Cited by 1,757Genomics and Phylogenetic StudiesGenomics and Chromatin DynamicsChromosomal and Genetic Variations

The DOI matches its Crossref record; 27 of the 28 references it cites were found in a registry or an index.

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

Open access

Davydov, Eugene V., Goode, David L., Sirota, Marina, Cooper, Gregory M., Sidow, Arend, Batzoglou, Serafim·2010·PLoS Computational Biology

DOI 10.1371/journal.pcbi.1001025PMC PMC2996323

Open this paper in CoChat — free account Open PDF

Abstract

Computational efforts to identify functional elements within genomes leverage comparative sequence information by looking for regions that exhibit evidence of selective constraint. One way of detecting constrained elements is to follow a bottom-up approach by computing constraint scores for individual positions of a multiple alignment and then defining constrained elements as segments of contiguous, highly scoring nucleotide positions. Here we present GERP++, a new tool that uses maximum likelihood evolutionary rate estimation for position-specific scoring and, in contrast to previous bottom-up methods, a novel dynamic programming approach to subsequently define constrained elements. GERP++ evaluates a richer set of candidate element breakpoints and ranks them based on statistical significance, eliminating the need for biased heuristic extension techniques. Using GERP++ we identify over 1.3 million constrained elements spanning over 7% of the human genome. We predict a higher fraction than earlier estimates largely due to the annotation of longer constrained elements, which improves one to one correspondence between predicted elements with known functional sequences. GERP++ is an efficient and effective tool to provide both nucleotide- and element-level constraint scores within deep multiple sequence alignments.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1371/journal.pcbi.1001025

Cites

27 of 27 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
Maximum Likelihood from Incomplete Data Via the EM Algorithm
Dempster, A. P., Laird, N. M., & Rubin, D. B. (1977) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1977.tb01600.x · Cited by 50,444
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
Kimura, M. (1980) · Journal of Molecular Evolution · doi:10.1007/bf01731581 · Cited by 29,778
Numerical recipes in C: the art of scientific computing
(1993) · Choice Reviews Online · doi:10.5860/choice.30-5638 · Cited by 17,933
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571
Numerical recipes in Pascal: the art of scientific computing
(1990) · Choice Reviews Online · doi:10.5860/choice.27-5158 · Cited by 12,040
Evolution of Protein Molecules
JUKES, T. H., & CANTOR, C. R. (1969) · Mammalian Protein Metabolism · doi:10.1016/b978-1-4832-3211-9.50009-7 · Cited by 11,032
The Human Genome Browser at UCSC
Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., & Haussler, A. D. (2002) · Genome Research · doi:10.1101/gr.229102 · Cited by 10,400
Dating of the human–ape splitting by a molecular clock of mitochondrial DNA.
Hasegawa, M., Kishino, H., & Yano, T.-A. (1985) · Journal of Molecular Evolution · doi:10.1007/bf02101694 · Cited by 8,687
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
The ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223

Flagged first, then by citations

Show all 28 references

1 of the 28 references couldn’t be matched to a known paper.

