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Items: 14


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.

Cell. 2019 Jun 13;177(7):1888-1902.e21. doi: 10.1016/j.cell.2019.05.031. Epub 2019 Jun 6.


Developmental diversification of cortical inhibitory interneurons.

Mayer C, Hafemeister C, Bandler RC, Machold R, Batista Brito R, Jaglin X, Allaway K, Butler A, Fishell G, Satija R.

Nature. 2018 Mar 22;555(7697):457-462. doi: 10.1038/nature25999. Epub 2018 Mar 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.

Nat Methods. 2017 Sep;14(9):865-868. doi: 10.1038/nmeth.4380. Epub 2017 Jul 31.


EGRINs (Environmental Gene Regulatory Influence Networks) in Rice That Function in the Response to Water Deficit, High Temperature, and Agricultural Environments.

Wilkins O, Hafemeister C, Plessis A, Holloway-Phillips MM, Pham GM, Nicotra AB, Gregorio GB, Jagadish SV, Septiningsih EM, Bonneau R, Purugganan M.

Plant Cell. 2016 Oct;28(10):2365-2384. Epub 2016 Sep 21.


Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions.

Plessis A, Hafemeister C, Wilkins O, Gonzaga ZJ, Meyer RS, Pires I, Müller C, Septiningsih EM, Bonneau R, Purugganan M.

Elife. 2015 Nov 26;4. pii: e08411. doi: 10.7554/eLife.08411.


An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network.

Arrieta-Ortiz ML, Hafemeister C, Bate AR, Chu T, Greenfield A, Shuster B, Barry SN, Gallitto M, Liu B, Kacmarczyk T, Santoriello F, Chen J, Rodrigues CD, Sato T, Rudner DZ, Driks A, Bonneau R, Eichenberger P.

Mol Syst Biol. 2015 Nov 17;11(11):839. doi: 10.15252/msb.20156236.


Genotet: An Interactive Web-based Visual Exploration Framework to Support Validation of Gene Regulatory Networks.

Yu B, Doraiswamy H, Chen X, Miraldi E, Arrieta-Ortiz ML, Hafemeister C, Madar A, Bonneau R, Silva CT.

IEEE Trans Vis Comput Graph. 2014 Dec;20(12):1903-12. doi: 10.1109/TVCG.2014.2346753.


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.

Bioinformatics. 2015 Feb 15;31(4):501-8. doi: 10.1093/bioinformatics/btu570. Epub 2014 Aug 22.


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

Greenfield A, Hafemeister C, Bonneau R.

Bioinformatics. 2013 Apr 15;29(8):1060-7. doi: 10.1093/bioinformatics/btt099. Epub 2013 Mar 21.


Identification of global alteration of translational regulation in glioma in vivo.

Helmy K, Halliday J, Fomchenko E, Setty M, Pitter K, Hafemeister C, Holland EC.

PLoS One. 2012;7(10):e46965. doi: 10.1371/journal.pone.0046965. Epub 2012 Oct 3.


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

Hafemeister C, Krause R, Schliep A.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Nov-Dec;8(6):1642-52. doi: 10.1109/TCBB.2011.39.


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

Hafemeister C, Costa IG, Schönhuth A, Schliep A.

Bioinformatics. 2011 Apr 1;27(7):946-52. doi: 10.1093/bioinformatics/btr037. Epub 2011 Jan 25.


Constrained mixture estimation for analysis and robust classification of clinical time series.

Costa IG, Schönhuth A, Hafemeister C, Schliep A.

Bioinformatics. 2009 Jun 15;25(12):i6-14. doi: 10.1093/bioinformatics/btp222.


Inferring differentiation pathways from gene expression.

Costa IG, Roepcke S, Hafemeister C, Schliep A.

Bioinformatics. 2008 Jul 1;24(13):i156-64. doi: 10.1093/bioinformatics/btn153.

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