Hiller, Michael

GREAT improves functional interpretation of cis-regulatory regions

McLean, C. Y., Bristor, D., Hiller, M., Clarke, S. L., Schaar, B. T., Lowe, C. B., Wenger, A. M., & Bejerano, G. (2010) · Nature Biotechnology

Genomics and Chromatin DynamicsBioinformatics and Genomic Networks

Cited by 4,502

Towards complete and error-free genome assemblies of all vertebrate species

Rhie, A., McCarthy, S. A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano-Silva, M., Chow, W., Fungtammasan, A., Kim, J., et al. (2021) · Nature

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 3,097

Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates

Damas, J., Hughes, G. M., Keough, K. C., Painter, C. A., Persky, N. S., Corbo, M., Hiller, M., Koepfli, K.-P., Pfenning, A. R., Zhao, H., et al. (2020) · Proceedings of the National Academy of Sciences

SARS-CoV-2 and COVID-19 ResearchAnimal Virus Infections Studies

Cited by 633

How genomics can help biodiversity conservation

Theissinger, K., Fernandes, C., Formenti, G., Bista, I., Berg, P. R., Bleidorn, C., Bombarely, A., Crottini, A., Gallo, G. R., Godoy, J. A., et al. (2023) · Trends in Genetics

Genomics and Phylogenetic StudiesGenetic diversity and population structure

Cited by 401

Six reference-quality genomes reveal evolution of bat adaptations

Jebb, D., Huang, Z., Pippel, M., Hughes, G. M., Lavrichenko, K., Devanna, P., Winkler, S., Jermiin, L. S., Skirmuntt, E. C., Katzourakis, A., et al. (2020) · Nature

Bat Biology and Ecology StudiesGenomics and Phylogenetic Studies

Cited by 361

The era of reference genomes in conservation genomics

Formenti, G., Theissinger, K., Fernandes, C., Bista, I., Bombarely, A., Bleidorn, C., Ciofi, C., Crottini, A., Godoy, J. A., Höglund, J., et al. (2022) · Trends in Ecology & Evolution

Genomics and Phylogenetic StudiesGenetic diversity and population structure

Cited by 340

A genomics approach reveals insights into the importance of gene losses for mammalian adaptations

Sharma, V., Hecker, N., Roscito, J. G., Foerster, L., Langer, B. E., & Hiller, M. (2018) · Nature Communications

Genomics and Phylogenetic StudiesEvolution and Paleontology Studies

Cited by 237

A “forward genomics” approach links genotype to phenotype using independent phenotypic losses among related species

Hiller, M., Schaar, B. T., Indjeian, V. B., Kingsley, D. M., Hagey, L. R., & Bejerano, G. (2012) · Cell Reports

Genomics and Phylogenetic StudiesEvolution and Genetic Dynamics

Cited by 144

Three-dimensional genome rewiring in loci with human accelerated regions

Keough, K. C., Whalen, S., Inoue, F., Przytycki, P. F., Fair, T., Deng, C., Steyert, M., Ryu, H., Lindblad-Toh, K., Karlsson, E., et al. (2023) · Science

Genomics and Chromatin DynamicsChromosomal and Genetic Variations

Cited by 113

Reference-quality bat genomes illuminate adaptations to viral tolerance and disease resistance

Morales, A., Dong, Y., Brown, T., Baid, K., Kontopoulos, D., Gonzalez, V., Huang, Z., Ahmed, A., Hilgers, L., Winkler, S., et al. (2023) · Nature

Bat Biology and Ecology Studiesinterferon and immune responses

Cited by 78

Bat genomes illuminate adaptations to viral tolerance and disease resistance

Morales, A. E., Dong, Y., Brown, T., Baid, K., Kontopoulos, D. G., Gonzalez, V., Huang, Z., Ahmed, A.-W., Bhuinya, A., Hilgers, L., et al. (2025) · Nature

Bat Biology and Ecology Studiesinterferon and immune responses

Cited by 78

Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish

Hiller, M., Agarwal, S., Notwell, J. H., Parikh, R., Guturu, H., Wenger, A. M., & Bejerano, G. (2013) · Nucleic Acids Research