Sorted by citations

Items 701–800 of 1,000

Cancer driver mutation prediction through Bayesian integration of multi-omic data
Wang, Z., Ng, P. K., Chen, T., Kim, T., Wang, F., Shaw, K. M., Scott, K. L., Meric‐Bernstam, F., Mills, G. B., & Chen, K. (2018) · PLoS ONE · doi:10.1371/journal.pone.0196939 · Cited by 21
Prioritization of Variants Detected by Next Generation Sequencing According to the Mutation Tolerance and Mutational Architecture of the Corresponding Genes
Roca, I., Marmiesse, A. F., Gouveia, S., Segovia, M., & Couce, M. L. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19061584 · Cited by 22
Novel compound mutations in the mitochondrial translation elongation factor (TSFM) gene cause severe cardiomyopathy with myocardial fibro-adipose replacement
Perli, E., Pisano, A., Glasgow, R. I. C., Carbo, M., Hardy, S. A., Falkous, G., He, L., Cerbelli, B., Pignataro, M. G., Zacara, E., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-41483-9 · Cited by 21
Correlation between Genotype and Phenotype in 69 Chinese Patients with USH2A Mutations: A comparative study of the patients with Usher Syndrome and Nonsyndromic Retinitis Pigmentosa
Meng, X., Liu, X., Li, Y., Guo, T., & Yang, L. (2020) · Acta Ophthalmologica · doi:10.1111/aos.14626 · Cited by 21
Genetic Determinants and Genotype-Phenotype Correlations in Vietnamese Patients With Dilated Cardiomyopathy
Nguyen, V., Vu, M. T. T., Do, T. N. P., Tran, T. H. N., Hao, T., Nguyen, T. M. H., Huynh, B. N. T., Le, L. A., Pham, N. T. N., Nguyen, T. D. A., et al. (2021) · Circulation Journal · doi:10.1253/circj.cj-21-0077 · Cited by 21
Radionuclide partitioning coefficients in soils and plants and their correlation.
Sheppard, M. I. (1985) · PubMed · Cited by 21
Machine Learning Classification and Structure–Functional Analysis of Cancer Mutations Reveal Unique Dynamic and Network Signatures of Driver Sites in Oncogenes and Tumor Suppressor Genes
Agajanian, S., Odeyemi, O., Bischoff, N., Ratra, S., & Verkhivker, G. M. (2018) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.8b00414 · Cited by 20
A Deep Learning Framework Identifies Pathogenic Noncoding Somatic Mutations from Personal Prostate Cancer Genomes
Wang, C., & Li, J. (2020) · Cancer Research · doi:10.1158/0008-5472.can-20-1791 · Cited by 21
SuRFing the genomics wave: an R package for prioritising SNPs by functionality
Ryan, N., Morris, S. W., Porteous, D. J., Taylor, M. S., & Evans, K. L. (2014) · Genome Medicine · doi:10.1186/s13073-014-0079-1 · Cited by 21
Integration of mtDNA pseudogenes into the nuclear genome coincides with speciation of the human genus. A hypothesis
Владимирович, Г. К., Peshkin, L., Popadin, K. Y., Annis, S., Ackermann, R., & Khrapko, K. (2016) · Mitochondrion · doi:10.1016/j.mito.2016.12.001 · Cited by 20
A homozygous mutation p.Arg2167Trp in FREM2 causes isolated cryptophthalmos
Qian, Y., Lin, B., Xie, S., Gao, S., Li, W., Liu, Y., Wang, H., Huang, D., & Xie, Z. (2018) · Human Molecular Genetics · doi:10.1093/hmg/ddy144 · Cited by 20
Genetic Variation in Pan Species Is Shaped by Demographic History and Harbors Lineage-Specific Functions
Han, S., Andrés, A. M., Marquès‐Bonet, T., & Kuhlwilm, M. (2019) · Genome Biology and Evolution · doi:10.1093/gbe/evz047 · Cited by 20
Heterozygous TLR3 Mutation in Patients with Hantavirus Encephalitis
Partanen, T., Chen, J., Lehtonen, J., Kuismin, O., Rusanen, H., Vapalahti, O., Vaheri, A. I., Anttila, V., Bode, M. K., Hautala, N. M., et al. (2020) · Journal of Clinical Immunology · doi:10.1007/s10875-020-00834-2 · Cited by 20
DGAT1 mutations leading to delayed chronic diarrhoea: a case report
Xu, L., Gu, W., Luo, Y., Lou, J., & Chen, J. (2020) · BMC Medical Genetics · doi:10.1186/s12881-020-01164-1 · Cited by 20
Detection of Disease-Causing SNVs/Indels and CNVs in Single Test Based on Whole Exome Sequencing: A Retrospective Case Study in Epileptic Encephalopathies
Sun, D., Liu, Y., Cai, W., Ma, J., Ni, K., Chen, M., Wang, C., Liu, Y., Zhu, Y., Liu, Z., et al. (2021) · Frontiers in Pediatrics · doi:10.3389/fped.2021.635703 · Cited by 20
RNA polymerase mapping in plants identifies intergenic regulatory elements enriched in causal variants
Lozano, R. D., Booth, G. T., Yonis, B. O., Li, B., Buckler, E. S., Lis, J. T., Carpio, D. P. D., & Jannink, J. (2021) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkab273 · Cited by 23
Recessive variants in COL25A1 gene as novel cause of arthrogryposis multiplex congenita with ocular congenital cranial dysinnervation disorder
