Hafemeister C - Search Results

1

Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data.

Tanevski J, Nguyen T, Truong B, Karaiskos N, Ahsen ME, Zhang X, Shu C, Xu K, Liang X, Hu Y, Pham HV, Xiaomei L, Le TD, Tarca AL, Bhatti G, Romero R, Karathanasis N, Loher P, Chen Y, Ouyang Z, Mao D, Zhang Y, Zand M, Ruan J, Hafemeister C, Qiu P, Tran D, Nguyen T, Gabor A, Yu T, Guinney J, Glaab E, Krause R, Banda P; DREAM SCTC Consortium; Stolovitzky G, Rajewsky N, Saez-Rodriguez J, Meyer P. Tanevski J, et al. Among authors: hafemeister c. Life Sci Alliance. 2020 Sep 24;3(11):e202000867. doi: 10.26508/lsa.202000867. Print 2020 Nov. Life Sci Alliance. 2020. PMID: 32972997 Free PMC article.

2

Inter-species pathway perturbation prediction via data-driven detection of functional homology.

Hafemeister C, Romero R, Bilal E, Meyer P, Norel R, Rhrissorrakrai K, Bonneau R, Tarca AL. Hafemeister C, et al. Bioinformatics. 2015 Feb 15;31(4):501-8. doi: 10.1093/bioinformatics/btu570. Epub 2014 Aug 22. Bioinformatics. 2015. PMID: 25150249 Free PMC article.

3

Selecting oligonucleotide probes for whole-genome tiling arrays with a cross-hybridization potential.

Hafemeister C, Krause R, Schliep A. Hafemeister C, et al. IEEE/ACM Trans Comput Biol Bioinform. 2011 Nov-Dec;8(6):1642-52. doi: 10.1109/TCBB.2011.39. IEEE/ACM Trans Comput Biol Bioinform. 2011. PMID: 21358006

4

Comprehensive Integration of Single-Cell Data.

Stuart T, Butler A, Hoffman P, Hafemeister C, Papalexi E, Mauck WM 3rd, Hao Y, Stoeckius M, Smibert P, Satija R. Stuart T, et al. Among authors: hafemeister c. Cell. 2019 Jun 13;177(7):1888-1902.e21. doi: 10.1016/j.cell.2019.05.031. Epub 2019 Jun 6. Cell. 2019. PMID: 31178118 Free PMC article.

5

Simultaneous epitope and transcriptome measurement in single cells.

Stoeckius M, Hafemeister C, Stephenson W, Houck-Loomis B, Chattopadhyay PK, Swerdlow H, Satija R, Smibert P. Stoeckius M, et al. Among authors: hafemeister c. Nat Methods. 2017 Sep;14(9):865-868. doi: 10.1038/nmeth.4380. Epub 2017 Jul 31. Nat Methods. 2017. PMID: 28759029 Free PMC article.

6

Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression.

Hafemeister C, Satija R. Hafemeister C, et al. Genome Biol. 2019 Dec 23;20(1):296. doi: 10.1186/s13059-019-1874-1. Genome Biol. 2019. PMID: 31870423 Free PMC article.

7

Optimized design of single-cell RNA sequencing experiments for cell-type-specific eQTL analysis.

Mandric I, Schwarz T, Majumdar A, Hou K, Briscoe L, Perez R, Subramaniam M, Hafemeister C, Satija R, Ye CJ, Pasaniuc B, Halperin E. Mandric I, et al. Among authors: hafemeister c. Nat Commun. 2020 Oct 30;11(1):5504. doi: 10.1038/s41467-020-19365-w. Nat Commun. 2020. PMID: 33127880 Free PMC article.

8

Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks.

Greenfield A, Hafemeister C, Bonneau R. Greenfield A, et al. Among authors: hafemeister c. Bioinformatics. 2013 Apr 15;29(8):1060-7. doi: 10.1093/bioinformatics/btt099. Epub 2013 Mar 21. Bioinformatics. 2013. PMID: 23525069 Free PMC article.

9

Inferring differentiation pathways from gene expression.

Costa IG, Roepcke S, Hafemeister C, Schliep A. Costa IG, et al. Among authors: hafemeister c. Bioinformatics. 2008 Jul 1;24(13):i156-64. doi: 10.1093/bioinformatics/btn153. Bioinformatics. 2008. PMID: 18586709 Free PMC article.

10

Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions.

Hafemeister C, Costa IG, Schönhuth A, Schliep A. Hafemeister C, et al. Bioinformatics. 2011 Apr 1;27(7):946-52. doi: 10.1093/bioinformatics/btr037. Epub 2011 Jan 25. Bioinformatics. 2011. PMID: 21266444

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