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ArticlesPeer ReviewedFull Text
Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data
Author / Creator:Andrews, Tallulah S. ; Kiselev, Vladimir Yu ; McCarthy, Davis ; Hemberg, Martin
Publisher:London: Nature Publishing Group UK
Journal title:Nature protocols, 2021-01, Vol.16 (1), p.1-9
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scmap: projection of single-cell RNA-seq data across data sets
Author / Creator:Kiselev, Vladimir Yu ; Yiu, Andrew ; Hemberg, Martin
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2018-05, Vol.15 (5), p.359-362
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Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes
Author / Creator:Heaton, Haynes ; Talman, Arthur M. ; Knights, Andrew ; Imaz, Maria ; Gaffney, Daniel J. ; Durbin, Richard ; Hemberg, Martin ; Lawniczak, Mara K. N.
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2020-06, Vol.17 (6), p.615-620
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Astrocyte layers in the mammalian cerebral cortex revealed by a single-cell in situ transcriptomic map
Author / Creator:Bayraktar, Omer Ali ; Bartels, Theresa ; Holmqvist, Staffan ; Kleshchevnikov, Vitalii ; Martirosyan, Araks ; Polioudakis, Damon ; Ben Haim, Lucile ; Young, Adam M. H. ; Batiuk, Mykhailo Y. ; Prakash, Kirti ; Brown, Alexander ; Roberts, Kenny ; Paredes, Mercedes F. ; Kawaguchi, Riki ; Stockley, John H. ; Sabeur, Khalida ; Chang, Sandra M. ; Huang, Eric ; Hutchinson, Peter ; Ullian, Erik M. ; Hemberg, Martin ; Coppola, Giovanni ; Holt, Matthew G. ; Geschwind, Daniel H. ; Rowitch, David H.
Publisher:New York: Nature Publishing Group US
Journal title:Nature neuroscience, 2020-04, Vol.23 (4), p.500-509
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The Human Cell Atlas
Author / Creator:Regev, Aviv ; Teichmann, Sarah A ; Lander, Eric S ; Amit, Ido ; Benoist, Christophe ; Birney, Ewan ; Bodenmiller, Bernd ; Campbell, Peter ; Carninci, Piero ; Clatworthy, Menna ; Clevers, Hans ; Deplancke, Bart ; Dunham, Ian ; Eberwine, James ; Eils, Roland ; Enard, Wolfgang ; Farmer, Andrew ; Fugger, Lars ; Göttgens, Berthold ; Hacohen, Nir ; Haniffa, Muzlifah ; Hemberg, Martin ; Kim, Seung ; Klenerman, Paul ; Kriegstein, Arnold ; Lein, Ed ; Linnarsson, Sten ; Lundberg, Emma ; Lundeberg, Joakim ; Majumder, Partha ; Marioni, John C ; Merad, Miriam ; Mhlanga, Musa ; Nawijn, Martijn ; Netea, Mihai ; Nolan, Garry ; Pe'er, Dana ; Phillipakis, Anthony ; Ponting, Chris P ; Quake, Stephen ; Reik, Wolf ; Rozenblatt-Rosen, Orit ; Sanes, Joshua ; Satija, Rahul ; Schumacher, Ton N ; Shalek, Alex ; Shapiro, Ehud ; Sharma, Padmanee ; Shin, Jay W ; Stegle, Oliver ; Stratton, Michael ; Stubbington, Michael J T ; Theis, Fabian J ; Uhlen, Matthias ; van Oudenaarden, Alexander ; Wagner, Allon ; Watt, Fiona ; Weissman, Jonathan ; Wold, Barbara ; Xavier, Ramnik ; Yosef, Nir
Publisher:England: eLife Science Publications, Ltd
Journal title:eLife, 2017-12, Vol.6
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Alternative splicing modulation by G-quadruplexes
Author / Creator:Georgakopoulos-Soares, Ilias ; Parada, Guillermo E. ; Wong, Hei Yuen ; Medhi, Ragini ; Furlan, Giulia ; Munita, Roberto ; Miska, Eric A. ; Kwok, Chun Kit ; Hemberg, Martin
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2022-05, Vol.13 (1), p.2404-2404, Article 2404
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SC3s: efficient scaling of single cell consensus clustering to millions of cells
Author / Creator:Quah, Fu Xiang ; Hemberg, Martin
Publisher:England: BioMed Central Ltd
Journal title:BMC bioinformatics, 2022-12, Vol.23 (1), p.536-536, Article 536
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Obstacles to detecting isoforms using full-length scRNA-seq data
Author / Creator:Westoby, Jennifer ; Artemov, Pavel ; Hemberg, Martin ; Ferguson-Smith, Anne
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2020-03, Vol.21 (1), p.74-74, Article 74
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Mining alternative splicing patterns in scRNA-seq data using scASfind
Author / Creator:Song, Yuyao ; Parada, Guillermo ; Lee, Jimmy Tsz Hang ; Hemberg, Martin
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2024-07, Vol.25 (1), p.197-197, Article 197
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Absent from DNA and protein: genomic characterization of nullomers and nullpeptides across functional categories and evolution
Author / Creator:Georgakopoulos-Soares, Ilias ; Yizhar-Barnea, Ofer ; Mouratidis, Ioannis ; Hemberg, Martin ; Ahituv, Nadav
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2021-08, Vol.22 (1), p.245-245, Article 245
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Joint analysis of mutational and transcriptional landscapes in human cancer reveals key perturbations during cancer evolution
Author / Creator:Cho, Jae-Won ; Cao, Jingyi ; Hemberg, Martin
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2024-03, Vol.25 (1), p.65-65, Article 65
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Transcription-coupled repair and mismatch repair contribute towards preserving genome integrity at mononucleotide repeat tracts
Author / Creator:Georgakopoulos-Soares, Ilias ; Koh, Gene ; Momen, Sophie E. ; Jiricny, Josef ; Hemberg, Martin ; Nik-Zainal, Serena
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2020-04, Vol.11 (1), p.1980-9, Article 1980
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Genome-wide identification and characterization of functional neuronal activity–dependent enhancers
Author / Creator:Malik, Athar N ; Vierbuchen, Thomas ; Hemberg, Martin ; Rubin, Alex A ; Ling, Emi ; Couch, Cameron H ; Stroud, Hume ; Spiegel, Ivo ; Farh, Kyle Kai-How ; Harmin, David A ; Greenberg, Michael E
Publisher:New York: Nature Publishing Group US
Journal title:Nature neuroscience, 2014-10, Vol.17 (10), p.1330-1339
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Widespread transcription at neuronal activity-regulated enhancers
Author / Creator:Kim, Tae-Kyung ; Hemberg, Martin ; Gray, Jesse M. ; Costa, Allen M. ; Bear, Daniel M. ; Wu, Jing ; Harmin, David A. ; Laptewicz, Mike ; Barbara-Haley, Kellie ; Kuersten, Scott ; Markenscoff-Papadimitriou, Eirene ; Kuhl, Dietmar ; Bito, Haruhiko ; Worley, Paul F. ; Kreiman, Gabriel ; Greenberg, Michael E.
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2010-05, Vol.465 (7295), p.182-187
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High-throughput techniques enable advances in the roles of DNA and RNA secondary structures in transcriptional and post-transcriptional gene regulation
Author / Creator:Georgakopoulos-Soares, Ilias ; Chan, Candace S. Y. ; Ahituv, Nadav ; Hemberg, Martin
Publisher:London: BioMed Central Ltd
Journal title:Genome Biology, 2022-07, Vol.23 (1), p.159-159, Article 159
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A robust activity marking system for exploring active neuronal ensembles
Author / Creator:Sørensen, Andreas T ; Cooper, Yonatan A ; Baratta, Michael V ; Weng, Feng-Ju ; Zhang, Yuxiang ; Ramamoorthi, Kartik ; Fropf, Robin ; LaVerriere, Emily ; Xue, Jian ; Young, Andrew ; Schneider, Colleen ; Gøtzsche, Casper René ; Hemberg, Martin ; Yin, Jerry CP ; Maier, Steven F ; Lin, Yingxi
Publisher:England: eLife Science Publications, Ltd
Journal title:eLife, 2016-09, Vol.5
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Genomic positional conservation identifies topological anchor point RNAs linked to developmental loci
Author / Creator:Amaral, Paulo P. ; Leonardi, Tommaso ; Han, Namshik ; Viré, Emmanuelle ; Gascoigne, Dennis K. ; Arias-Carrasco, Raúl ; Büscher, Magdalena ; Pandolfini, Luca ; Zhang, Anda ; Pluchino, Stefano ; Maracaja-Coutinho, Vinicius ; Nakaya, Helder I. ; Hemberg, Martin ; Shiekhattar, Ramin ; Enright, Anton J. ; Kouzarides, Tony
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2018-03, Vol.19 (1), p.32-32, Article 32
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Fast searches of large collections of single-cell data using scfind
Author / Creator:Lee, Jimmy Tsz Hang ; Patikas, Nikolaos ; Kiselev, Vladimir Yu ; Hemberg, Martin
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2021-03, Vol.18 (3), p.262-271
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Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods
Author / Creator:Neavin, Drew ; Senabouth, Anne ; Arora, Himanshi ; Lee, Jimmy Tsz Hang ; Ripoll-Cladellas, Aida ; Franke, Lude ; Prabhakar, Shyam ; Ye, Chun Jimmie ; McCarthy, Davis J. ; Melé, Marta ; Hemberg, Martin ; Powell, Joseph E.
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2024-04, Vol.25 (1), p.94-94, Article 94
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ArticlesPeer ReviewedFull Text
Publisher Correction: Challenges in unsupervised clustering of single-cell RNA-seq data
Author / Creator:Kiselev, Vladimir Yu ; Andrews, Tallulah S. ; Hemberg, Martin
Publisher:London: Nature Publishing Group UK
Journal title:Nature reviews. Genetics, 2019-05, Vol.20 (5), p.310-310
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Showing 1 to 20 of 92 results