Benito, D. N., Jurgens, J. A., Yeung, A., Zaharieva, I. T., Manzur, A. Y., DiTroia, S. P., Gioia, S. A. D., Pais, L. S., Pini, V., Barry, B. J., et al. (2022) · Human Mutation · doi:10.1002/humu.24333 · Cited by 20
The PRC2-binding long non-coding RNAs in human and mouse genomes are associated with predictive sequence features
Tu, S., Yuan, G., & Shao, Z. (2017) · Scientific Reports · doi:10.1038/srep41669 · Cited by 20
Population genomics of the muskox' resilience in the near absence of genetic variation
Pečnerová, P., Lord, E., Garcia‐Erill, G., Hanghøj, K., Rasmussen, M. S., Meisner, J., Liu, X., van der Valk, T., Santander, C. G., Quinn, L., et al. (2024) · Molecular Ecology · doi:10.1111/mec.17205 · Cited by 19
The Spectra of Disease-Causing Mutations in the Ferroportin 1 (SLC40A1) Encoding Gene and Related Iron Overload Phenotypes (Hemochromatosis Type 4 and Ferroportin Disease)
Uguen, K., Ka, C., Collod‐Béroud, G., Tertre, M. L., Guellec, J., Férec, C., Béroud, C., Callebaut, I., & Gac, G. L. (2023) · Human Mutation · doi:10.1155/2023/5162256 · Cited by 21
Rational Redomestication for Future Agriculture
Wang, N., Li, H., & Huang, S. (2025) · Annual Review of Plant Biology · doi:10.1146/annurev-arplant-083123-064726 · Cited by 19
Functional assessment of all ATM SNVs using prime editing and deep learning
Lee, K. S., Min, J.-G., Cheong, Y., Oh, H.-C., Jung, S.-Y., Park, J., Song, M., Seo, J. H., Cho, S., & Kim, S. (2025) · Cell · doi:10.1016/j.cell.2025.05.046 · Cited by 24
Pathways systematically associated to Hirschsprung’s disease
Fernández, R. M., Bleda, M., Luzón‐Toro, B., García‐Alonso, L., Arnold, S. M., Sribudiani, Y., Besmond, C., Lantieri, F., Doan, B. Q., Ceccherini, I., et al. (2013) · Orphanet Journal of Rare Diseases · doi:10.1186/1750-1172-8-187 · Cited by 19
What does the distribution of fitness effects of new mutations reflect? Insights from plants
Chen, J., Bataillon, T. M., Glémin, S., & Lascoux, M. (2021) · New Phytologist · doi:10.1111/nph.17826 · Cited by 19
Prevalence of Monogenic Bone Disorders in a Dutch Cohort of Atypical Femur Fracture Patients
Zhou, W. Z., van Rooij, J., van de Laarschot, D. M., Zervou, Z., Brüggenwirth, H. T., Appelman‐Dijkstra, N. M., Ebeling, P. R., Demirdas, S., Verkerk, A. J. M. H., & Zillikens, M. C. (2020) · Journal of Bone and Mineral Research · doi:10.1002/jbmr.4801 · Cited by 19
Poison exon annotations improve the yield of clinically relevant variants in genomic diagnostic testing
Felker, S. A., Lawlor, J. M. J., Hiatt, S. M., Thompson, M. L., Latner, D. R., Finnila, C. R., Bowling, K. M., Bonnstetter, Z. T., Bonini, K. E., Kelly, N., et al. (2023) · Genetics in Medicine · doi:10.1016/j.gim.2023.100884 · Cited by 19
Self-citation
Variants in the WDR44 WD40-repeat domain cause a spectrum of ciliopathy by impairing ciliogenesis initiation
Accogli, A., Shakya, S., Yang, T., Insinna, C., Kim, S. Y., Bell, D. R., Butov, K. R., Severino, M., Niceta, M., Scala, M., et al. (2024) · Nature Communications · doi:10.1038/s41467-023-44611-2 · Cited by 19
Resolving clinical diagnoses for syndromic cleft lip and/or palate phenotypes using whole‐exome sequencing
Pengelly, R. J., Upstill‐Goddard, R., Arias, L., Martínez, J., Gibson, J., Knut, M., Collins, A., Ennis, S., Collins, A., & Briceno, I. (2014) · Clinical Genetics · doi:10.1111/cge.12547 · Cited by 19
Transcription initiation arising from E-cadherin/CDH1 intron2: a novel protein isoform that increases gastric cancer cell invasion and angiogenesis†
Pinheiro, H. C., Carvalho, J., Oliveira, P., Ferreira, D. A., Pinto, M. T., Osório, H., Licastro, D., Bordeira–Carriço, R., Jordan, P., Lazarević, D., et al. (2012) · Human Molecular Genetics · doi:10.1093/hmg/dds248 · Cited by 20
POLG2 deficiency causes adult‐onset syndromic sensory neuropathy, ataxia and parkinsonism
Maldergem, L. V., Besse, A., Paepe, B. D., Blakely, E. L., Appadurai, V., Humble, M. M., Piard, J., Craig, K., He, L., Hella, P., et al. (2016) · Annals of Clinical and Translational Neurology · doi:10.1002/acn3.361 · Cited by 19
Exome Sequencing Analysis: A Guide to Disease Variant Detection
Isakov, O., Perrone, M. E., & Shomron, N. (2013) · Methods in molecular biology · doi:10.1007/978-1-62703-514-9_8 · Cited by 19
Genotype-phenotype correlations and expansion of the molecular spectrum of AP4M1-related hereditary spastic paraplegia
