, Shiri ; Soon, Erin ; Greenbaum, Shirley ; Risom, Tyler ; Hollmann, Travis ; Bendall, Sean C. ; Keren, Leeat ; Graf, William ; Angelo, Michael ; Van Valen, David
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2022-04, Vol.40 (4), p.555-565
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Deciphering spatial domains from spatially resolved transcriptomics with an adaptive graph attention auto-encoder
Author / Creator:Dong, Kangning ; Zhang, Shihua
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2022-04, Vol.13 (1), p.1739-12, Article 1739
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Haplotype-resolved assembly of diploid genomes without parental data
Author / Creator:Cheng, Haoyu ; Jarvis, Erich D. ; Fedrigo, Olivier ; Koepfli, Klaus-Peter ; Urban, Lara ; Gemmell, Neil J. ; Li, Heng
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2022-09, Vol.40 (9), p.1332-1335
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ArticlesPeer ReviewedFull Text
Multi-omics single-cell data integration and regulatory inference with graph-linked embedding
Author / Creator:Cao, Zhi-Jie ; Gao, Ge
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2022-10, Vol.40 (10), p.1458-1466
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ArticlesPeer ReviewedFull Text
Deep learning
Author / Creator:Rusk, Nicole
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2016-01, Vol.13 (1), p.35-35
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Fast and accurate long-read assembly with wtdbg2
Author / Creator:Ruan, Jue ; Li, Heng
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2020-02, Vol.17 (2), p.155-158
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TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines
Author / Creator:Ershov, Dmitry ; Phan, Minh-Son ; Pylvänäinen, Joanna W. ; Rigaud, Stéphane U. ; Le Blanc, Laure ; Charles-Orszag, Arthur ; Conway, James R. W. ; Laine, Romain F. ; Roy, Nathan H. ; Bonazzi, Daria ; Duménil, Guillaume ; Jacquemet, Guillaume ; Tinevez, Jean-Yves
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2022-07, Vol.19 (7), p.829-832
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Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs
Author / Creator:Bepler, Tristan ; Morin, Andrew ; Rapp, Micah ; Brasch, Julia ; Shapiro, Lawrence ; Noble, Alex J. ; Berger, Bonnie
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2019-11, Vol.16 (11), p.1153-1160
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Philosopher: a versatile toolkit for shotgun proteomics data analysis
Author / Creator:da Veiga Leprevost, Felipe ; Haynes, Sarah E. ; Avtonomov, Dmitry M. ; Chang, Hui-Yin ; Shanmugam, Avinash K. ; Mellacheruvu, Dattatreya ; Kong, Andy T. ; Nesvizhskii, Alexey I.
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2020-09, Vol.17 (9), p.869-870
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ArticlesPeer ReviewedFull Text
SLEAP: A deep learning system for multi-animal pose tracking
Author / Creator:Pereira, Talmo D. ; Tabris, Nathaniel ; Matsliah, Arie ; Turner, David M. ; Li, Junyu ; Ravindranath, Shruthi ; Papadoyannis, Eleni S. ; Normand, Edna ; Deutsch, David S. ; Wang, Z. Yan ; McKenzie-Smith, Grace C. ; Mitelut, Catalin C. ; Castro, Marielisa Diez ; D’Uva, John ; Kislin, Mikhail ; Sanes, Dan H. ; Kocher, Sarah D. ; Wang, Samuel S.-H. ; Falkner, Annegret L. ; Shaevitz, Joshua W. ; Murthy, Mala
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2022-04, Vol.19 (4), p.486-495
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ArticlesPeer ReviewedFull Text
ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation
Author / Creator:Bentsen, Mette ; Goymann, Philipp ; Schultheis, Hendrik ; Klee, Kathrin ; Petrova, Anastasiia ; Wiegandt, René ; Fust, Annika ; Preussner, Jens ; Kuenne, Carsten ; Braun, Thomas ; Kim, Johnny ; Looso, Mario
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2020-08, Vol.11 (1), p.4267-4267, Article 4267
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ArticlesPeer ReviewedFull Text
GOATOOLS: A Python library for Gene Ontology analyses
Author / Creator:Klopfenstein, D. V. ; Zhang, Liangsheng ; Pedersen, Brent S. ; Ramírez, Fidel ; Warwick Vesztrocy, Alex ; Naldi, Aurélien ; Mungall, Christopher J. ; Yunes, Jeffrey M. ; Botvinnik, Olga ; Weigel, Mark ; Dampier, Will ; Dessimoz, Christophe ; Flick, Patrick ; Tang, Haibao
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2018-07, Vol.8 (1), p.10872-17, Article 10872
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ArticlesPeer ReviewedFull Text
Salmon provides fast and bias-aware quantification of transcript expression
Author / Creator:Patro, Rob ; Duggal, Geet ; Love, Michael I ; Irizarry, Rafael A ; Kingsford, Carl
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2017-04, Vol.14 (4), p.417-419
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ArticlesPeer ReviewedFull Text
MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy
Author / Creator:Zheng, Shawn Q ; Palovcak, Eugene ; Armache, Jean-Paul ; Verba, Kliment A ; Cheng, Yifan ; Agard, David A
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2017-04, Vol.14 (4), p.331-332
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KBase: The United States Department of Energy Systems Biology Knowledgebase
