Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302 · see citing works

Trimmomatic: a flexible trimmer for Illumina sequence data

Bolger, A. M., Lohse, M., & Usadel, B. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu170 · Cited by 65,548 · see citing works

The Sequence Alignment/Map format and SAMtools

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041 · see citing works

Fast gapped-read alignment with Bowtie 2

Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400 · see citing works

MUSCLE: multiple sequence alignment with high accuracy and high throughput

Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662 · see citing works

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

Kumar, S., Stecher, G., & Tamura, K. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw054 · Cited by 43,923 · see citing works

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Stamatakis, A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu033 · Cited by 32,291 · see citing works

HISAT: a fast spliced aligner with low memory requirements

Kim, D., Langmead, B., & Salzberg, S. L. (2015) · Nature Methods · doi:10.1038/nmeth.3317 · Cited by 24,112 · see citing works

BLAST+: architecture and applications

Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-421 · Cited by 22,074 · see citing works

The variant call format and VCFtools

Danecek, P., Auton, A., Abecasis, G. R., Albers, C. A., Banks, E., DePristo, M. A., Handsaker, R. E., Lunter, G. A., Marth, G., Sherry, S. T., et al. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr330 · Cited by 16,008 · see citing works

The sequence of the human genome

Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) · Science · doi:10.1126/science.1058040 · Cited by 13,909 · see citing works

PAML 4: Phylogenetic Analysis by Maximum Likelihood

Yang, Z. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm088 · Cited by 13,879 · see citing works

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V., & Zdobnov, E. M. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv351 · Cited by 13,344 · see citing works

BEAST: Bayesian evolutionary analysis by sampling trees

Drummond, A. J., & Rambaut, A. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-214 · Cited by 12,898 · see citing works

APE: Analyses of Phylogenetics and Evolution in R language

Paradis, E., Claude, J., & Strimmer, K. (2004) · Bioinformatics · doi:10.1093/bioinformatics/btg412 · Cited by 12,037 · see citing works

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w ¹¹¹⁸ ; iso-2; iso-3

Cingolani, P., Platts, A., Wang, L. L., Coon, M., Nguyen, T., Wang, L., Land, S. J., Lu, X., & Ruden, D. M. (2012) · Fly · doi:10.4161/fly.19695 · Cited by 11,816 · see citing works

Circos: An information aesthetic for comparative genomicsPreprint

Krzywinski, M. I., Schein, J. E., Birol, İ., Connors, J. M., Gascoyne, R. D., Horsman, D. E., Jones, S. J. M., & Marra, M. A. (2009) · Genome Research · doi:10.1101/gr.092759.109 · Cited by 10,838 · see citing works

Tandem repeats finder: a program to analyze DNA sequences

Benson, G. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.2.573 · Cited by 9,374 · see citing works

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

Thorvaldsdottir, H., Robinson, J. T., & Mesirov, J. P. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbs017 · Cited by 9,049 · see citing works

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

Li, H. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr509 · Cited by 6,283 · see citing works

Pfam: the protein families database

Finn, R. D., Bateman, A., Clements, J., Coggill, P., Eberhardt, R. Y., Eddy, S. R., Heger, A., Hetherington, K., Holm, L., Mistry, J., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1223 · Cited by 6,148 · see citing works

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

Li, L., Stoeckert, C. J., & Roos, D. S. (2003) · Genome Research · doi:10.1101/gr.1224503 · Cited by 5,707 · see citing works

Mammal Species of the World: A Taxonomic and Geographic Reference

Schmid, R., Wilson, D. E., & Reeder, D. M. (1993) · Taxon · doi:10.2307/1223169 · Cited by 5,384 · see citing works

KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases

Xie, C., Mao, X., Huang, J., Ding, Y., Wu, J., Dong, S., Kong, L., Gao, G., Li, C., & Wei, L. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr483 · Cited by 5,078 · see citing works

Quality control and preprocessing of metagenomic datasets

Schmieder, R., & Edwards, R. A. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr026 · Cited by 4,989 · see citing works

Wound Healing--Aiming for Perfect Skin Regeneration

Martin, P. B. (1997) · Science · doi:10.1126/science.276.5309.75 · Cited by 4,814 · see citing works

miRBase: annotating high confidence microRNAs using deep sequencing data

Kozomara, A., & Griffiths-Jones, S. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1181 · Cited by 4,629 · see citing works