Bettencourt, C., Salpietro, V., Efthymiou, S., Chelban, V., Hughes, D., Pittman, A. M., Federoff, M., Bourinaris, T., Spilioti, M. G., Deretzi, G., et al. (2017) · Orphanet Journal of Rare Diseases · doi:10.1186/s13023-017-0721-2 · Cited by 19
Towards a map of cis-regulatory sequences in the human genome
Niu, M., Tabari, E. S., Ni, P., & Su, Z. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky338 · Cited by 19
De novopattern discovery enables robust assessment of functional consequences of non-coding variants
Hai, Y., Chen, R., Wang, Q., Wei, Q., Ji, Y., Zheng, G., Zhong, X. Y., Cox, N. J., & Li, B. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty826 · Cited by 19
Regulatory genome variants in human susceptibility to infection
Telenti, A., & di Iulio, J. (2019) · Human Genetics · doi:10.1007/s00439-019-02091-9 · Cited by 19
Expanding Clinical Presentations Due to Variations in THOC2 mRNA Nuclear Export Factor
Kumar, R., Palmer, E. E., Gardner, A. E., Carroll, R., Banka, S., Abdelhadi, O., Donnai, D., Elgersma, Y., Curry, C. J., Gardham, A., et al. (2020) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2020.00012 · Cited by 20
Factor 8 Gene Mutation Spectrum of 270 Patients with Haemophilia A: Identification of 36 Novel Mutations
Atık, T., Işık, E., Önay, H., Akgün, B., Kavaklı, K., Evim, M. S., Tüysüz, G., Özbek, N. Y., Şahin, F., Şalcıoğlu, Z., et al. (2020) · Turkish Journal of Hematology · doi:10.4274/tjh.galenos.2020.2019.0262 · Cited by 19
Improving the informativeness of Mendelian disease-derived pathogenicity scores for common disease
Kim, S. S., Dey, K. K., Weissbrod, O., Márquez‐Luna, C., Gazal, S., & Price, A. L. (2020) · Nature Communications · doi:10.1038/s41467-020-20087-2 · Cited by 19
DGCR8-dependent efficient pri-miRNA processing of human pri-miR-9-2
Nogami, M., Miyamoto, K., Hayakawa‐Yano, Y., Nakanishi, A., Yano, M., & Okano, H. (2021) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2021.100409 · Cited by 19
Massive parallel sequencing questions the pathogenic role of missense variants in dilated cardiomyopathy
Dalin, M. G., Engström, P. G., Ivarsson, E. G., Unneberg, P., Light, S., Schaufelberger, M., Gilljam, T., Andersson, B., & Bergö, M. O. (2016) · International Journal of Cardiology · doi:10.1016/j.ijcard.2016.11.066 · Cited by 19
Axon guidance pathways served as common targets for human speech/language evolution and related disorders
Lei, H., Yan, Z., Sun, X., Zhang, Y., Wang, J., Ma, C., Xu, Q., Wang, R., Jarvis, E. D., & Sun, Z. (2017) · Brain and Language · doi:10.1016/j.bandl.2017.06.007 · Cited by 18
Integrating population genomics and environmental data to predict adaptation to climate change in post-bottleneck Tibetan macaques
Teng, Y., Li, W., Wang, X., Zhang, R., Shen, Y., Wu, R., Liu, J., Zhang, M., Roos, C., Li, J., et al. (2025) · Science Advances · doi:10.1126/sciadv.adw0562 · Cited by 18
From Genome-Wide Association Studies to Functional Genomics: New Insights Into Cardiovascular Disease
McPherson, R. (2012) · Canadian Journal of Cardiology · doi:10.1016/j.cjca.2012.08.017 · Cited by 18
Genome sequencing data analysis for rare disease gene discovery
Umlai, U. I., Bangarusamy, D. K., Estivill, X., & Jithesh, P. V. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab363 · Cited by 20
BayesPI-BAR: a new biophysical model for characterization of regulatory sequence variations
Wang, J., & Batmanov, K. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv733 · Cited by 18
Exome sequencing of a patient with suspected mitochondrial disease reveals a likely multigenic etiology
Craigen, W. J., Graham, B. H., Wong, L. C., Scaglia, F., Lewis, R. A., & Bonnen, P. E. (2013) · BMC Medical Genetics · doi:10.1186/1471-2350-14-83 · Cited by 18
EP300基因通过调控一氧化氮合成帮助藏族人群适应高原低氧环境
郭永博, Zheng, W.-S., 和耀喜, 崔超英, Deji, Q., 白马康卓, 多吉卓玛, Duoji, Z., 边巴, 彭忆, et al. (2017) · 动物学研究 · doi:10.24272/j.issn.2095-8137.2017.036 · Cited by 18
Natural selection beyond genes: Identification and analyses of evolutionarily conserved elements in the genome of the collared flycatcher (Ficedula albicollis)
Craig, R. J., Suh, A., Mi, W., & Ellegren, H. (2017) · Molecular Ecology · doi:10.1111/mec.14462 · Cited by 18
Association of IL17RC and COL6A1 genetic polymorphisms with susceptibility to ossification of the thoracic posterior longitudinal ligament in Chinese patients
Wang, P., Liu, X., Zhu, B., Ma, Y., Lei, Y. H., Teng, Z., Liang, C., He, G., & Liu, X. (2018) · Journal of Orthopaedic Surgery and Research · doi:10.1186/s13018-018-0817-y · Cited by 18
