Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 44

1.

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

Kiselev VY, Andrews TS, Hemberg M.

Nat Rev Genet. 2019 Jan 22. doi: 10.1038/s41576-019-0095-5. [Epub ahead of print]

PMID:
30670832
2.

Challenges in unsupervised clustering of single-cell RNA-seq data.

Kiselev VY, Andrews TS, Hemberg M.

Nat Rev Genet. 2019 Jan 7. doi: 10.1038/s41576-018-0088-9. [Epub ahead of print] Review. Erratum in: Nat Rev Genet. 2019 Jan 22;:.

PMID:
30617341
3.

M3Drop: Dropout-based feature selection for scRNASeq.

Andrews TS, Hemberg M.

Bioinformatics. 2018 Dec 24. doi: 10.1093/bioinformatics/bty1044. [Epub ahead of print]

PMID:
30590489
4.

Simulation-based benchmarking of isoform quantification in single-cell RNA-seq.

Westoby J, Herrera MS, Ferguson-Smith AC, Hemberg M.

Genome Biol. 2018 Nov 7;19(1):191. doi: 10.1186/s13059-018-1571-5.

5.

Noncanonical secondary structures arising from non-B DNA motifs are determinants of mutagenesis.

Georgakopoulos-Soares I, Morganella S, Jain N, Hemberg M, Nik-Zainal S.

Genome Res. 2018 Sep;28(9):1264-1271. doi: 10.1101/gr.231688.117. Epub 2018 Aug 13.

PMID:
30104284
6.

Single-cell genomics.

Hemberg M.

Brief Funct Genomics. 2018 Jul 1;17(4):207-208. doi: 10.1093/bfgp/ely025. No abstract available.

7.

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

Kiselev VY, Yiu A, Hemberg M.

Nat Methods. 2018 May;15(5):359-362. doi: 10.1038/nmeth.4644. Epub 2018 Apr 2.

PMID:
29608555
8.

Single-cell transcriptomics reveals a new dynamical function of transcription factors during embryonic hematopoiesis.

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.

Elife. 2018 Mar 20;7. pii: e29312. doi: 10.7554/eLife.29312.

9.

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

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.

Genome Biol. 2018 Mar 15;19(1):32. doi: 10.1186/s13059-018-1405-5.

10.

The Human Cell Atlas.

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; Human Cell Atlas Meeting Participants.

Elife. 2017 Dec 5;6. pii: e27041. doi: 10.7554/eLife.27041.

11.

Temporal Tracking of Microglia Activation in Neurodegeneration at Single-Cell Resolution.

Mathys H, Adaikkan C, Gao F, Young JZ, Manet E, Hemberg M, De Jager PL, Ransohoff RM, Regev A, Tsai LH.

Cell Rep. 2017 Oct 10;21(2):366-380. doi: 10.1016/j.celrep.2017.09.039.

12.

The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription.

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.

Dev Cell. 2017 Aug 7;42(3):241-255.e6. doi: 10.1016/j.devcel.2017.07.002.

13.

Identifying cell populations with scRNASeq.

Andrews TS, Hemberg M.

Mol Aspects Med. 2018 Feb;59:114-122. doi: 10.1016/j.mam.2017.07.002. Epub 2017 Jul 25. Review.

14.

Proliferation Drives Aging-Related Functional Decline in a Subpopulation of the Hematopoietic Stem Cell Compartment.

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.

Cell Rep. 2017 May 23;19(8):1503-1511. doi: 10.1016/j.celrep.2017.04.074.

15.

SC3: consensus clustering of single-cell RNA-seq data.

Kiselev VY, Kirschner K, Schaub MT, Andrews T, Yiu A, Chandra T, Natarajan KN, Reik W, Barahona M, Green AR, Hemberg M.

Nat Methods. 2017 May;14(5):483-486. doi: 10.1038/nmeth.4236. Epub 2017 Mar 27.

16.

Summing up the parts of the hypothalamus.

Hemberg M.

Nat Neurosci. 2017 Feb 23;20(3):378-379. doi: 10.1038/nn.4515. No abstract available.