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 4,408 · cited 1× · see citing works

Prediction of complete gene structures in human genomic DNA

Burge, C., & Karlin, S. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.0951 · Cited by 4,211 · see citing works

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

Haas, B. J., Salzberg, S. L., Zhu, W., Pertea, M., Allen, J., Orvis, J., White, O. R., Buell, C. R., & Wortman, J. R. (2008) · Genome biology · doi:10.1186/gb-2008-9-1-r7 · Cited by 4,051 · see citing works

Genome-wide efficient mixed-model analysis for association studies

Zhou, X., & Stephens, M. (2012) · Nature Genetics · doi:10.1038/ng.2310 · Cited by 3,627 · see citing works

Gene finding in novel genomes

Korf, I. F. (2004) · BMC Bioinformatics · doi:10.1186/1471-2105-5-59 · Cited by 3,160 · see citing works

Pathogen Recognition and Inflammatory Signaling in Innate Immune Defenses

Mogensen, T. H. (2009) · Clinical Microbiology Reviews · doi:10.1128/cmr.00046-08 · Cited by 3,122 · see citing works

Repbase Update, a database of repetitive elements in eukaryotic genomes

Bao, W., Kojima, K. K., & Kohany, O. (2015) · Mobile DNA · doi:10.1186/s13100-015-0041-9 · Cited by 3,014 · see citing works

De novo assembly of human genomes with massively parallel short read sequencing

Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G., Kristiansen, K., et al. (2010) · Genome Research · doi:10.1101/gr.097261.109 · Cited by 2,926 · see citing works

AUGUSTUS: ab initio prediction of alternative transcripts

Stanke, M., Keller, O., Gunduz, I., Hayes, A., Waack, S., & Morgenstern, B. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl200 · Cited by 2,829 · see citing works

GeneWise and GenomewisePreprint

Birney, E., Clamp, M. E., & Durbin, R. M. (2004) · Genome Research · doi:10.1101/gr.1865504 · Cited by 2,799 · see citing works

LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons

Xu, Z., & Wang, H. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm286 · Cited by 2,618 · see citing works

Inference of human population history from individual whole-genome sequences

Li, H., & Durbin, R. (2011) · Nature · doi:10.1038/nature10231 · Cited by 2,590 · see citing works

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

Zhang, C., Rabiee, M., Sayyari, E., & Mirarab, S. (2018) · BMC Bioinformatics · doi:10.1186/s12859-018-2129-y · Cited by 2,471 · see citing works

Scaffolding pre-assembled contigs using SSPACE.

Boetzer, M., Henkel, C. V., Jansen, H. J., Butler, D., & Pirovano, W. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btq683 · Cited by 2,337 · see citing works

Sideband cooling of micromechanical motion to the quantum ground state

Teufel, J. D., Donner, T., Li, D., Harlow, J., Allman, M., Cicak, K., Sirois, A. J., Whittaker, J. D., Lehnert, K. W., & Simmonds, R. W. (2011) · Nature · doi:10.1038/nature10261 · Cited by 2,100 · see citing works

The delayed rise of present-day mammals

Bininda-Emonds, O. R. P., Cardillo, M., Jones, K. E., MacPhee, R. D. E., Beck, R. M. D., Grenyer, R., Price, S. A., Vos, R. A., Gittleman, J. L., & Purvis, A. (2007) · Nature · doi:10.1038/nature05634 · Cited by 2,082 · see citing works

TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders

Majoros, W. H., Pertea, M., & Salzberg, S. L. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth315 · Cited by 1,938 · see citing works

r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock

Sanderson, M. J. (2003) · Bioinformatics · doi:10.1093/bioinformatics/19.2.301 · Cited by 1,906 · see citing works

Whole-genome analyses resolve early branches in the tree of life of modern birds

Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., Ho, S. Y. W., Faircloth, B. C., Nabholz, B., Howard, J. T., et al. (2014) · Science · doi:10.1126/science.1253451 · Cited by 1,901 · see citing works

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

Hahn, C., Bachmann, L., & Chevreux, B. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt371 · Cited by 1,854 · see citing works