A Pipeline for Classifying Deleterious Coding Mutations in Agricultural Plants
Kovalev, M. S., Igolkina, A. A., Samsonova, M. G., & Nuzhdin, S. V. (2018) · Frontiers in Plant Science · doi:10.3389/fpls.2018.01734 · Cited by 18
Actionable Pharmacogenetic Variation in the Slovenian Genomic Database
Hočevar, K., Maver, A., & Peterlin, B. (2019) · Frontiers in Pharmacology · doi:10.3389/fphar.2019.00240 · Cited by 19
FunSPU: A versatile and adaptive multiple functional annotation-based association test of whole-genome sequencing data
Ma, Y., & Wei, P. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008081 · Cited by 19
Comprehensive functional annotation of susceptibility variants associated with asthma
Gautam, Y., Afanador, Y., Ghandikota, S. K., & Baye, T. M. (2020) · Human Genetics · doi:10.1007/s00439-020-02151-5 · Cited by 18
Phenotypic expansion in KIF1A ‐related dominant disorders: A description of novel variants and review of published cases
Montenegro‐Garreaud, X., Hansen, A. W., Khayat, M. M., Chander, V., Grochowski, C. M., Jiang, Y., Li, H., Mitani, T., Kessler, E., Jayaseelan, J. C., et al. (2020) · Human Mutation · doi:10.1002/humu.24118 · Cited by 18
Strong Heterogeneity in Mutation Rate Causes Misleading Hallmarks of Natural Selection on Indel Mutations in the Human Genome
Kvikstad, E. M., & Duret, L. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst185 · Cited by 18
Analysis of CH25H in multiple sclerosis and neuromyelitis optica
Forwell, A. L., Bernales, C. Q., Ross, J. P., Yee, I. M. L., Encarnacion, M. J., Lee, J. D., Sadovnick, A. D., Traboulsee, A. L., & Vilariño‐Güell, C. (2015) · Journal of Neuroimmunology · doi:10.1016/j.jneuroim.2015.12.014 · Cited by 18
Innovation in cancer pharmacotherapy through integrative consideration of germline and tumor genomes
Tremmel, R., Hübschmann, D., Schaeffeler, E., Pirmann, S., Fröhling, S., & Schwab, M. (2024) · Pharmacological Reviews · doi:10.1124/pharmrev.124.001049 · Cited by 17
Cis-regulatory elements: systematic identification and horticultural applications
Li, T., Zeng, W., Zhu, F., & Lü, P. (2025) · aBIOTECH · doi:10.1007/s42994-025-00237-0 · Cited by 17
Identification of missense MAB21L1 variants in microphthalmia and aniridia
Seese, S. E., Reis, L. M., Deml, B., Griffith, C. B., Reich, A., Jamieson, R. V., & Semina, E. V. (2021) · Human Mutation · doi:10.1002/humu.24218 · Cited by 17
VIP‐HL: Semi‐automated ACMG/AMP variant interpretation platform for genetic hearing loss
Peng, J., Xiang, J., Jin, X., Meng, J., Song, N., Chen, L., Tayoun, A. N. A., & Peng, Z. (2021) · Human Mutation · doi:10.1002/humu.24277 · Cited by 17
Estimated prevalence of Niemann–Pick type C disease in Quebec
Labrecque, M., Touma, L., Bhérer, C., Duquette, A., & Tétreault, M. (2021) · Scientific Reports · doi:10.1038/s41598-021-01966-0 · Cited by 17
An Integrated Phenotypic and Genotypic Approach Reveals a High‐Risk Subtype Association for EBF3 Missense Variants Affecting the Zinc Finger Domain
Deisseroth, C. A., Lerma, V. C., Magyar, C. L., Pfliger, J. M., Nayak, A., Bliss, N. D., LeMaire, A. W., Narayanan, V., Balak, C. D., Zanni, G., et al. (2022) · Annals of Neurology · doi:10.1002/ana.26359 · Cited by 17
Deleterious Mutations and the Rare Allele Burden on Rice Gene Expression
Lye, Z. N., Choi, J. Y., & Purugganan, M. D. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac193 · Cited by 17
Pathogenic variants inGCSHencoding the moonlighting H-protein cause combined nonketotic hyperglycinemia and lipoate deficiency
Arribas‐Carreira, L., Dallabona, C., Swanson, M. A., Farris, J. D., Østergaard, E., Tsiakas, K., Hempel, M., Acquaviva, C., Koutsoukos, S. A., Stence, N. V., et al. (2022) · Human Molecular Genetics · doi:10.1093/hmg/ddac246 · Cited by 17
Loss-of-function variants in KCTD19 cause non-obstructive azoospermia in humans
Liu, J., Rahim, F., Zhou, J., Fan, S., Jiang, H., Yu, C., Chen, J., Xu, J., Yang, G., Shah, W., et al. (2023) · iScience · doi:10.1016/j.isci.2023.107193 · Cited by 17
Strategies to Design and Analyze Targeted Sequencing Data
Lin, H., Wang, M., Brody, J. A., Bis, J. C., Dupuis, J., Lumley, T., McKnight, B., Rice, K. M., Sitlani, C. M., Reid, J. G., et al. (2014) · Circulation Cardiovascular Genetics · doi:10.1161/circgenetics.113.000350 · Cited by 17
Truncating and missense PPM1D mutations in early‐onset and/or familial/hereditary prostate cancer patients