PMID:
28230849
17.

A robust activity marking system for exploring active neuronal ensembles.

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.

Elife. 2016 Sep 23;5. pii: e13918. doi: 10.7554/eLife.13918.

18.

MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments.

Georgakopoulos-Soares I, Jain N, Gray JM, Hemberg M.

Bioinformatics. 2017 Jan 1;33(1):137-138. doi: 10.1093/bioinformatics/btw584. Epub 2016 Sep 6.

19.

Chromatin remodeling inactivates activity genes and regulates neural coding.

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.

Science. 2016 Jul 15;353(6296):300-305. doi: 10.1126/science.aad4225.

20.

High-throughput functional comparison of promoter and enhancer activities.

Nguyen TA, Jones RD, Snavely AR, Pfenning AR, Kirchner R, Hemberg M, Gray JM.

Genome Res. 2016 Aug;26(8):1023-33. doi: 10.1101/gr.204834.116. Epub 2016 Jun 16.

21.

f-divergence cutoff index to simultaneously identify differential expression in the integrated transcriptome and proteome.

Tang S, Hemberg M, Cansizoglu E, Belin S, Kosik K, Kreiman G, Steen H, Steen J.

Nucleic Acids Res. 2016 Jun 2;44(10):e97. doi: 10.1093/nar/gkw157. Epub 2016 Mar 14.

22.

Discrete distributional differential expression (D3E)--a tool for gene expression analysis of single-cell RNA-seq data.

Delmans M, Hemberg M.

BMC Bioinformatics. 2016 Feb 29;17:110. doi: 10.1186/s12859-016-0944-6.

23.

MEF2D drives photoreceptor development through a genome-wide competition for tissue-specific enhancers.

Andzelm MM, Cherry TJ, Harmin DA, Boeke AC, Lee C, Hemberg M, Pawlyk B, Malik AN, Flavell SW, Sandberg MA, Raviola E, Greenberg ME.

Neuron. 2015 Apr 8;86(1):247-63. doi: 10.1016/j.neuron.2015.02.038. Epub 2015 Mar 19.

24.

Disruption of DNA-methylation-dependent long gene repression in Rett syndrome.

Gabel HW, Kinde B, Stroud H, Gilbert CS, Harmin DA, Kastan NR, Hemberg M, Ebert DH, Greenberg ME.

Nature. 2015 Jun 4;522(7554):89-93. doi: 10.1038/nature14319. Epub 2015 Mar 11.

25.

Enhancer RNAs: a class of long noncoding RNAs synthesized at enhancers.

Kim TK, Hemberg M, Gray JM.

Cold Spring Harb Perspect Biol. 2015 Jan 5;7(1):a018622. doi: 10.1101/cshperspect.a018622. Review.

26.

Quantitative profiling of peptides from RNAs classified as noncoding.

Prabakaran S, Hemberg M, Chauhan R, Winter D, Tweedie-Cullen RY, Dittrich C, Hong E, Gunawardena J, Steen H, Kreiman G, Steen JA.

Nat Commun. 2014 Nov 18;5:5429. doi: 10.1038/ncomms6429.

27.

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

Malik AN, Vierbuchen T, Hemberg M, Rubin AA, Ling E, Couch CH, Stroud H, Spiegel I, Farh KK, Harmin DA, Greenberg ME.

Nat Neurosci. 2014 Oct;17(10):1330-9. doi: 10.1038/nn.3808. Epub 2014 Sep 7.

28.

Promoter decommissioning by the NuRD chromatin remodeling complex triggers synaptic connectivity in the mammalian brain.

Yamada T, Yang Y, Hemberg M, Yoshida T, Cho HY, Murphy JP, Fioravante D, Regehr WG, Gygi SP, Georgopoulos K, Bonni A.

Neuron. 2014 Jul 2;83(1):122-34. doi: 10.1016/j.neuron.2014.05.039.

29.

Tau promotes neurodegeneration through global chromatin relaxation.

