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Items: 1 to 20 of 43

1.

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.

PMID:
30617341
2.

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
3.

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.

4.

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
5.

Single-cell genomics.

Hemberg M.

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

6.

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
7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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
16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

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