Defining the role of common variation in the genomic and biological architecture of adult human height

The Electronic Medical Records and Genomics (eMERGE) Consortium, Wood, A. R., The MIGen Consortium, The PAGE Consortium, Study, T. L. C., Esko, T., Yang, J., Vedantam, S., Pers, T. H., Gustafsson, S., et al. (2014) · Nature Genetics · doi:10.1038/ng.3097 · Cited by 1,853 · see citing works

CAFE: a computational tool for the study of gene family evolution

De Bie, T., Cristianini, N., Demuth, J. P., & Hahn, M. W. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl097 · Cited by 1,790 · see citing works

Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks

Huson, D. H., & Scornavacca, C. (2012) · Systematic Biology · doi:10.1093/sysbio/sys062 · Cited by 1,674 · see citing works

A deletion in the bovine myostatin gene causes the double–muscled phenotype in cattle

Grobet, L., Royo Martin, L. J., Poncelet, D., Pirottin, D., Brouwers, B., Riquet, J., Schoeberlein, A., Dunner, S., Ménissier, F., Massabanda, J., et al. (1997) · Nature Genetics · doi:10.1038/ng0997-71 · Cited by 1,556 · see citing works

Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification

Meredith, R. W., Janečka, J. E., Gatesy, J., Ryder, O. A., Fisher, C. A., Teeling, E. C., Goodbla, A., Eizirik, E., Simão, T. L. L., Stadler, T., et al. (2011) · Science · doi:10.1126/science.1211028 · Cited by 1,464 · see citing works

Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner

Blanchette, M., Kent, W. J., Riemer, C., Elnitski, L., Smit, A. F. A., Roskin, K. M., Baertsch, R., Rosenbloom, K., Clawson, H., Green, E. D., et al. (2004) · Genome Research · doi:10.1101/gr.1933104 · Cited by 1,452 · see citing works

Analyses of pig genomes provide insight into porcine demography and evolution

Groenen, M. A. M., Archibald, A. L., Uenishi, H., Tuggle, C. K., Takeuchi, Y., Rothschild, M. F., Rogel-Gaillard, C., Park, C., Denis Milan, A., Megens, H., et al. (2012) · Nature · doi:10.1038/nature11622 · Cited by 1,386 · see citing works

Testing for ancient admixture between closely related populations

Durand, E. Y., Patterson, N., Reich, D., & Slatkin, M. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr048 · Cited by 1,375 · see citing works

Adaptive seeds tame genomic sequence comparisonPreprint

Kiełbasa, S. M., Wan, R., Sato, K., Horton, P., & Frith, M. C. (2011) · Genome Research · doi:10.1101/gr.113985.110 · Cited by 1,252 · see citing works

The sequence and de novo assembly of the giant panda genome

Li, R., Fan, W., Tian, G., Zhu, H., He, L., Cai, J., Huang, Q., Cai, Q., Li, B., Bai, Y., et al. (2010) · Nature · doi:10.1038/nature08696 · Cited by 1,180 · see citing works

A whole-genome assembly of the domestic cow, Bos taurus

Zimin, A. V., Delcher, A. L., Florea, L., Kelley, D. R., Schatz, M. C., Puiu, D., Hanrahan, F., Pertea, G. M., Tassell, C. P. V., Sonstegard, T. S., et al. (2009) · Genome biology · doi:10.1186/gb-2009-10-4-r42 · Cited by 1,143 · see citing works

Assessing the Causes of Late Pleistocene Extinctions on the Continents

Barnosky, A. D., Koch, P. L., Feranec, R. S., Wing, S. L., & Shabel, A. B. (2004) · Science · doi:10.1126/science.1101476 · Cited by 1,084 · see citing works

Inconsistency of Phylogenetic Estimates from Concatenated Data under Coalescence

Kubatko, L. S., & Degnan, J. H. (2007) · Systematic Biology · doi:10.1080/10635150601146041 · Cited by 1,041 · see citing works

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

Kajitani, R., Toshimoto, K., Noguchi, H., Toyoda, A., Ogura, Y., Okuno, M., Yabana, M., Harada, M., Nagayasu, E., Maruyama, H., et al. (2014) · Genome Research · doi:10.1101/gr.170720.113 · Cited by 1,017 · see citing works

