This is a selection of publications from members of the lab. For a complete list, please see the ORCID profiles of individual members or look up their publications on PubMed, Google Scholar or other services like Scopus or Web of Sciences.

 

2024

Deciphering the impact of genomic variation on function.
IGVF Consortium
Nature 2024.

STIGMA: Single-cell tissue-specific gene prioritization using machine learning.
S. Balachandran, C. A. Prada-Medina, M. A. Mensah, J. Glaser, N. Kakar, I. Nagel, J. Pozojevic, E. Audain, M. P. Hitz, M. Kircher, V. KA. Sreenivasan, M. Spielmann
American Journal of Human Genetics 2024.

CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods.
Critical Assessment of Genome Interpretation Consortium
Genome Biology 2024.

CADD v1.7: using protein language models, regulatory CNNs and other nucleotide-level scores to improve genome-wide variant predictions.
M. Schubach, T. Maass, L. Nazaretyan, S. Röner, M. Kircher
Nucleic Acids Research 2024.

2023

GCparagon: evaluating and correcting GC biases in cell-free DNA at the fragment level.
Spiegl B, Kapidzic F, Röner S, Kircher M, Speicher MR.
NAR Genomics and Bioinformatics 2023.

Predicting the pathogenicity of missense variants using features derived from AlphaFold2.
A. Schmidt, S. Röner, K. Mai, H. Klinkhammer, M. Kircher, K. U. Ludwig
Bioinformatics 2023.

The Regulatory Mendelian Mutation score for GRCh38.
M. Schubach, L. Nazaretyan, M. Kircher
GigaScience 2023.

2022

Boosting tissue-specific prediction of active cis-regulatory regions through deep learning and Bayesian optimization techniques.
L. Cappelletti, A. Petrini, J. Gliozzo, E. Casiraghi, M. Schubach, M. Kircher, G. Valentini
BMC Bioinformatics 2022.

Systematic assays and resources for the functional annotation of non-coding variants.
M. Kircher & K.U. Ludwig
Medizinische Genetik 2022.

Computational and experimental methods for classifying variants of unknown clinical significance.
M. Spielmann & M. Kircher.
Cold Spring Harb Mol Case Stud 2022.

A framework to score the effects of structural variants in health and disease.
P. Kleinert & M. Kircher.
Genome Research 2022.

2021

CADD-Splice - improving genome-wide variant effect prediction using deep learning-derived splice scores.
P. Rentzsch, M. Schubach, J. Shendure, M. Kircher.
Genome Medicine 2021.

2020

lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements.
M.G. Gordon*, F. Inoue*, B. Martin*, M. Schubach*, V. Agarwal, S. Whalen, S. Feng, J. Zhao, T. Ashuach, R. Ziffra, A. Kreimer, I. Georgakopoulous-Soares, N. Yosef, C.J. Ye, K.S. Pollard, J. Shendure, M. Kircher, N. Ahituv.
Nature Protocols 2020.

HemoMIPs - Automated analysis and result reporting pipeline for targeted sequencing data.
P. Kleinert, B. Martin, M. Kircher.
PLOS Computational Biology 2020.

The impact of different negative training data on regulatory sequence predictions.
LM. Krützfeldt, M. Schubach, M. Kircher.
PLOS ONE 2020.

2019

Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution.
M. Kircher*, C. Xiong*, B. Martin*, M. Schubach*, F. Inoue, R. JA. Bell, J. F. Costello, J. Shendure & N. Ahituv.
Nature Communications 2019.

2018

CADD: predicting the deleteriousness of variants throughout the human genome.
P. Rentzsch, D. Witten, G.M. Cooper, J. Shendure, M. Kircher.
Nucleic Acids Research 2018.

2017

A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity.
F. Inoue*, M. Kircher*, B. Martin, G.M. Cooper, D.M. Witten, M.T. McManus, N. Ahituv, J. Shendure.
Genome Research 2017.

2016

Cell-free DNA comprises an in vivo nucleosome footprint that informs its tissues-of-origin.
M.W. Snyder*, M. Kircher*, A.J. Hill, R.M. Daza, and J. Shendure.
Cell 2016.

2014

A general framework for estimating the relative pathogenicity of human genetic variants.
M. Kircher*, D.M. Witten*, P. Jain, B.J. O'Roak, G.M. Cooper, and J. Shendure.
Nature Genetics 2014.

2012

A high coverage genome sequence from an archaic Denisovan individual.
M. Meyer*, M. Kircher*, M. Gansauge, H. Li, F. Racimo, S. Mallick, J.G. Schraiber, F. Jay, K. Prüfer, C. de Filippo, P.H. Sudmant, C. Alkan, Q. Fu, R. Do, N. Rohland, A. Tandon, M. Siebauer, R.E. Green, K. Bryc, A.W. Briggs, U. Stenzel, J. Dabney, J. Shendure, J. Kitzman, M.F. Hammer, M.V. Shunkov, A.P. Derevianko, N. Patterson, A.M. Andrés, E.E. Eichler, M. Slatkin, D. Reich, J. Kelso, and S. Pääbo.
Science 2012.

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform.
M. Kircher, S. Sawyer, and M. Meyer.
Nucleic Acids Research 2012.

2011

Addressing challenges in the production and analysis of Illumina sequencing data.
M. Kircher, P. Heyn, and J. Kelso.
BMC Genomics 2011.

2010

Genetic history of an archaic hominin group from Denisova Cave in Siberia.
D. Reich*, R.E. Green*, M. Kircher*, J. Krause*, N. Patterson*, E.Y. Durand*, B. Viola*, A.W. Briggs, U. Stenzel, P.L.F. Johnson, T. Maricic, J.M. Good, T. Marques-Bonet, C. Alkan, Q. Fu, S. Mallick, H. Li, M. Meyer, E.E. Eichler, M. Stoneking, M. Richards, S. Talamo, M.V. Shunkov, A.P. Derevianko, J.-J. Hublin, J. Kelso, M. Slatkin, and S. Pääbo.
Nature 2010.

2009

Improved base calling for the Illumina Genome Analyzer using machine learning strategies.
M. Kircher, U. Stenzel, and J. Kelso.
Genome Biology 2009.