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Martin Hemberg, Ph.D.


Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Chazarra-Gil R, van Dongen S, Kiselev VY, Hemberg M. Flexible comparison of batch correction methods for single-cell RNA-seq using BatchBench. Nucleic Acids Res. 2021 04 19; 49(7):e42. PMID: 33524142.
    Citations: 1     Fields:    
  2. Lee JTH, Patikas N, Kiselev VY, Hemberg M. Fast searches of large collections of single-cell data using scfind. Nat Methods. 2021 03; 18(3):262-271. PMID: 33649586.
    Citations:    Fields:    Translation:AnimalsCells
  3. Parada GE, Munita R, Georgakopoulos-Soares I, Fernandes HJR, Kedlian VR, Metzakopian E, Andres ME, Miska EA, Hemberg M. MicroExonator enables systematic discovery and quantification of microexons across mouse embryonic development. Genome Biol. 2021 Jan 22; 22(1):43. PMID: 33482885.
    Citations:    Fields:    
  4. Georgakopoulos-Soares I, Mouratidis I, Parada GE, Matharu N, Hemberg M, Ahituv N. Asymmetron: a toolkit for the identification of strand asymmetry patterns in biological sequences. Nucleic Acids Res. 2021 01 11; 49(1):e4. PMID: 33211865.
    Citations:    Fields:    Translation:HumansCells
  5. Cahan P, Cacchiarelli D, Dunn SJ, Hemberg M, de Sousa Lopes SMC, Morris SA, Rackham OJL, Del Sol A, Wells CA. Computational Stem Cell Biology: Open Questions and Guiding Principles. Cell Stem Cell. 2021 Jan 07; 28(1):20-32. PMID: 33417869.
    Citations:    Fields:    
  6. Andrews TS, Kiselev VY, McCarthy D, Hemberg M. Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data. Nat Protoc. 2021 01; 16(1):1-9. PMID: 33288955.
    Citations: 1     Fields:    Translation:HumansAnimalsCells
  7. 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, Pe'er D, Tabar V. Adult Human Glioblastomas Harbor Radial Glia-like Cells. Stem Cell Reports. 2020 07 14; 15(1):275-277. PMID: 32668221.
    Citations: 1     Fields:    
  8. 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. Nat Methods. 2020 06; 17(6):615-620. PMID: 32366989.
    Citations: 8     Fields:    Translation:HumansCells
  9. 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. Nat Commun. 2020 04 24; 11(1):1980. PMID: 32332764.
    Citations: 5     Fields:    Translation:HumansCells
  10. Westoby J, Artemov P, Hemberg M, Ferguson-Smith A. Obstacles to detecting isoforms using full-length scRNA-seq data. Genome Biol. 2020 03 23; 21(1):74. PMID: 32293520.
    Citations: 2     Fields:    Translation:Cells
  11. 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, Sabeur K, Chang SM, Huang E, Hutchinson P, Ullian EM, Hemberg M, Coppola G, Holt MG, Geschwind DH, Rowitch DH. Astrocyte layers in the mammalian cerebral cortex revealed by a single-cell in situ transcriptomic map. Nat Neurosci. 2020 04; 23(4):500-509. PMID: 32203496.
    Citations: 27     Fields:    Translation:HumansAnimalsCells
  12. 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, Pe'er D, Tabar V. Adult Human Glioblastomas Harbor Radial Glia-like Cells. Stem Cell Reports. 2020 02 11; 14(2):338-350. PMID: 32004492.
    Citations: 2     Fields:    Translation:HumansCells
  13. Lee JTH, Hemberg M. Supervised clustering for single-cell analysis. Nat Methods. 2019 10; 16(10):965-966. PMID: 31501544.
    Citations:    Fields:    
  14. Howick VM, Russell AJC, Andrews T, Heaton H, Reid AJ, Natarajan K, Butungi H, Metcalf T, Verzier LH, Rayner JC, Berriman M, Herren JK, Billker O, Hemberg M, Talman AM, Lawniczak MKN. The Malaria Cell Atlas: Single parasite transcriptomes across the complete Plasmodium life cycle. Science. 2019 08 23; 365(6455). PMID: 31439762.
    Citations: 30     Fields:    Translation:HumansAnimalsCells
  15. Andrews TS, Hemberg M. M3Drop: dropout-based feature selection for scRNASeq. Bioinformatics. 2019 08 15; 35(16):2865-2867. PMID: 30590489.
    Citations: 32     Fields:    
  16. Kiselev VY, Andrews TS, Hemberg M. Challenges in unsupervised clustering of single-cell RNA-seq data. Nat Rev Genet. 2019 05; 20(5):273-282. PMID: 30617341.