The genomic substrate for adaptive radiation in African cichlid fish

Brawand, D., Wagner, C. E., Li, Y., Malinsky, M., Keller, I., Fan, S., Simakov, O., Ng, A. Y. J., Lim, Z. W., Bezault, É., et al. (2014) · Nature · doi:10.1038/nature13726 · Cited by 989 · see citing works

The yak genome and adaptation to life at high altitude

Qiu, Q., Zhang, G., Ma, T., Qian, W., Wang, J., Ye, Z., Cao, C., Hu, Q., Kim, J., Larkin, D. M., et al. (2012) · Nature Genetics · doi:10.1038/ng.2343 · Cited by 971 · see citing works

Divergence time and evolutionary rate estimation with multilocus data.

Thorne, J. L., & Kishino, H. (2002) · Systematic Biology · doi:10.1080/10635150290102456 · Cited by 962 · see citing works

Factors That Alter Rumen Microbial Ecology

Russell, J. B., & Rychlik, J. L. (2001) · Science · doi:10.1126/science.1058830 · Cited by 954 · see citing works

Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies

Sayyari, E., & Mirarab, S. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw079 · Cited by 872 · see citing works

Ballgown bridges the gap between transcriptome assembly and expression analysis

Frazee, A. C., Pertea, G. M., Jaffe, A. E., Langmead, B., Salzberg, S. L., & Leek, J. T. (2015) · Nature Biotechnology · doi:10.1038/nbt.3172 · Cited by 853 · see citing works

Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels

Li, H., Peng, Z., Yang, X., Wang, W., Fu, J., Wang, J., Han, Y., Chai, Y., Guo, T., Yang, N., et al. (2012) · Nature Genetics · doi:10.1038/ng.2484 · Cited by 841 · see citing works

Genome Sequence, Comparative Analysis, and Population Genetics of the Domestic Horse

Wade, C. M., Giulotto, E., Sigurdsson, S., Zoli, M., Gnerre, S., Imsland, F., Lear, T. L., Adelson, D. L., Bailey, E., Bellone, R. R., et al. (2009) · Science · doi:10.1126/science.1178158 · Cited by 822 · see citing works

Direct determination of diploid genome sequences

Weisenfeld, N. I., Kumar, V., Shah, P., Church, D. M., & Jaffe, D. B. (2017) · Genome Research · doi:10.1101/gr.214874.116 · Cited by 803 · see citing works

Mutations in SBDS are associated with Shwachman–Diamond syndrome

Boocock, G. R. B., Morrison, J. A., Popovic, M., Richards, N., Ellis, L. E., Durie, P. R., & Rommens, J. M. (2002) · Nature Genetics · doi:10.1038/ng1062 · Cited by 785 · see citing works

Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes

Vlastaridis, P., Kyriakidou, P., Chaliotis, A., de Peer, Y. V., Oliver, S. G., & Amoutzias, G. D. (2017) · GigaScience · doi:10.1093/gigascience/giw015 · Cited by 732 · see citing works

Species-specific responses of Late Quaternary megafauna to climate and humans

Lorenzen, E. D., Nogués‐Bravo, D., Orlando, L., Weinstock, J., Binladen, J., Marske, K. A., Ugan, A., Borregaard, M. K., Gilbert, M. T. P., Nielsen, R., et al. (2011) · Nature · doi:10.1038/nature10574 · Cited by 691 · see citing works

Animal Genome Size Database

Gregory, T. R. (2002) · Cited by 663 · see citing works

Pattern and timing of diversification of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes

Hassanin, A., Delsuc, F., Ropiquet, A., Hammer, C., Jansen van Vuuren, B., Matthee, C., Ruiz-Garcia, M., Catzeflis, F., Areskoug, V., Nguyen, T. T., et al. (2011) · Comptes Rendus. Biologies · doi:10.1016/j.crvi.2011.11.002 · Cited by 638 · see citing works

Mechanisms of Leukocyte Transendothelial Migration

Müller, W. A. (2011) · Annual Review of Pathology Mechanisms of Disease · doi:10.1146/annurev-pathol-011110-130224 · Cited by 627 · see citing works

