Publications by authors named "Martin Kircher"

65Publications

The impact of different negative training data on regulatory sequence predictions.

PLoS One 2020 1;15(12):e0237412. Epub 2020 Dec 1.

Charité-Universitätsmedizin Berlin, Berlin, Germany.

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January 2021

A systematic evaluation of the design and context dependencies of massively parallel reporter assays.

Nat Methods 2020 11 12;17(11):1083-1091. Epub 2020 Oct 12.

Department of Genome Sciences, University of Washington, Seattle, WA, USA.

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November 2020

HemoMIPs-Automated analysis and result reporting pipeline for targeted sequencing data.

PLoS Comput Biol 2020 06 4;16(6):e1007956. Epub 2020 Jun 4.

Berlin Institute of Health (BIH), Berlin, Germany.

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June 2020

Concurrent genome and epigenome editing by CRISPR-mediated sequence replacement.

BMC Biol 2019 11 18;17(1):90. Epub 2019 Nov 18.

Department of Genome Sciences, University of Washington, Seattle, WA, USA.

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November 2019

Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution.

Nat Commun 2019 08 8;10(1):3583. Epub 2019 Aug 8.

Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA.

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August 2019

Bi-allelic POLR3A Loss-of-Function Variants Cause Autosomal-Recessive Wiedemann-Rautenstrauch Syndrome.

Am J Hum Genet 2018 12 7;103(6):968-975. Epub 2018 Nov 7.

Division of Nutrition Metabolic Diseases, Department of Internal Medicine, Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. Electronic address:

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December 2018

CADD: predicting the deleteriousness of variants throughout the human genome.

Nucleic Acids Res 2019 01;47(D1):D886-D894

Berlin Institute of Health (BIH), 10178 Berlin, Germany.

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January 2019

Mutations in the fourth β-propeller domain of LRP4 are associated with isolated syndactyly with fusion of the third and fourth fingers.

Hum Mutat 2018 06 22;39(6):811-815. Epub 2018 Mar 22.

Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California.

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June 2018

Encephalopathy caused by novel mutations in the CMP-sialic acid transporter, SLC35A1.

Am J Med Genet A 2017 Nov 29;173(11):2906-2911. Epub 2017 Aug 29.

Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California.

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November 2017

Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin.

Cell 2016 Jan;164(1-2):57-68

Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA. Electronic address:

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January 2016

Running spell-check to identify regulatory variants.

Nat Genet 2015 Aug;47(8):853-5

Department of Genome Sciences, University of Washington, Seattle, Washington, USA.

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August 2015

Whole exome sequencing identifies de novo heterozygous CAV1 mutations associated with a novel neonatal onset lipodystrophy syndrome.

Am J Med Genet A 2015 Aug 21;167A(8):1796-806. Epub 2015 Apr 21.

Department of Internal Medicine and the Center for Human Nutrition, Division of Nutrition and Metabolic Diseases, UT Southwestern Medical Center, Dallas, Texas.

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August 2015

Evaluating intra- and inter-individual variation in the human placental transcriptome.

Genome Biol 2015 Mar 19;16:54. Epub 2015 Mar 19.

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

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March 2015

Biallelic mutations in BRCA1 cause a new Fanconi anemia subtype.

Cancer Discov 2015 Feb 3;5(2):135-42. Epub 2014 Dec 3.

Department of Cancer Biology, Abramson Family Cancer Research Institute, Basser Research Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania. Department of Pathology, Abramson Family Cancer Research Institute, Basser Research Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.

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February 2015

Somatic mutations in cerebral cortical malformations.

