Martin Hemberg, Ph.D. - Publications

Sanger Institute 

41 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Salmen F, De Jonghe J, Kaminski TS, Alemany A, Parada GE, Verity-Legg J, Yanagida A, Kohler TN, Battich N, van den Brekel F, Ellermann AL, Arias AM, Nichols J, Hemberg M, Hollfelder F, et al. High-throughput total RNA sequencing in single cells using VASA-seq. Nature Biotechnology. PMID 35760914 DOI: 10.1038/s41587-022-01361-8  0.339
2020 Heaton H, Talman AM, Knights A, Imaz M, Gaffney DJ, Durbin R, Hemberg M, Lawniczak MKN. Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes. Nature Methods. PMID 32366989 DOI: 10.1038/S41592-020-0820-1  0.384
2020 Georgakopoulos-Soares I, Koh G, Momen SE, Jiricny J, Hemberg M, Nik-Zainal S. Transcription-coupled repair and mismatch repair contribute towards preserving genome integrity at mononucleotide repeat tracts. Nature Communications. 11: 1980. PMID 32332764 DOI: 10.1038/S41467-020-15901-W  0.367
2020 Westoby J, Artemov P, Hemberg M, Ferguson-Smith A. Obstacles to detecting isoforms using full-length scRNA-seq data. Genome Biology. 21: 74. PMID 32293520 DOI: 10.1186/S13059-020-01981-W  0.414
2020 Bayraktar OA, Bartels T, Holmqvist S, Kleshchevnikov V, Martirosyan A, Polioudakis D, Ben Haim L, Young AMH, Batiuk MY, Prakash K, Brown A, Roberts K, Paredes MF, Kawaguchi R, Stockley JH, ... ... Hemberg M, et al. Astrocyte layers in the mammalian cerebral cortex revealed by a single-cell in situ transcriptomic map. Nature Neuroscience. PMID 32203496 DOI: 10.1038/S41593-020-0602-1  0.312
2020 Wang R, Sharma R, Shen X, Laughney AM, Funato K, Clark PJ, Shpokayte M, Morgenstern P, Navare M, Xu Y, Harbi S, Masilionis I, Nanjangud G, Yang Y, Duran-Rehbein G, ... Hemberg M, et al. Adult Human Glioblastomas Harbor Radial Glia-like Cells. Stem Cell Reports. PMID 32004492 DOI: 10.1016/J.Stemcr.2020.01.007  0.347
2019 Kiselev VY, Andrews TS, Hemberg M. Challenges in unsupervised clustering of single-cell RNA-seq data. Nature Reviews. Genetics. PMID 30617341 DOI: 10.1038/S41576-018-0088-9  0.369
2018 Andrews TS, Hemberg M. False signals induced by single-cell imputation. F1000research. 7: 1740. PMID 30906525 DOI: 10.12688/F1000Research.16613.2  0.41
2018 Andrews TS, Hemberg M. M3Drop: Dropout-based feature selection for scRNASeq. Bioinformatics (Oxford, England). PMID 30590489 DOI: 10.1093/Bioinformatics/Bty1044  0.347
2018 Westoby J, Herrera MS, Ferguson-Smith AC, Hemberg M. Simulation-based benchmarking of isoform quantification in single-cell RNA-seq. Genome Biology. 19: 191. PMID 30404663 DOI: 10.1186/S13059-018-1571-5  0.423
2018 Hemberg M. Single-cell genomics. Briefings in Functional Genomics. 17: 207-208. PMID 30060035 DOI: 10.1093/Bfgp/Ely025  0.33
2018 Kiselev VY, Yiu A, Hemberg M. scmap: projection of single-cell RNA-seq data across data sets. Nature Methods. PMID 29608555 DOI: 10.1038/Nmeth.4644  0.38
2018 Bergiers I, Andrews T, Vargel Bölükbaşı Ö, Buness A, Janosz E, Lopez-Anguita N, Ganter K, Kosim K, Celen C, Itır Perçin G, Collier P, Baying B, Benes V, Hemberg M, Lancrin C. Single-cell transcriptomics reveals a new dynamical function of transcription factors during embryonic hematopoiesis. Elife. 7. PMID 29555020 DOI: 10.7554/Elife.29312  0.436
2018 Amaral PP, Leonardi T, Han N, Viré E, Gascoigne DK, Arias-Carrasco R, Büscher M, Pandolfini L, Zhang A, Pluchino S, Maracaja-Coutinho V, Nakaya HI, Hemberg M, Shiekhattar R, Enright AJ, et al. Genomic positional conservation identifies topological anchor point RNAs linked to developmental loci. Genome Biology. 19: 32. PMID 29540241 DOI: 10.1186/S13059-018-1405-5  0.405
