Publications by authors named "Ines Hellmann"

35Publications

A systematic evaluation of single cell RNA-seq analysis pipelines.

Nat Commun 2019 10 11;10(1):4667. Epub 2019 Oct 11.

Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Munich, Germany.

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http://dx.doi.org/10.1038/s41467-019-12266-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6789098PMC
October 2019

Sensitive and powerful single-cell RNA sequencing using mcSCRB-seq.

Nat Commun 2018 07 26;9(1):2937. Epub 2018 Jul 26.

Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University, Großhaderner Straße 2, 82152, Martinsried, Germany.

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http://www.nature.com/articles/s41467-018-05347-6
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http://dx.doi.org/10.1038/s41467-018-05347-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6062574PMC
July 2018

zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs.

Gigascience 2018 06;7(6)

Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Grosshaderner Str. 2, 82152 Martinsried, Germany.

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http://dx.doi.org/10.1093/gigascience/giy059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6007394PMC
June 2018

Quantitative single-cell transcriptomics.

Brief Funct Genomics 2018 07;17(4):220-232

Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, Martinsried, Germany.

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http://dx.doi.org/10.1093/bfgp/ely009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6063296PMC
July 2018

powsimR: power analysis for bulk and single cell RNA-seq experiments.

Bioinformatics 2017 Nov;33(21):3486-3488

Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, 82152 Munich, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btx435DOI Listing
November 2017

Initial high-resolution microscopic mapping of active and inactive regulatory sequences proves non-random 3D arrangements in chromatin domain clusters.

Epigenetics Chromatin 2017 08 7;10(1):39. Epub 2017 Aug 7.

LMU Biocenter, Department Biology II, Ludwig Maximilians-Universität (LMU Munich), Grosshadernerstr. 2, 82152, Martinsried, Germany.

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http://dx.doi.org/10.1186/s13072-017-0146-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5547466PMC
August 2017

Comparative Analysis of Single-Cell RNA Sequencing Methods.

Mol Cell 2017 Feb;65(4):631-643.e4

Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Straße 2, 82152 Martinsried, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2017.01.023DOI Listing
February 2017

The impact of amplification on differential expression analyses by RNA-seq.

Sci Rep 2016 05 9;6:25533. Epub 2016 May 9.

Anthropology &Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, 82152 Martinsried, Germany.

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http://dx.doi.org/10.1038/srep25533DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4860583PMC
May 2016

SweepFinder2: increased sensitivity, robustness and flexibility.

Bioinformatics 2016 06 15;32(12):1895-7. Epub 2016 Feb 15.

Department of Integrative Biology, University of California, Berkeley, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw051DOI Listing
June 2016

Detecting recent selective sweeps while controlling for mutation rate and background selection.

Mol Ecol 2016 Jan 7;25(1):142-56. Epub 2015 Sep 7.

Departments of Integrative Biology and Statistics, University of California, Berkeley, CA, USA.

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http://biorxiv.org/content/biorxiv/early/2015/04/30/018697.f
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http://doi.wiley.com/10.1111/mec.13351
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http://dx.doi.org/10.1111/mec.13351DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5082542PMC
January 2016

Mutation rate distribution inferred from coincident SNPs and coincident substitutions.

Genome Biol Evol 2011 13;3:842-50. Epub 2011 May 13.

Department of Biology, Emory University, Atlanta, Georgia, USA.

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http://dx.doi.org/10.1093/gbe/evr044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3172574PMC
December 2011

Population genetic inference from genomic sequence variation.

Genome Res 2010 Mar 12;20(3):291-300. Epub 2010 Jan 12.

Department of Integrative Biology, University of California, Berkeley, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1101/gr.079509.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2840988PMC
March 2010

The effects of probe binding affinity differences on gene expression measurements and how to deal with them.

Bioinformatics 2009 Nov 18;25(21):2772-9. Epub 2009 Aug 18.

Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btp492DOI Listing
November 2009

Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals.

Genome Res 2008 Jul 14;18(7):1020-9. Epub 2008 Apr 14.

Departments of Integrative Biology and Statistics, University of California, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1101/gr.074187.107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2493391PMC
July 2008

Recent and ongoing selection in the human genome.

Nat Rev Genet 2007 Nov;8(11):857-68

Center for Comparative Genomics, University of Copenhagen, Universitetsparken 15, 2100 Kbh Ø, Denmark.

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http://dx.doi.org/10.1038/nrg2187DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2933187PMC
November 2007

Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome.

Nat Genet 2007 Apr 4;39(4):457-66. Epub 2007 Mar 4.

Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland.

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http://dx.doi.org/10.1038/ng1990DOI Listing
April 2007

Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees.

Science 2005 Sep 1;309(5742):1850-4. Epub 2005 Sep 1.

Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany.

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http://www.sciencemag.org/cgi/doi/10.1126/science.1108296
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http://dx.doi.org/10.1126/science.1108296DOI Listing
September 2005

Why do human diversity levels vary at a megabase scale?

Genome Res 2005 Sep;15(9):1222-31

Max-Planck-Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.

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http://dx.doi.org/10.1101/gr.3461105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1199536PMC
September 2005

A neutral model of transcriptome evolution.

PLoS Biol 2004 May 11;2(5):E132. Epub 2004 May 11.

Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.

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http://dx.doi.org/10.1371/journal.pbio.0020132DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC406393PMC
May 2004

A neutral explanation for the correlation of diversity with recombination rates in humans.

Am J Hum Genet 2003 Jun 8;72(6):1527-35. Epub 2003 May 8.

Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1180312PMC
http://dx.doi.org/10.1086/375657DOI Listing
June 2003

Selection on human genes as revealed by comparisons to chimpanzee cDNA.

Genome Res 2003 May;13(5):831-7

Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.

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http://dx.doi.org/10.1101/gr.944903DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC430916PMC
May 2003