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

Bickhart, D. M., Rosen, B. D., Koren, S., Sayre, B. L., Hastie, A. R., Chan, S., Lee, J., Lam, E. T., Liachko, I., Sullivan, S. T., et al. (2017) · Nature Genetics · doi:10.1038/ng.3802 · Cited by 620 · see citing works

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

Liu, L., Yu, L., & Edwards, S. V. (2010) · BMC Evolutionary Biology · doi:10.1186/1471-2148-10-302 · Cited by 607 · see citing works

The bonobo genome compared with the chimpanzee and human genomes

Prüfer, K., Munch, K., Hellmann, I., Akagi, K., Miller, J. R., Walenz, B., Koren, S., Sutton, G., Kodira, C., Winer, R., et al. (2012) · Nature · doi:10.1038/nature11128 · Cited by 579 · see citing works

Changes in genetic selection differentials and generation intervals in US Holstein dairy cattle as a result of genomic selection

García-Ruíz, A., Cole, J. B., VanRaden, P. M., Wiggans, G. R., Lopez, F. J., & Tassell, C. P. V. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1519061113 · Cited by 574 · see citing works

The Dog Genome: Survey Sequencing and Comparative Analysis

Kirkness, E. F., Bafna, V., Halpern, A. L., Levy, S., Remington, K., Rusch, D. B., Delcher, A. L., Pop, M., Wang, W., Fraser, C. M., et al. (2003) · Science · doi:10.1126/science.1086432 · Cited by 548 · see citing works

Invited Review: Role of livestock in human nutrition and health for poverty reduction in developing countries1,2,3

Randolph, T. F., Schelling, E., Grace, D., Nicholson, C. F., Leroy, J. L., Cole, D. C., Demment, M. W., Omore, A. O., Zinsstag, J., & Ruel, M. T. (2007) · Journal of Animal Science · doi:10.2527/jas.2007-0467 · Cited by 543 · see citing works

THE EVOLUTIONARY STRATEGY OF THE EQUIDAE AND THE ORIGINS OF RUMEN AND CECAL DIGESTION

Janis, C. M. (1976) · Evolution · doi:10.1111/j.1558-5646.1976.tb00957.x · Cited by 540 · see citing works

Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny

dos Reis, M., Inoue, J., Hasegawa, M., Asher, R. J., Donoghue, P. C. J., & Yang, Z. (2012) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2012.0683 · Cited by 526 · cited 1× · see citing works

The sheep genome illuminates biology of the rumen and lipid metabolism

Jiang, Y., Xie, M., Chen, W., Talbot, R., Maddox, J. F., Faraut, T., Wu, C., Muzny, D. M., Li, Y., Zhang, W., et al. (2014) · Science · doi:10.1126/science.1252806 · Cited by 514 · see citing works

PHAST and RPHAST: phylogenetic analysis with space/time models

Hubisz, M. J., Pollard, K. S., & Siepel, A. (2011) · Briefings in Bioinformatics · doi:10.1093/bib/bbq072 · Cited by 490 · see citing works

On the origin of modern humans: Asian perspectives

Bae, C. J., Douka, K., & Petraglia, M. D. (2017) · Science · doi:10.1126/science.aai9067 · Cited by 471 · see citing works

BMP signaling controls muscle mass

Sartori, R., Schirwis, E., Blaauw, B., Bortolanza, S., Zhao, J., Enzo, E., Stantzou, A., Mouisel, E., Toniolo, L., Ferry, A., et al. (2013) · Nature Genetics · doi:10.1038/ng.2772 · Cited by 467 · see citing works

Human-livestock interactions: The stockperson and the productivity and welfare of intensively farmed animals

(2010) · CABI eBooks · doi:10.1079/9781845936730.0000 · Cited by 463 · see citing works

Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

Song, S., Liu, L., Edwards, S. V., & Wu, S. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1211733109 · Cited by 461 · see citing works

PhyloNetworks: A Package for Phylogenetic Networks

Solís‐Lemus, C., Bastide, P., & Ané, C. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx235 · Cited by 457 · see citing works

Convergent evolution of the genomes of marine mammals

Foote, A. D., Liu, Y., Thomas, G. W. C., Vinař, T., Alföldi, J., Deng, J., Dugan, S., van Elk, C. E., Hunter, M. E., Joshi, V., et al. (2015) · Nature Genetics · doi:10.1038/ng.3198 · Cited by 453 · see citing works