N Engl J Med 2014 Aug;371(8):733-43

From the Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute (S.S.J., A.-T.N.L., A.M.D., B.J.B., X.Z., R.S.H., J.N.P., A.R., S.S., B.K.M., T.W.Y., C.A.W.), and the Departments of Laboratory Medicine (J.W., Y.S., B.L.W.) and Neurology (M.S., A.P.), Boston Children's Hospital, the Departments of Pediatrics (S.S.J., A.-T.N.L., A.M.D., B.J.B., X.Z., R.S.H., J.N.P., A.R., S.S., B.K.M., T.W.Y., C.A.W.), Neurology (S.S.J., A.-T.N.L., A.M.D., B.J.B., X.Z., R.S.H., J.N.P., A.R., S.S., B.K.M., T.W.Y., C.A.W., M.S., A.P.), and Pathology (Y.S., B.L.W.), Harvard Medical School, the Department of Neurology, Beth Israel Deaconess Medical Center (B.S.C.), and the Department of Neurology, Massachusetts General Hospital (T.W.Y.) - all in Boston; the Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Singapore (S.S.J.); the Department of Genome Sciences, University of Washington, Seattle (M.K., M.B., D.A.N., J.S.); the Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai (J.W., Y.S.); the Division of Neurology, Department of Pediatrics, Hacettepe University School of Medicine, Sihhiye, Ankara, Turkey (M.T.); the Neurogenetics Unit, Montreal Neurological Hospital and Institute, Department of Neurology and Neurosurgery (D.A., E.A.) and Department of Human Genetics (E.A.), McGill University, Montreal; the Department of Neurology, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels (B.D.); the Pediatric Neurology Unit and Laboratories, Children's Hospital A. Meyer-University of Florence, Florence, Italy (E.P., R.G.); the Department of Medicine, University of Melbourne, Austin Health, Heidelberg (I.E.S., S.F.B.), Department of Paediatrics, Royal Children's Hospital, University of Melbourne, and the Florey Institute of Neuroscience and Mental Health, Melbourne (I.E.S.), and the Department of Neurology, Royal Children's Hospital, Murdoch Children'

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August 2014

Primate iPS cells as tools for evolutionary analyses.

Stem Cell Res 2014 May 8;12(3):622-9. Epub 2014 Feb 8.

Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany; Department Biology II, Ludwig Maximilian University Munich, D-82152 Martinsried, Germany. Electronic address:

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May 2014

A general framework for estimating the relative pathogenicity of human genetic variants.

Nat Genet 2014 Mar 2;46(3):310-5. Epub 2014 Feb 2.

Department of Genome Sciences, University of Washington, Seattle, Washington, USA.

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March 2014

The earliest transcribed zygotic genes are short, newly evolved, and different across species.

Cell Rep 2014 Jan 16;6(2):285-92. Epub 2014 Jan 16.

Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany. Electronic address:

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January 2014

A new congenital disorder of glycosylation caused by a mutation in SSR4, the signal sequence receptor 4 protein of the TRAP complex.

Hum Mol Genet 2014 Mar 11;23(6):1602-5. Epub 2013 Nov 11.

Genetic Disease Program, Sanford Children's Health Research Center, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA.

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March 2014

freeIbis: an efficient basecaller with calibrated quality scores for Illumina sequencers.

Bioinformatics 2013 May 6;29(9):1208-9. Epub 2013 Mar 6.

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

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May 2013

Analysis of high-throughput ancient DNA sequencing data.

Authors:
Martin Kircher

Methods Mol Biol 2012 ;840:197-228

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

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May 2012

Deep proteome and transcriptome mapping of a human cancer cell line.

Mol Syst Biol 2011 Nov 8;7:548. Epub 2011 Nov 8.

Department for Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.

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November 2011

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform.

Nucleic Acids Res 2012 Jan 21;40(1):e3. Epub 2011 Oct 21.

Max Planck Institute for Evolutionary Anthropology, Department of Evolutionary Genetics, 04103 Leipzig, Germany.

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January 2012

Addressing challenges in the production and analysis of illumina sequencing data.

BMC Genomics 2011 Jul 29;12:382. Epub 2011 Jul 29.

Max Planck Institute for Evolutionary Anthropology, Department of Evolutionary Genetics Deutscher Platz 6 04103 Leipzig, Germany.

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July 2011

Road blocks on paleogenomes--polymerase extension profiling reveals the frequency of blocking lesions in ancient DNA.

Nucleic Acids Res 2010 Sep 28;38(16):e161. Epub 2010 Jun 28.

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

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September 2010

Illumina sequencing library preparation for highly multiplexed target capture and sequencing.

Cold Spring Harb Protoc 2010 Jun;2010(6):pdb.prot5448

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

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June 2010

High-throughput DNA sequencing--concepts and limitations.

Bioessays 2010 Jun;32(6):524-36

Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.

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June 2010

A complete mtDNA genome of an early modern human from Kostenki, Russia.

Curr Biol 2010 Feb 31;20(3):231-6. Epub 2009 Dec 31.

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

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February 2010

Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA.

Nucleic Acids Res 2010 Apr 22;38(6):e87. Epub 2009 Dec 22.

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

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April 2010

Improved base calling for the Illumina Genome Analyzer using machine learning strategies.

Genome Biol 2009 14;10(8):R83. Epub 2009 Aug 14.

Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz, 04103 Leipzig, Germany.

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October 2009