2017 Mathys H, Adaikkan C, Gao F, Young JZ, Manet E, Hemberg M, De Jager PL, Ransohoff RM, Regev A, Tsai LH. Temporal Tracking of Microglia Activation in Neurodegeneration at Single-Cell Resolution. Cell Reports. 21: 366-380. PMID 29020624 DOI: 10.1016/J.Celrep.2017.09.039  0.36
2017 Akay A, Di Domenico T, Suen KM, Nabih A, Parada GE, Larance M, Medhi R, Berkyurek AC, Zhang X, Wedeles CJ, Rudolph KLM, Engelhardt J, Hemberg M, Ma P, Lamond AI, et al. The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription. Developmental Cell. 42: 241-255.e6. PMID 28787591 DOI: 10.1016/J.Devcel.2017.07.002  0.445
2017 Andrews TS, Hemberg M. Identifying cell populations with scRNASeq. Molecular Aspects of Medicine. PMID 28712804 DOI: 10.1016/J.Mam.2017.07.002  0.362
2017 Kiselev VY, Kirschner K, Schaub MT, Andrews T, Yiu A, Chandra T, Natarajan KN, Reik W, Barahona M, Green AR, Hemberg M. SC3: consensus clustering of single-cell RNA-seq data. Nature Methods. PMID 28346451 DOI: 10.1038/Nmeth.4236  0.359
2017 Bergiers I, Andrews T, Bölükbaşı ÖV, Buness A, Janosz E, Lopez-Anguita N, Ganter K, Kosim K, Celen C, Perçin GI, Collier P, Baying B, Benes V, Hemberg M, Lancrin C. Author response: Single-cell transcriptomics reveals a new dynamical function of transcription factors during embryonic hematopoiesis Elife. DOI: 10.7554/Elife.29312.055  0.361
2016 Sørensen AT, Cooper YA, Baratta MV, Weng FJ, Zhang Y, Ramamoorthi K, Fropf R, LaVerriere E, Xue J, Young A, Schneider C, Gøtzsche CR, Hemberg M, Yin JC, Maier SF, et al. A robust activity marking system for exploring active neuronal ensembles. Elife. 5. PMID 27661450 DOI: 10.7554/Elife.13918  0.342
2016 Yang Y, Yamada T, Hill KK, Hemberg M, Reddy NC, Cho HY, Guthrie AN, Oldenborg A, Heiney SA, Ohmae S, Medina JF, Holy TE, Bonni A. Chromatin remodeling inactivates activity genes and regulates neural coding. Science (New York, N.Y.). 353: 300-5. PMID 27418512 DOI: 10.1126/Science.Aad4225  0.421
2016 Nguyen TA, Jones RD, Snavely A, Pfenning A, Kirchner R, Hemberg M, Gray JM. High-throughput functional comparison of promoter and enhancer activities. Genome Research. PMID 27311442 DOI: 10.1101/Gr.204834.116  0.403
2016 Tang S, Hemberg M, Cansizoglu E, Belin S, Kosik K, Kreiman G, Steen H, Steen J. f-divergence cutoff index to simultaneously identify differential expression in the integrated transcriptome and proteome. Nucleic Acids Research. PMID 26980280 DOI: 10.1093/Nar/Gkw157  0.591
2016 Delmans M, Hemberg M. Discrete distributional differential expression (D(3)E) - a tool for gene expression analysis of single-cell RNA-seq data. Bmc Bioinformatics. 17: 110. PMID 26927822 DOI: 10.1186/S12859-016-0944-6  0.434
2015 Andzelm MM, Cherry TJ, Harmin DA, Boeke AC, Lee C, Hemberg M, Pawlyk B, Malik AN, Flavell SW, Sandberg MA, Raviola E, Greenberg ME. MEF2D drives photoreceptor development through a genome-wide competition for tissue-specific enhancers. Neuron. 86: 247-63. PMID 25801704 DOI: 10.1016/J.Neuron.2015.02.038  0.394
2015 Gabel HW, Kinde B, Stroud H, Gilbert CS, Harmin DA, Kastan NR, Hemberg M, Ebert DH, Greenberg ME. Disruption of DNA-methylation-dependent long gene repression in Rett syndrome. Nature. 522: 89-93. PMID 25762136 DOI: 10.1038/Nature14319  0.397
2015 Kim TK, Hemberg M, Gray JM. Enhancer RNAs: a class of long noncoding RNAs synthesized at enhancers. Cold Spring Harbor Perspectives in Biology. 7: a018622. PMID 25561718 DOI: 10.1101/Cshperspect.A018622  0.408
2015 Kiselev V, Schaub M, Andrews TS, Barahona M, Hemberg M. SC 3 - consensus clustering of single-cell RNA-Seq data F1000research. 4. DOI: 10.7490/F1000Research.1110908.1  0.365