Bone morphogenetic protein-3 is a negative regulator of bone density

Daluiski, A., Engstrand, T., Bahamonde, M. E., Gamer, L. W., Agius, E., Stevenson, S., Cox, K. A., Rosen, V., & Lyons, K. M. (2001) · Nature Genetics · doi:10.1038/83810 · Cited by 427 · see citing works

Epithelial sodium channel (ENaC) family: Phylogeny, structure–function, tissue distribution, and associated inherited diseases

Hanukoglu, I., & Hanukoglu, A. (2016) · Gene · doi:10.1016/j.gene.2015.12.061 · Cited by 387 · see citing works

The Evolution of Artiodactyls

Prothero, D. R. (2007) · Johns Hopkins University Press eBooks · doi:10.56021/9780801887352 · Cited by 375 · see citing works

A complete estimate of the phylogenetic relationships in Ruminantia: a dated species-level supertree of the extant ruminants

Fernández, M. H., & Vrba, E. S. (2005) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1017/s1464793104006670 · Cited by 362 · see citing works

Inferring Phylogenetic Networks Using PhyloNet

Wen, D., Yu, Y., Zhu, J., & Nakhleh, L. K. (2018) · Systematic Biology · doi:10.1093/sysbio/syy015 · Cited by 352 · see citing works

Targeted disruption of the mouse NHERF-1 gene promotes internalization of proximal tubule sodium-phosphate cotransporter type IIa and renal phosphate wasting

Shenolikar, S., Voltz, J. W., Minkoff, C., Wade, J. B., & Weinman, E. J. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.162232699 · Cited by 332 · see citing works

Origin of Whales from Early Artiodactyls: Hands and Feet of Eocene Protocetidae from Pakistan

Gingerich, P. D., Haq, M. U., Zalmout, I. S., Khan, I. H., & Malkani, M. S. (2001) · Science · doi:10.1126/science.1063902 · Cited by 321 · see citing works

Generation length for mammals

Marco, M. D., Pacifici, M., Santini, L., Baisero, D., Francucci, L., Marasini, G. G., Visconti, P., & Rondinini, C. (2013) · Nature Conservation · doi:10.3897/natureconservation.5.5734 · Cited by 315 · see citing works

Camelid genomes reveal evolution and adaptation to desert environments

Wu, H., Guang, X., Al‐Fageeh, M. B., Cao, J., Pan, S., Zhou, H., Zhang, L., Abutarboush, M. H., Xing, Y., Xie, Z., et al. (2014) · Nature Communications · doi:10.1038/ncomms6188 · Cited by 314 · see citing works

The tiger genome and comparative analysis with lion and snow leopard genomes

Cho, Y. S., Hu, L., Hou, H., Lee, H., Xu, J., Kwon, S., Oh, S., Kim, H.-M., Jho, S., Kim, S., et al. (2013) · Nature Communications · doi:10.1038/ncomms3433 · Cited by 312 · see citing works

The Association of Sport Performance with ACE and ACTN3 Genetic Polymorphisms: A Systematic Review and Meta-Analysis

Ma, F., Yang, Y., Li, X., Zhou, F., Gao, C., Li, M., & Gao, L. (2013) · PLoS ONE · doi:10.1371/journal.pone.0054685 · Cited by 310 · see citing works

The gene tree delusion

Springer, M. S., & Gatesy, J. (2015) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2015.07.018 · Cited by 281 · see citing works

Draft genome sequence of the Tibetan antelope

Ge, R.-L., Cai, Q., Shen, Y., San, A., Ma, L., Zhang, Y., Yi, X., Chen, Y., Yang, L., Huang, Y., et al. (2013) · Nature Communications · doi:10.1038/ncomms2860 · Cited by 279 · see citing works

Multiplex sequencing of pooled mitochondrial genomes—a crucial step toward biodiversity analysis using mito-metagenomics

Tang, M., Tan, M., Meng, G., Yang, S., Su, X., Liu, S., Song, W., Li, Y., Wu, Q., Zhang, A., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku917 · Cited by 278 · see citing works