    Citations: 94     Fields:    Translation:HumansCells
  17. Kiselev VY, Andrews TS, Hemberg M. Publisher Correction: Challenges in unsupervised clustering of single-cell RNA-seq data. Nat Rev Genet. 2019 05; 20(5):310. PMID: 30670832.
    Citations: 5     Fields:    
  18. Westoby J, Herrera MS, Ferguson-Smith AC, Hemberg M. Simulation-based benchmarking of isoform quantification in single-cell RNA-seq. Genome Biol. 2018 11 07; 19(1):191. PMID: 30404663.
    Citations: 5     Fields:    Translation:AnimalsCells
  19. Andrews TS, Hemberg M. False signals induced by single-cell imputation. F1000Res. 2018; 7:1740. PMID: 30906525.
    Citations: 27     Fields:    Translation:Humans
  20. Georgakopoulos-Soares I, Morganella S, Jain N, Hemberg M, Nik-Zainal S. Noncanonical secondary structures arising from non-B DNA motifs are determinants of mutagenesis. Genome Res. 2018 09; 28(9):1264-1271. PMID: 30104284.
    Citations: 14     Fields:    Translation:HumansCells
  21. Hemberg M. Single-cell genomics. Brief Funct Genomics. 2018 07 01; 17(4):207-208. PMID: 30060035.
    Citations: 1     Fields:    
  22. Kiselev VY, Yiu A, Hemberg M. scmap: projection of single-cell RNA-seq data across data sets. Nat Methods. 2018 05; 15(5):359-362. PMID: 29608555.
    Citations: 89     Fields:    Translation:Cells
  23. Bergiers I, Andrews T, Vargel Bölükbasi Ö, Buness A, Janosz E, Lopez-Anguita N, Ganter K, Kosim K, Celen C, Itir 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. 2018 03 20; 7. PMID: 29555020.
    Citations: 6     Fields:    Translation:AnimalsCells
  24. 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, Kouzarides T. Genomic positional conservation identifies topological anchor point RNAs linked to developmental loci. Genome Biol. 2018 03 15; 19(1):32. PMID: 29540241.
    Citations: 31     Fields:    Translation:HumansAnimalsCells
  25. Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N. The Human Cell Atlas. Elife. 2017 12 05; 6. PMID: 29206104.
    Citations: 282     Fields:    Translation:HumansCells
  26. 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 Rep. 2017 Oct 10; 21(2):366-380. PMID: 29020624.
    Citations: 124     Fields:    Translation:AnimalsCells
  27. 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, Claycomb JM, Miska EA. The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription. Dev Cell. 2017 08 07; 42(3):241-255.e6. PMID: 28787591.
    Citations: 11     Fields:    Translation:AnimalsCells
  28. Andrews TS, Hemberg M. Identifying cell populations with scRNASeq. Mol Aspects Med. 2018 02; 59:114-122. PMID: 28712804.
    Citations: 46     Fields:    Translation:HumansCells
  29. Kirschner K, Chandra T, Kiselev V, Flores-Santa Cruz D, Macaulay IC, Park HJ, Li J, Kent DG, Kumar R, Pask DC, Hamilton TL, Hemberg M, Reik W, Green AR. Proliferation Drives Aging-Related Functional Decline in a Subpopulation of the Hematopoietic Stem Cell Compartment. Cell Rep. 2017 05 23; 19(8):1503-1511. PMID: 28538171.
    Citations: 22     Fields:    Translation:AnimalsCells
  30. 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. Nat Methods. 2017 May; 14(5):483-486. PMID: 28346451.
    Citations: 247     Fields:    Translation:HumansCells
  31. Hemberg M. Summing up the parts of the hypothalamus. Nat Neurosci. 2017 02 23; 20(3):378-379. PMID: 28230849.
    Citations: 1     Fields:    
  32. 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, Lin Y. A robust activity marking system for exploring active neuronal ensembles. Elife. 2016 Sep 23; 5. PMID: 27661450.
    Citations: 33     Fields:    
  33. Georgakopoulos-Soares I, Jain N, Gray JM, Hemberg M. MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments. Bioinformatics. 2017 01 01; 33(1):137-138. PMID: 27605100.
    Citations: 1     Fields:    
  34. 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. 2016 Jul 15; 353(6296):300-305. PMID: 27418512.
    Citations: 33     Fields:    Translation:AnimalsCells
  35. Nguyen TA, Jones RD, Snavely AR, Pfenning AR, Kirchner R, Hemberg M, Gray JM. High-throughput functional comparison of promoter and enhancer activities. Genome Res. 2016 08; 26(8):1023-33. PMID: 27311442.
    Citations: 31     Fields:    Translation:AnimalsCells
  36. 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 Res. 2016 06 02; 44(10):e97. PMID: 26980280.
    Citations: 1     Fields:    
  37. Delmans M, Hemberg M. Discrete distributional differential expression (D3E)--a tool for gene expression analysis of single-cell RNA-seq data. BMC Bioinformatics. 2016 Feb 29; 17:110. PMID: 26927822.