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Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data

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scmap: projection of single-cell RNA-seq data across data sets

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Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes

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Astrocyte layers in the mammalian cerebral cortex revealed by a single-cell in situ transcriptomic map

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The Human Cell Atlas

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Alternative splicing modulation by G-quadruplexes

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SC3s: efficient scaling of single cell consensus clustering to millions of cells

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Obstacles to detecting isoforms using full-length scRNA-seq data

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Mining alternative splicing patterns in scRNA-seq data using scASfind

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Absent from DNA and protein: genomic characterization of nullomers and nullpeptides across functional categories and evolution

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Joint analysis of mutational and transcriptional landscapes in human cancer reveals key perturbations during cancer evolution

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Transcription-coupled repair and mismatch repair contribute towards preserving genome integrity at mononucleotide repeat tracts

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Genome-wide identification and characterization of functional neuronal activity–dependent enhancers

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Widespread transcription at neuronal activity-regulated enhancers

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High-throughput techniques enable advances in the roles of DNA and RNA secondary structures in transcriptional and post-transcriptional gene regulation

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A robust activity marking system for exploring active neuronal ensembles

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Genomic positional conservation identifies topological anchor point RNAs linked to developmental loci

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Fast searches of large collections of single-cell data using scfind

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Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods

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Publisher Correction: Challenges in unsupervised clustering of single-cell RNA-seq data

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