Cardoso, M., Paulo, P., Maia, S., & Teixeira, M. R. (2016) · Genes Chromosomes and Cancer · doi:10.1002/gcc.22393 · Cited by 17
Genome Sequence Variability Predicts Drug Precautions and Withdrawals from the Market
Lee, K. H., Baik, S. Y., Lee, S., Park, C. H., Park, P. J., & Kim, J. H. (2016) · PLoS ONE · doi:10.1371/journal.pone.0162135 · Cited by 17
The Cumulative Effects of the MYH7-V878A and CACNA1C-A1594V Mutations in a Chinese Family with Hypertrophic Cardiomyopathy
Wang, B., Guo, R., Wang, J., Yang, F., Zuo, L., Liu, Y., Shao, H., Ju, Y., Sun, C., Xu, L., et al. (2017) · Cardiology · doi:10.1159/000478900 · Cited by 17
A novel mutation of the EYA4 gene associated with post-lingual hearing loss in a proband is co-segregating with a novel PAX3 mutation in two congenitally deaf family members
Cesca, F., Bettella, E., Polli, R., Cama, E., Scimemi, P., Santarelli, R., & Murgia, A. (2017) · International Journal of Pediatric Otorhinolaryngology · doi:10.1016/j.ijporl.2017.10.042 · Cited by 17
Germline Variants in the POT1-Gene in High-Risk Melanoma Patients in Austria
Müller, C., Krunic, M., Wendt, J., von Haeseler, A., & Okamoto, I. (2018) · G3 Genes Genomes Genetics · doi:10.1534/g3.117.300394 · Cited by 17
Predicting variant deleteriousness in non-human species: applying the CADD approach in mouse
Groß, C., de Ridder, D., & Reinders, M. J. T. (2018) · BMC Bioinformatics · doi:10.1186/s12859-018-2337-5 · Cited by 17
ARMC5 Variants and Risk of Hypertension in Blacks: MH‐GRID Study
Zilbermint, M. F., Gaye, A., Berthon, A. S., Hannah‐Shmouni, F., Faucz, F. R., Lodish, M. B., Davis, A. R., Gibbons, G. H., & Stratakis, C. A. (2019) · Journal of the American Heart Association · doi:10.1161/jaha.119.012508 · Cited by 18
A Recurrent Rare SOX9 Variant (M469V) is Associated with Congenital Vertebral Malformations
Wu, N., Wang, L., Hu, J., Zhao, S., Liu, B., Li, Y., Du, H., Zhang, Y., Li, X., Yan, Z., et al. (2019) · Current Gene Therapy · doi:10.2174/1566523219666190924120307 · Cited by 17
MosaicBase: A Knowledgebase of Postzygotic Mosaic Variants in Noncancer Disease-Related and Healthy Human Individuals
Yang, X., Yang, C., Zheng, X., Xiong, L., Tao, Y., Wang, M., Ye, A. Y., Wu, Q., Dou, Y., Luo, J., et al. (2020) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2020.05.002 · Cited by 17
SVPath: an accurate pipeline for predicting the pathogenicity of human exon structural variants
Yang, Y., Wang, X., Zhou, D., Wei, D., & Peng, S. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac014 · Cited by 17
Whole exome sequencing in inborn errors of immunity: use the power but mind the limits
Bucciol, G., Nieuwenhove, E. V., Moens, L., Itan, Y., & Meyts, I. (2017) · Current Opinion in Allergy and Clinical Immunology · doi:10.1097/aci.0000000000000398 · Cited by 18
Generalising better: Applying deep learning to integrate deleteriousness prediction scores for whole-exome SNV studies
Korvigo, I. O., Afanasyev, A., Romashchenko, N., & Skoblov, M. Y. (2018) · PLoS ONE · doi:10.1371/journal.pone.0192829 · Cited by 17
Expanding the mutational spectrum of monogenic hypogonadotropic hypogonadism: novel mutations in ANOS1 and FGFR1 genes
Gach, A., Pinkier, I., Szarras‐Czapnik, M., Sakowicz, A., & Jakubowski, L. (2020) · Reproductive Biology and Endocrinology · doi:10.1186/s12958-020-0568-6 · Cited by 17
Bardet–Biedl syndrome in two unrelated patients with identical compound heterozygous SCLT1 mutations
Morisada, N., Hamada, R., Miura, K., Ye, M. J., Nozu, K., Hattori, M., & Iijima, K. (2020) · CEN Case Reports · doi:10.1007/s13730-020-00472-y · Cited by 17
Regulation of Sex Determination in Mice by a Non-coding Genomic Region
Arboleda, V. A., Fleming, A. A., Barseghyan, H., Délot, E. C., Sinsheimer, J. S., & Vilain, E. J. N. (2014) · Genetics · doi:10.1534/genetics.113.160259 · Cited by 16
Phylogenomic analysis points to a South American origin of Manihot and illuminates the primary gene pool of cassava
Simon, M. F., F., J. M. M., Liu, H., Martins, M. L. L., Drovetski, S. V., Przelomska, N. A. S., Loiselle, H., Cavalcanti, T. B., Inglis, P. W., Mueller, N. G., et al. (2021) · New Phytologist · doi:10.1111/nph.17743 · Cited by 17
Familial Exudative Vitreoretinopathy With and Without Pathogenic Variants of Norrin/β-Catenin Signaling Genes
Kondo, H., Tsukahara‐Kawamura, T., Matsushita, I., Nagata, T., Hayashi, T., Nishina, S., Higasa, K., Uchio, E., Kondo, M., Sakamoto, T., et al. (2024) · Ophthalmology Science · doi:10.1016/j.xops.2024.100514 · Cited by 16