RUMINANT NUTRITION SYMPOSIUM: Molecular adaptation of ruminal epithelia to highly fermentable diets1

Penner, G. B., Steele, M. A., Aschenbach, J. R., & McBride, B. W. (2010) · Journal of Animal Science · doi:10.2527/jas.2010-3378 · Cited by 272 · see citing works

Detection and Polarization of Introgression in a Five-Taxon Phylogeny

Pease, J. B., & Hahn, M. W. (2015) · Systematic Biology · doi:10.1093/sysbio/syv023 · Cited by 268 · see citing works

A multi-calibrated mitochondrial phylogeny of extant Bovidae (Artiodactyla, Ruminantia) and the importance of the fossil record to systematics

Bibi, F. (2013) · BMC Evolutionary Biology · doi:10.1186/1471-2148-13-166 · Cited by 265 · see citing works

Statistical binning enables an accurate coalescent-based estimation of the avian tree

Mirarab, S., Bayzid, M. S., Boussau, B., & Warnow, T. (2014) · Science · doi:10.1126/science.1250463 · Cited by 257 · see citing works

Regulation of bone development and maintenance by Runx2

Komori, T. (2007) · Frontiers in bioscience · doi:10.2741/2730 · Cited by 254 · see citing works

Molecular and Morphological Phylogenies of Ruminantia and the Alternative Position of the Moschidae

Hassanin, A., & Douzery, E. (2003) · Systematic Biology · doi:10.1080/10635150390192726 · Cited by 253 · see citing works

Carbohydrate and Lipid Metabolism in Farm Animals1

Nafikov, R. A., & Beitz, D. C. (2007) · Journal of Nutrition · doi:10.1093/jn/137.3.702 · Cited by 250 · see citing works

ExaML version 3: a tool for phylogenomic analyses on supercomputers

Kozlov, A. M., Aberer, A. J., & Stamatakis, A. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv184 · Cited by 239 · see citing works

Relationships of Cetacea (Artiodactyla) Among Mammals: Increased Taxon Sampling Alters Interpretations of Key Fossils and Character Evolution

Spaulding, M., O’Leary, M. A., & Gatesy, J. (2009) · PLoS ONE · doi:10.1371/journal.pone.0007062 · Cited by 227 · see citing works

Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics

Decker, J. E., Pires, J. C., Conant, G. C., McKay, S., Heaton, M. P., Chen, K., Cooper, A., Vilkki, J., Seabury, C. M., Caetano, A. R., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0904691106 · Cited by 224 · see citing works

The Phusion Assembler

Mullikin, J. C., & Ning, Z. (2003) · Genome Research · doi:10.1101/gr.731003 · Cited by 222 · see citing works

More genes underwent positive selection in chimpanzee evolution than in human evolution

Bakewell, M. A., Shi, P., & Zhang, J. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0701705104 · Cited by 219 · see citing works

Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selectionPreprint

Hobolth, A., Dutheil, J. Y., Hawks, J. D., Schierup, M. H., & Mailund, T. (2011) · Genome Research · doi:10.1101/gr.114751.110 · Cited by 213 · see citing works

Three-dimensional morphometric ontogeny of mollusc shells by micro-computed tomography and geometric analysis

Monnet, C., Zollikofer, C., Bucher, H., & Goudemand, N. (2009) · Zurich Open Repository and Archive (University of Zurich) · doi:10.5167/uzh-23587 · Cited by 212 · see citing works

Chromosomal Redistribution of Male-Biased Genes in Mammalian Evolution with Two Bursts of Gene Gain on the X Chromosome

Zhang, Y. E., Vibranovski, M. D., Landback, P., Marais, G. A. B., & Long, M. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000494 · Cited by 206 · see citing works

Loss of keratin 6 (K6) proteins reveals a function for intermediate filaments during wound repair

Wong, P., & Coulombe, P. A. (2003) · The Journal of Cell Biology · doi:10.1083/jcb.200305032 · Cited by 199 · see citing works

Transcriptional regulation of bone formation by the osteoblast-specific transcription factor Osx

Zhang, C. (2010) · Journal of Orthopaedic Surgery and Research · doi:10.1186/1749-799x-5-37 · Cited by 192 · see citing works

