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Martin Hemberg, Ph.D. - Publications

Affiliations: 
Sanger Institute 
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29 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
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2014 Frost B, Hemberg M, Lewis J, Feany MB. Tau promotes neurodegeneration through global chromatin relaxation. Nature Neuroscience. 17: 357-66. PMID 24464041 DOI: 10.1038/nn.3639  1
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  1
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  1
2012 McDermott J, Swafford JM, Hemberg M, Byrne J, Hemberg E, Fenton M, McNally C, Shotton E, O'Neill M. String-rewriting grammars for evolutionary architectural design Environment and Planning B: Planning and Design. 39: 713-731. DOI: 10.1068/b38037  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2008 Hemberg M, Barahona M. A dominated coupling from the past algorithm for the stochastic simulation of networks of biochemical reactions. Bmc Systems Biology. 2: 42. PMID 18466612 DOI: 10.1186/1752-0509-2-42  1
2007 Thompson RM, Hemberg M, Starzomski BM, Shurin JB. Trophic levels and trophic tangles: the prevalence of omnivory in real food webs. Ecology. 88: 612-7. PMID 17503589 DOI: 10.1890/05-1454  1
2007 Hemberg M, Barahona M. Perfect sampling of the master equation for gene regulatory networks. Biophysical Journal. 93: 401-10. PMID 17468171 DOI: 10.1529/biophysj.106.099390  1
2007 O'Reilly UM, Hemberg M. Integrating generative growth and evolutionary computation for form exploration Genetic Programming and Evolvable Machines. 8: 163-186. DOI: 10.1007/s10710-007-9025-y  1
2006 Hemberg M, Yaliraki SN, Barahona M. Stochastic kinetics of viral capsid assembly based on detailed protein structures. Biophysical Journal. 90: 3029-42. PMID 16473916 DOI: 10.1529/biophysj.105.076737  1
2004 Hemberg M, O'Reilly UM. Extending Grammatical Evolution to Evolve Digital Surfaces with Genr8 Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3003: 299-308.  1
2004 O'Reilly UM, Hemberg M, Menges A. Evolutionary computation and artificial life in architecture: Exploring the potential of generative and genetic algorithms as operative design tools Architectural Design. 74: 49-53.  1
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