PHACTboost: A Phylogeny-Aware Pathogenicity Predictor for Missense Mutations via Boosting
Dereli, O., Kuru, N., Akkoyun, E., Bırcan, A., Taştan, Ö., & Adebalı, O. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae136 · Cited by 17
Inference of Evolutionary Forces Acting on Human Biological Pathways
Daub, J. T., Dupanloup, I., Robinson‐Rechavi, M., & Excoffier, L. (2015) · Genome Biology and Evolution · doi:10.1093/gbe/evv083 · Cited by 17
Novel HARS2 missense variants identified in individuals with sensorineural hearing impairment and Perrault syndrome
Karstensen, H. G., Rendtorff, N. D., Hindbæk, L. S., Colombo, R., Stein, A., Birkebæk, N., Hartmann‐Petersen, R., Lindorff‐Larsen, K., Højland, A. T., Petersen, M. B., et al. (2019) · European Journal of Medical Genetics · doi:10.1016/j.ejmg.2019.103733 · Cited by 16
Functional disease architectures reveal unique biological role of transposable elements
Hormozdiari, F., van de Geijn, B., Nasser, J., Weissbrod, O., Gazal, S., Ju, C. J. ‐., O’Connor, L. J., Hujoel, M. L. A., Engreitz, J., Hormozdiari, F., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-11957-5 · Cited by 17
Genetic variations in olfactory receptor gene OR2AG2 in a large multigenerational family with asthma
Chakraborty, S., Dakle, P., Sinha, A., Vishweswaraiah, S., Nagori, A., Salimath, S., Prakash, Y. S., Lodha, R., Kabra, S. K., Ghosh, B., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-54718-6 · Cited by 16
Statistical Methods in Genome-Wide Association Studies
Sun, N., & Zhao, H. (2020) · Annual Review of Biomedical Data Science · doi:10.1146/annurev-biodatasci-030320-041026 · Cited by 16
Identification of a Pathogenic TGFBR2 Variant in a Patient With Loeys–Dietz Syndrome
Luo, X., Deng, S., Jiang, Y., Wang, X., Al-raimi, A. M. A., Wu, L., Liu, X., Song, Y., Chen, X., & Zhu, F. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.00479 · Cited by 16
Positive natural selection of N6-methyladenosine on the RNAs of processed pseudogenes
Tan, L., Cheng, W., Liu, F., Wang, D. O., Wu, L., Cao, N., & Wang, J. (2021) · Genome biology · doi:10.1186/s13059-021-02402-2 · Cited by 16
Landscape of TP53 Alterations in Chronic Lymphocytic Leukemia via Data Mining Mutation Databases
Soussi, T., & Baliakas, P. (2022) · Frontiers in Oncology · doi:10.3389/fonc.2022.808886 · Cited by 16
DVPred: a disease-specific prediction tool for variant pathogenicity classification for hearing loss
Bu, F., Zhong, M., Chen, Q., Wang, Y., Zhao, X., Zhang, Q., Li, X., Booth, K. T. A., Azaiez, H., Lu, Y., et al. (2022) · Human Genetics · doi:10.1007/s00439-022-02440-1 · Cited by 16
An expanded phenotype centric benchmark of variant prioritisation tools
Anderson, D. R., & Lassmann, T. (2022) · Human Mutation · doi:10.1002/humu.24362 · Cited by 18
Systematic elucidation of genetic mechanisms underlying cholesterol uptake
Hamilton, M. C., Fife, J. D., Akinci, E., Yu, T., Khowpinitchai, B., Cha, M., Barkal, S., Thi, T. T., Yeo, G. H. T., Ramos Barroso, J. P., et al. (2023) · Cell Genomics · doi:10.1016/j.xgen.2023.100304 · Cited by 16
Dual Function of DNA Sequences: Protein-Coding Sequences Function as Transcriptional Enhancers
Hirsch, N., & Birnbaum, R. Y. (2015) · Perspectives in biology and medicine · doi:10.1353/pbm.2015.0026 · Cited by 17
Germline mutations in DNA repair genes may predict neoadjuvant therapy response in triple negative breast patients
Spugnesi, L., Gabriele, M., Scarpitta, R., Tancredi, M., Maresca, L., Gambino, G., Collavoli, A., Aretini, P., Bertolini, I., Salvadori, B., et al. (2016) · Genes Chromosomes and Cancer · doi:10.1002/gcc.22389 · Cited by 16
REforge associates transcription factor binding site divergence in regulatory elements with phenotypic differences between species
Langer, B. E., Roscito, J. G., & Hiller, M. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy187 · Cited by 8
A genome-wide association study identifies susceptibility loci for primary central nervous system lymphoma at 6p25.3 and 3p22.1: a LOC Network study
Labrèche, K., Daniau, M., Sud, A., Law, P., Royer-Perron, L., Holroyd, A., Broderick, P., Went, M., Benazra, M., Ahle, G., et al. (2019) · Neuro-Oncology · doi:10.1093/neuonc/noz088 · Cited by 16
PsyMuKB: An Integrative De Novo Variant Knowledge Base for Developmental Disorders
Lin, G. N., Guo, S., Xian, T., Wang, W., Qian, W., Song, W., Wang, J., Yu, S., Wang, Z., Cui, D., et al. (2019) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2019.10.002 · Cited by 16