Author / Creator:Arkin, Adam P ; Cottingham, Robert W ; Henry, Christopher S ; Harris, Nomi L ; Stevens, Rick L ; Maslov, Sergei ; Dehal, Paramvir ; Ware, Doreen ; Perez, Fernando ; Canon, Shane ; Sneddon, Michael W ; Henderson, Matthew L ; Riehl, William J ; Murphy-Olson, Dan ; Chan, Stephen Y ; Kamimura, Roy T ; Kumari, Sunita ; Drake, Meghan M ; Brettin, Thomas S ; Glass, Elizabeth M ; Chivian, Dylan ; Gunter, Dan ; Weston, David J ; Allen, Benjamin H ; Baumohl, Jason ; Best, Aaron A ; Bowen, Ben ; Brenner, Steven E ; Bun, Christopher C ; Chandonia, John-Marc ; Chia, Jer-Ming ; Colasanti, Ric ; Conrad, Neal ; Davis, James J ; Davison, Brian H ; DeJongh, Matthew ; Devoid, Scott ; Dietrich, Emily ; Dubchak, Inna ; Edirisinghe, Janaka N ; Fang, Gang ; Faria, José P ; Frybarger, Paul M ; Gerlach, Wolfgang ; Gerstein, Mark ; Greiner, Annette ; Gurtowski, James ; Haun, Holly L ; He, Fei ; Jain, Rashmi ; Joachimiak, Marcin P ; Keegan, Kevin P ; Kondo, Shinnosuke ; Kumar, Vivek ; Land, Miriam L ; Meyer, Folker ; Mills, Marissa ; Novichkov, Pavel S ; Oh, Taeyun ; Olsen, Gary J ; Olson, Robert ; Parrello, Bruce ; Pasternak, Shiran ; Pearson, Erik ; Poon, Sarah S ; Price, Gavin A ; Ramakrishnan, Srividya ; Ranjan, Priya ; Ronald, Pamela C ; Schatz, Michael C ; Seaver, Samuel M D ; Shukla, Maulik ; Sutormin, Roman A ; Syed, Mustafa H ; Thomason, James ; Tintle, Nathan L ; Wang, Daifeng ; Xia, Fangfang ; Yoo, Hyunseung ; Yoo, Shinjae ; Yu, Dantong
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2018-07, Vol.36 (7), p.566-569
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ArticlesPeer ReviewedFull Text
Muscle5: High-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny
Author / Creator:Edgar, Robert C.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2022-11, Vol.13 (1), p.6968-6968, Article 6968
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ilastik: interactive machine learning for (bio)image analysis
Author / Creator:Berg, Stuart ; Kutra, Dominik ; Kroeger, Thorben ; Straehle, Christoph N. ; Kausler, Bernhard X. ; Haubold, Carsten ; Schiegg, Martin ; Ales, Janez ; Beier, Thorsten ; Rudy, Markus ; Eren, Kemal ; Cervantes, Jaime I ; Xu, Buote ; Beuttenmueller, Fynn ; Wolny, Adrian ; Zhang, Chong ; Koethe, Ullrich ; Hamprecht, Fred A. ; Kreshuk, Anna
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2019-12, Vol.16 (12), p.1226-1232
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ArticlesPeer ReviewedFull Text
Accurate detection of complex structural variations using single-molecule sequencing
Author / Creator:Sedlazeck, Fritz J. ; Rescheneder, Philipp ; Smolka, Moritz ; Fang, Han ; Nattestad, Maria ; von Haeseler, Arndt ; Schatz, Michael C.
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2018-06, Vol.15 (6), p.461-468
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ArticlesPeer ReviewedFull Text
CHARMM36m: an improved force field for folded and intrinsically disordered proteins
Author / Creator:Huang, Jing ; Rauscher, Sarah ; Nawrocki, Grzegorz ; Ran, Ting ; Feig, Michael ; de Groot, Bert L ; Grubmüller, Helmut ; MacKerell, Alexander D
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2017-01, Vol.14 (1), p.71-73
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Select record 40
ArticlesPeer ReviewedFull Text
SignalP 5.0 improves signal peptide predictions using deep neural networks
Author / Creator:Almagro Armenteros, José Juan ; Tsirigos, Konstantinos D. ; Sønderby, Casper Kaae ; Petersen, Thomas Nordahl ; Winther, Ole ; Brunak, Søren ; von Heijne, Gunnar ; Nielsen, Henrik
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2019-04, Vol.37 (4), p.420-423
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Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning

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Deciphering spatial domains from spatially resolved transcriptomics with an adaptive graph attention auto-encoder

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Haplotype-resolved assembly of diploid genomes without parental data

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Multi-omics single-cell data integration and regulatory inference with graph-linked embedding

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Deep learning

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Fast and accurate long-read assembly with wtdbg2

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TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines

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Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs

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Philosopher: a versatile toolkit for shotgun proteomics data analysis

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SLEAP: A deep learning system for multi-animal pose tracking

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ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation

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GOATOOLS: A Python library for Gene Ontology analyses

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Salmon provides fast and bias-aware quantification of transcript expression

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MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy

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KBase: The United States Department of Energy Systems Biology Knowledgebase

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Muscle5: High-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny

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ilastik: interactive machine learning for (bio)image analysis

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Accurate detection of complex structural variations using single-molecule sequencing

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CHARMM36m: an improved force field for folded and intrinsically disordered proteins

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SignalP 5.0 improves signal peptide predictions using deep neural networks

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