| Year |
Citation |
Score |
| 2024 |
Abnizova I, Stapel C, Boekhorst RT, Lee JTH, Hemberg M. Integrative analysis of transcriptomic and epigenomic data reveals distinct patterns for developmental and housekeeping gene regulation. Bmc Biology. 22: 78. PMID 38600550 DOI: 10.1186/s12915-024-01869-2 |
0.305 |
|
| 2023 |
Hepkema J, Lee NK, Stewart BJ, Ruangroengkulrith S, Charoensawan V, Clatworthy MR, Hemberg M. Predicting the impact of sequence motifs on gene regulation using single-cell data. Genome Biology. 24: 189. PMID 37582793 DOI: 10.1186/s13059-023-03021-9 |
0.37 |
|
| 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 |
0.338 |
|
| 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 |
0.366 |
|
| 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 |
0.413 |
|
| 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 |
0.348 |
|
| 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 |
0.409 |
|
| 2018 |
Andrews TS, Hemberg M. M3Drop: Dropout-based feature selection for scRNASeq. Bioinformatics (Oxford, England). PMID 30590489 DOI: 10.1093/Bioinformatics/Bty1044 |
0.346 |
|
| 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 |
0.422 |
|
| 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 |
0.403 |
|
| 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 |
0.443 |
|
| 2017 |
Andrews TS, Hemberg M. Identifying cell populations with scRNASeq. Molecular Aspects of Medicine. PMID 28712804 DOI: 10.1016/J.Mam.2017.07.002 |
0.363 |
|
| 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 |
0.341 |
|
| 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 |
0.419 |
|
| 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 |
0.402 |
|
| 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 |
0.587 |
|
| 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 |
0.433 |
|
| 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 |
0.393 |
|
| 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 |
0.396 |
|
| 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 |
0.405 |
|
| 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 |
0.364 |
|
| 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 |
0.615 |
|
| 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 |
0.428 |
|
| 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 |
0.394 |
|
| 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 |
0.596 |
|
| 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 |
0.373 |
|
| 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 |
0.358 |
|
| 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 |
0.605 |
|
| 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 |
0.423 |
|
| 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 |
0.622 |
|
| 2009 |
Ståhlberg 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 |
0.39 |
|
| 2008 |
Bengtsson M, Hemberg M, Rorsman P, Ståhlberg 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 |
0.372 |
|
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