2014 Prabakaran S, Hemberg M, Chauhan R, Winter D, Tweedie-Cullen RY, Dittrich C, Hong E, Gunawardena J, Steen H, Kreiman G, Steen JA. Quantitative profiling of peptides from RNAs classified as noncoding. Nature Communications. 5: 5429. PMID 25403355 DOI: 10.1038/Ncomms6429  0.619
2014 Malik AN, Vierbuchen T, Hemberg M, Rubin AA, Ling E, Couch CH, Stroud H, Spiegel I, Farh KK, Harmin DA, Greenberg ME. Genome-wide identification and characterization of functional neuronal activity-dependent enhancers. Nature Neuroscience. 17: 1330-9. PMID 25195102 DOI: 10.1038/Nn.3808  0.43
2014 Yamada T, Yang Y, Hemberg M, Yoshida T, Cho HY, Murphy JP, Fioravante D, Regehr WG, Gygi SP, Georgopoulos K, Bonni A. Promoter decommissioning by the NuRD chromatin remodeling complex triggers synaptic connectivity in the mammalian brain. Neuron. 83: 122-34. PMID 24991957 DOI: 10.1016/J.Neuron.2014.05.039  0.395
2012 Hemberg M, Gray JM, Cloonan N, Kuersten S, Grimmond S, Greenberg ME, Kreiman G. Integrated genome analysis suggests that most conserved non-coding sequences are regulatory factor binding sites. Nucleic Acids Research. 40: 7858-69. PMID 22684627 DOI: 10.1093/nar/gks477  0.602
2012 Ross SE, McCord AE, Jung C, Atan D, Mok SI, Hemberg M, Kim TK, Salogiannis J, Hu L, Cohen S, Lin Y, Harrar D, McInnes RR, Greenberg ME. Bhlhb5 and Prdm8 form a repressor complex involved in neuronal circuit assembly. Neuron. 73: 292-303. PMID 22284184 DOI: 10.1016/J.Neuron.2011.09.035  0.374
2011 Cohen S, Gabel HW, Hemberg M, Hutchinson AN, Sadacca LA, Ebert DH, Harmin DA, Greenberg RS, Verdine VK, Zhou Z, Wetsel WC, West AE, Greenberg ME. Genome-wide activity-dependent MeCP2 phosphorylation regulates nervous system development and function. Neuron. 72: 72-85. PMID 21982370 DOI: 10.1016/J.Neuron.2011.08.022  0.359
2011 Hemberg M, Kreiman G. Conservation of transcription factor binding events predicts gene expression across species. Nucleic Acids Research. 39: 7092-102. PMID 21622661 DOI: 10.1093/Nar/Gkr404  0.609
2010 Pfenning AR, Kim TK, Spotts JM, Hemberg M, Su D, West AE. Genome-wide identification of calcium-response factor (CaRF) binding sites predicts a role in regulation of neuronal signaling pathways. Plos One. 5: e10870. PMID 20523734 DOI: 10.1371/Journal.Pone.0010870  0.426
2010 Kim TK, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J, Harmin DA, Laptewicz M, Barbara-Haley K, Kuersten S, Markenscoff-Papadimitriou E, Kuhl D, Bito H, Worley PF, Kreiman G, et al. Widespread transcription at neuronal activity-regulated enhancers. Nature. 465: 182-7. PMID 20393465 DOI: 10.1038/Nature09033  0.627
2009 StÃ¥hlberg A, Bengtsson M, Hemberg M, Semb H. Quantitative transcription factor analysis of undifferentiated single human embryonic stem cells. Clinical Chemistry. 55: 2162-70. PMID 19815608 DOI: 10.1373/Clinchem.2009.131433  0.416
2008 Flavell SW, Kim TK, Gray JM, Harmin DA, Hemberg M, Hong EJ, Markenscoff-Papadimitriou E, Bear DM, Greenberg ME. Genome-wide analysis of MEF2 transcriptional program reveals synaptic target genes and neuronal activity-dependent polyadenylation site selection. Neuron. 60: 1022-38. PMID 19109909 DOI: 10.1016/J.Neuron.2008.11.029  0.392
2008 Bengtsson M, Hemberg M, Rorsman P, StÃ¥hlberg A. Quantification of mRNA in single cells and modelling of RT-qPCR induced noise. Bmc Molecular Biology. 9: 63. PMID 18631407 DOI: 10.1186/1471-2199-9-63  0.382
2008 Chang HH, Hemberg M, Barahona M, Ingber DE, Huang S. Transcriptome-wide noise controls lineage choice in mammalian progenitor cells. Nature. 453: 544-7. PMID 18497826 DOI: 10.1038/Nature06965  0.371
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