Frost B, Hemberg M, Lewis J, Feany MB.

Nat Neurosci. 2014 Mar;17(3):357-66. doi: 10.1038/nn.3639. Epub 2014 Jan 26.

30.

Integrated genome analysis suggests that most conserved non-coding sequences are regulatory factor binding sites.

Hemberg M, Gray JM, Cloonan N, Kuersten S, Grimmond S, Greenberg ME, Kreiman G.

Nucleic Acids Res. 2012 Sep;40(16):7858-69. doi: 10.1093/nar/gks477. Epub 2012 Jun 8.

31.

Bhlhb5 and Prdm8 form a repressor complex involved in neuronal circuit assembly.

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.

Neuron. 2012 Jan 26;73(2):292-303. doi: 10.1016/j.neuron.2011.09.035.

32.

Genome-wide activity-dependent MeCP2 phosphorylation regulates nervous system development and function.

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.

Neuron. 2011 Oct 6;72(1):72-85. doi: 10.1016/j.neuron.2011.08.022.

33.

Conservation of transcription factor binding events predicts gene expression across species.

Hemberg M, Kreiman G.

Nucleic Acids Res. 2011 Sep 1;39(16):7092-102. doi: 10.1093/nar/gkr404. Epub 2011 May 26.

34.

Genome-wide identification of calcium-response factor (CaRF) binding sites predicts a role in regulation of neuronal signaling pathways.

Pfenning AR, Kim TK, Spotts JM, Hemberg M, Su D, West AE.

PLoS One. 2010 May 27;5(5):e10870. doi: 10.1371/journal.pone.0010870.

35.

Widespread transcription at neuronal activity-regulated enhancers.

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.

Nature. 2010 May 13;465(7295):182-7. doi: 10.1038/nature09033. Epub 2010 Apr 14.

36.

Quantitative transcription factor analysis of undifferentiated single human embryonic stem cells.

Ståhlberg A, Bengtsson M, Hemberg M, Semb H.

Clin Chem. 2009 Dec;55(12):2162-70. doi: 10.1373/clinchem.2009.131433. Epub 2009 Oct 8.

37.

Genome-wide analysis of MEF2 transcriptional program reveals synaptic target genes and neuronal activity-dependent polyadenylation site selection.

Flavell SW, Kim TK, Gray JM, Harmin DA, Hemberg M, Hong EJ, Markenscoff-Papadimitriou E, Bear DM, Greenberg ME.

Neuron. 2008 Dec 26;60(6):1022-38. doi: 10.1016/j.neuron.2008.11.029.

38.

Quantification of mRNA in single cells and modelling of RT-qPCR induced noise.

Bengtsson M, Hemberg M, Rorsman P, Ståhlberg A.

BMC Mol Biol. 2008 Jul 17;9:63. doi: 10.1186/1471-2199-9-63.

39.

Transcriptome-wide noise controls lineage choice in mammalian progenitor cells.

Chang HH, Hemberg M, Barahona M, Ingber DE, Huang S.

Nature. 2008 May 22;453(7194):544-7. doi: 10.1038/nature06965.

40.

A dominated coupling from the past algorithm for the stochastic simulation of networks of biochemical reactions.

Hemberg M, Barahona M.

BMC Syst Biol. 2008 May 8;2:42. doi: 10.1186/1752-0509-2-42.

41.

Trophic levels and trophic tangles: the prevalence of omnivory in real food webs.

Thompson RM, Hemberg M, Starzomski BM, Shurin JB.

Ecology. 2007 Mar;88(3):612-7.

PMID:
17503589
42.

Perfect sampling of the master equation for gene regulatory networks.

Hemberg M, Barahona M.

Biophys J. 2007 Jul 15;93(2):401-10. Epub 2007 Apr 27.

43.

Stochastic kinetics of viral capsid assembly based on detailed protein structures.

Hemberg M, Yaliraki SN, Barahona M.

Biophys J. 2006 May 1;90(9):3029-42. Epub 2006 Feb 10.

44.

Supplemental Content

Loading ...
Support Center