Genomics and Phylogenetic StudiesGenomics and Chromatin Dynamics

Cited by 72

Controlling for phylogenetic relatedness and evolutionary rates improves the discovery of associations between species’ phenotypic and genomic differences

Prudent, X., Parra, G., Schwede, P., Roscito, J. G., & Hiller, M. (2016) · Molecular Biology and Evolution

Genomics and Phylogenetic StudiesEvolution and Genetic Dynamics

Cited by 71

The mole genome reveals regulatory rearrangements associated with adaptive intersexuality

M. Real, F., Haas, S. A., Franchini, P., Xiong, P., Simakov, O., Kuhl, H., Schöpflin, R., Heller, D., Moeinzadeh, M.-H., Heinrich, V., et al. (2020) · Science

Genetic and Clinical Aspects of Sex Determination and Chromosomal AbnormalitiesSexual Differentiation and Disorders

Cited by 66

Gene losses in the common vampire bat illuminate molecular adaptations to blood feeding

Blumer, M., Brown, T., Freitas, M. B., Destro, A. L., Oliveira, J. A., Morales, A. E., Schell, T., Greve, C., Pippel, M., Jebb, D., et al. (2022) · Science Advances

Bat Biology and Ecology StudiesGenomics and Phylogenetic Studies

Cited by 65

Single-nucleotide polymorphisms in NAGNAG acceptors are highly predictive for variations of alternative splicing

Hiller, M., Huse, K., Szafranski, K., Jahn, N., Hampe, J., Schreiber, S., Backofen, R., & Platzer, M. (2006) · The American Journal of Human Genetics

RNA Research and SplicingGenetic Associations and Epidemiology

Cited by 54

Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation

Sharma, V., Elghafari, A., & Hiller, M. (2016) · Nucleic Acids Research

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 47

Convergent and lineage-specific genomic differences in limb regulatory elements in limbless reptile lineages

Roscito, J. G., Sameith, K., Kirilenko, B. M., Hecker, N., Winkler, S., Dahl, A., Rodrigues, M. T., & Hiller, M. (2022) · Cell Reports

Developmental Biology and Gene RegulationChromosomal and Genetic Variations

Cited by 44

CESAR 2.0 substantially improves speed and accuracy of comparative gene annotation

Sharma, V., Schwede, P., & Hiller, M. (2017) · Bioinformatics

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 42

Transition to an aquatic habitat permitted the repeated loss of the pleiotropic KLK8 gene in mammals

Hecker, N., Sharma, V., & Hiller, M. (2017) · Genome Biology and Evolution

Evolution and Paleontology StudiesEvolution and Genetic Dynamics

Cited by 34

Quest for Orthologs in the Era of Biodiversity Genomics

Langschied, F., Bordin, N., Cosentino, S., Fuentes-Palacios, D., Glover, N., Hiller, M., Hu, Y., Huerta-Cepas, J., Coelho, L. P., Iwasaki, W., et al. (2024) · Genome Biology and Evolution

Genomics and Phylogenetic StudiesBioinformatics and Genomic Networks

Cited by 26

Vision-related convergent gene losses reveal SERPINE3’s unknown role in the eye

Indrischek, H., Hammer, J., Machate, A., Hecker, N., Kirilenko, B., Roscito, J., Hans, S., Norden, C., Brand, M., & Hiller, M. (2022) · eLife

Retinal Development and DisordersOcular Disorders and Treatments

Cited by 21

Accurate, comprehensive gene annotation and ortholog identification across thousands of vertebrate genomes with TOGA2

Malovichko, Y. V., Bein, B., Gonzales-Irribarren, A., Leushkin, E., Hilgers, L., Stephen, A., Yi, X., Albertini, M., Stadager, T., Zumpt, M., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory)

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 5

The landscape of gene loss and missense variation across the mammalian tree informs on gene essentiality

Liao, C., Ye, R., Ivankovic, F., Fu, J. M., Walters, R., Lowther, C., Valkanas, E., Churchhouse, C., Samocha, K. E., Lindblad-Toh, K., et al. (2026) · Nature Genetics

Genomics and Rare DiseasesGenetic Associations and Epidemiology

Cited by 0