Authors: Davydov, E. V., Goode, D. L., Sirota, M., Cooper, G. M., Sidow, A., & Batzoglou, S.
Affiliations: Stanford University (US)
Stanford Medicine (US)
Howard Hughes Medical Institute (US)
Corresponding author: Sidow, Arend
ORCID: Goode, David L.
Sirota, Marina
Cooper, Gregory M.
Sidow, Arend
Batzoglou, Serafim
Venue: PLoS Computational Biology
Publisher: Public Library of Science (PLoS)
Published: 2010-12-02
Volume: 6
Issue: 12
Pages: e1001025
ISSN: 1553-734X (ISSN-L)
1553-7358
DOI: 10.1371/journal.pcbi.1001025
PMC: PMC2996323
OpenAlex: W2038473742
Cited by: 1,757
References: 28
Citations by year: 2026: 105 · 2025: 116 · 2024: 128 · 2023: 134 · 2022: 142 · 2021: 174 · 2020: 156 · 2019: 164 · 2018: 134 · 2017: 107 · 2016: 118 · 2015: 100 · 2014: 69 · 2013: 71 · 2012: 25
FWCI: 14.08
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0/ (unspecified)
Locations: PLoS Computational Biology (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Figshare (submittedVersion, cc-by)
Minerva Access (University of Melbourne) (submittedVersion, cc-by)
Funders: National Science Foundation (0347952)
National Institutes of Health (LM007033)
National Human Genome Research Institute
U.S. National Library of Medicine (K22LM008261, LM007033, T15LM007033)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
Keywords: GERP, selective constraint, functional elements, human genome, sequence comparison, multiple sequence alignment, dynamic programming
MeSH terms: Algorithms, Animals, Humans, Mammals, Models, Genetic, Phylogeny, Software, User-Computer Interface, Genome, Human, Sequence Alignment, Sequence Analysis, DNA, Genomics

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks