This is a selection of publications from members of the lab, typically those with at least two lab members. 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.

 

2025

varCADD: large sets of standing genetic variation enable genome-wide pathogenicity prediction.
L. Nazaretyan, P. Rentzsch, M. Kircher
Genome Medicine 2025 Aug 4;17(1):84

Benchmarking machine learning methods for the identification of mislabeled data.
L. Nazaretyan, U. Leser, M. Kircher
Artificial Intelligence Review, 58, 310 (2025)

Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity.
M. Kosicki, D. Laboy Cintrón, P. Keukeleire, M. Schubach, N.F. Page, I. Georgakopoulos-Soares, J.A. Akiyama, I. Plajzer-Frick, C.S. Novak, M. Kato, R.D. Hunter, K. von Maydell, S. Barton, P. Godfrey, E. Beckman, S.J. Sanders, M. Kircher, L.A. Pennacchio, N. Ahituv.
Nature Communications 2025 May 23;16(1):4786

Massively parallel jumping assay decodes Alu retrotransposition activity.
N. Matharu, J. Zhao, A. Sohota, L. Deng, Y. Hung, Z. Li, K. An, J. Sims, S. Rattanasopha, T.J. Meyer, L. Carbone, M. Kircher, N. Ahituv
Nature Communications 2025 May 9;16(1):4310

Using individual barcodes to increase quantification power of massively parallel reporter assays.
P. Keukeleire, J.D. Rosen, A. Göbel-Knapp, K. Salomon, M. Schubach, M. Kircher
BMC Bioinformatics 2025

Massively parallel characterization of transcriptional regulatory elements.
V. Agarwal, F. Inoue, M. Schubach, D. Penzar D, B.K. Martin, P.M. Dash, P. Keukeleire, Z. Zhang, A. Sohota, J. Zhao, I. Georgakopoulos-Soares, W.S. Noble, G.G. Yardımcı, I.V. Kulakovskiy, M. Kircher, J. Shendure, N. Ahituv
Nature 2025

cfDNA UniFlow: a unified preprocessing pipeline for cell-free DNA data from liquid biopsies.
S. Röner, L. Burkard, M.R. Speicher, M. Kircher
Gigascience 2024

2024

Deciphering the impact of genomic variation on function.
IGVF Consortium
Nature 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.
B. Spiegl, F. Kapidzic, S. Röner, M. Kircher, M.R. Speicher
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