    Citations: 16     Fields:    Translation:Humans
  38. 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. 2015 Apr 08; 86(1):247-63. PMID: 25801704.
    Citations: 27     Fields:    Translation:AnimalsCells
  39. 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. 2015 Jun 04; 522(7554):89-93. PMID: 25762136.
    Citations: 196     Fields:    Translation:HumansAnimalsCells
  40. Kim TK, Hemberg M, Gray JM. Enhancer RNAs: a class of long noncoding RNAs synthesized at enhancers. Cold Spring Harb Perspect Biol. 2015 Jan 05; 7(1):a018622. PMID: 25561718.
    Citations: 47     Fields:    Translation:HumansAnimalsCells
  41. 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. Nat Commun. 2014 Nov 18; 5:5429. PMID: 25403355.
    Citations: 17     Fields:    Translation:AnimalsCells
  42. 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. Nat Neurosci. 2014 Oct; 17(10):1330-9. PMID: 25195102.
    Citations: 96     Fields:    Translation:HumansAnimalsCells
  43. 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. 2014 Jul 02; 83(1):122-34. PMID: 24991957.
    Citations: 40     Fields:    Translation:HumansAnimalsCells
  44. Frost B, Hemberg M, Lewis J, Feany MB. Tau promotes neurodegeneration through global chromatin relaxation. Nat Neurosci. 2014 Mar; 17(3):357-66. PMID: 24464041.
    Citations: 127     Fields:    Translation:HumansAnimalsCells
  45. 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 Res. 2012 Sep; 40(16):7858-69. PMID: 22684627.
    Citations: 12     Fields:    Translation:HumansAnimalsCells
  46. 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. 2012 Jan 26; 73(2):292-303. PMID: 22284184.
    Citations: 49     Fields:    Translation:AnimalsCells
  47. 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. 2011 Oct 06; 72(1):72-85. PMID: 21982370.
    Citations: 128     Fields:    Translation:AnimalsCells
  48. Hemberg M, Kreiman G. Conservation of transcription factor binding events predicts gene expression across species. Nucleic Acids Res. 2011 Sep 01; 39(16):7092-102. PMID: 21622661.
    Citations: 13     Fields:    Translation:HumansAnimalsCells
  49. 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. 2010 May 27; 5(5):e10870. PMID: 20523734.
    Citations: 11     Fields:    Translation:AnimalsCells
  50. 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, Greenberg ME. Widespread transcription at neuronal activity-regulated enhancers. Nature. 2010 May 13; 465(7295):182-7. PMID: 20393465.
    Citations: 1011     Fields:    Translation:AnimalsCells
  51. Ståhlberg A, Bengtsson M, Hemberg M, Semb H. Quantitative transcription factor analysis of undifferentiated single human embryonic stem cells. Clin Chem. 2009 Dec; 55(12):2162-70. PMID: 19815608.
    Citations: 12     Fields:    Translation:HumansCells
  52. 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. 2008 Dec 26; 60(6):1022-38. PMID: 19109909.
    Citations: 222     Fields:    Translation:HumansAnimalsCells
  53. Bengtsson M, Hemberg M, Rorsman P, Ståhlberg A. Quantification of mRNA in single cells and modelling of RT-qPCR induced noise. BMC Mol Biol. 2008 Jul 17; 9:63. PMID: 18631407.
    Citations: 44     Fields:    Translation:AnimalsCells
  54. Chang HH, Hemberg M, Barahona M, Ingber DE, Huang S. Transcriptome-wide noise controls lineage choice in mammalian progenitor cells. Nature. 2008 May 22; 453(7194):544-7. PMID: 18497826.
    Citations: 426     Fields:    Translation:AnimalsCells
  55. Hemberg M, Barahona M. A dominated coupling from the past algorithm for the stochastic simulation of networks of biochemical reactions. BMC Syst Biol. 2008 May 08; 2:42. PMID: 18466612.
    Citations:    Fields:    
  56. Hemberg M, Barahona M. Perfect sampling of the master equation for gene regulatory networks. Biophys J. 2007 Jul 15; 93(2):401-10. PMID: 17468171.
    Citations: 10     Fields:    
  57. Thompson RM, Hemberg M, Starzomski BM, Shurin JB. Trophic levels and trophic tangles: the prevalence of omnivory in real food webs. Ecology. 2007 Mar; 88(3):612-7. PMID: 17503589.
    Citations: 34     Fields:    Translation:Animals
  58. Hemberg M, Yaliraki SN, Barahona M. Stochastic kinetics of viral capsid assembly based on detailed protein structures. Biophys J. 2006 May 01; 90(9):3029-42. PMID: 16473916.
    Citations: 19     Fields:    Translation:Cells
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.