Morphology and locomotor adaptations of the bovid femur in relation to habitat

Kappelman, J. W. (1988) · Journal of Morphology · doi:10.1002/jmor.1051980111 · Cited by 187 · see citing works

Genetic basis of ruminant headgear and rapid antler regeneration

Wang, Y., Zhang, C., Wang, N., Li, Z., Heller, R., Liu, R., Zhao, Y., Han, J., Pan, X., Zheng, Z., et al. (2019) · Science · doi:10.1126/science.aav6335 · Cited by 186 · see citing works

Invited review: Ruminant ecology and evolution: Perspectives useful to ruminant livestock research and production

Hackmann, T. J., & Spain, J. N. (2010) · Journal of Dairy Science · doi:10.3168/jds.2009-2071 · Cited by 174 · see citing works

Enamel Defects and Ameloblast-specific Expression in Enam Knock-out/lacZ Knock-in Mice

Hu, J. C. ‐., Hu, Y., Smith, C. E., McKee, M. D., Wright, J. T., Yamakoshi, Y., Papagerakis, P., Hunter, G. K., Feng, J. Q., Yamakoshi, F., et al. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m710565200 · Cited by 170 · see citing works

Hidden Likelihood Support in Genomic Data: Can Forty-Five Wrongs Make a Right?

Gatesy, J., & Baker, R. H. (2005) · Systematic Biology · doi:10.1080/10635150590945368 · Cited by 151 · see citing works

DiscoVista: Interpretable visualizations of gene tree discordance

Sayyari, E., Whitfield, J. B., & Mirarab, S. (2018) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2018.01.019 · Cited by 149 · see citing works

Are Convergent and Parallel Amino Acid Substitutions in Protein Evolution More Prevalent Than Neutral Expectations?

Zou, Z., & Zhang, J. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv091 · Cited by 148 · see citing works

Body Size, Population Metabolism, and Habitat Specialization Among Large African Herbivores

Toit, D., & Owen‐Smith, N. (1989) · The American Naturalist · doi:10.1086/284949 · Cited by 145 · see citing works

Molecular Insights into the Evolution of the Family Bovidae: A Nuclear DNA Perspective

Matthee, C. A., & Davis, S. K. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003908 · Cited by 142 · see citing works

Variations in molar enamel thickness among primates

Shellis, R. P., Beynon, A. D., Reid, D. J., & Hiiemäe, K. M. (1998) · Journal of Human Evolution · doi:10.1006/jhev.1998.0238 · Cited by 140 · see citing works

Age-dependent chromosomal distribution of male-biased genes in DrosophilaPreprint

Zhang, Y. E., Vibranovski, M. D., Krinsky, B. H., & Long, M. (2010) · Genome Research · doi:10.1101/gr.107334.110 · Cited by 130 · see citing works

Genomic Signature of an Avian Lilliput Effect across the K-Pg Extinction

Berv, J. S., & Field, D. J. (2017) · Systematic Biology · doi:10.1093/sysbio/syx064 · Cited by 129 · see citing works

Genetics of Athletic Performance

Ostrander, E. A., Huson, H. J., & Ostrander, G. K. (2009) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-082908-150058 · Cited by 119 · see citing works

Error in Phylogenetic Estimation for Bushes in the Tree of Life

Patel, S. K. (2013) · Journal of Phylogenetics & Evolutionary Biology · doi:10.4172/2329-9002.1000110 · Cited by 118 · see citing works

Improved BLAST searches using longer words for protein seeding

Shiryev, S. A., Papadopoulos, J. S., Schäffer, A. A., & Agarwala, R. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm479 · Cited by 115 · see citing works

Serpins, Immunity and Autoimmunity: Old Molecules, New Functions

Gatto, M., Iaccarino, L., Ghirardello, A., Bassi, N., Pontisso, P., Punzi, L., Shoenfeld, Y., & Doria, A. (2013) · Clinical Reviews in Allergy & Immunology · doi:10.1007/s12016-013-8353-3 · Cited by 114 · see citing works

Evolution of ruminant headgear: a review

Davis, E., Brakora, K. A., & Lee, A. H. (2011) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2011.0938 · Cited by 107 · see citing works

Efficient Generation of Myostatin (MSTN) Biallelic Mutations in Cattle Using Zinc Finger Nucleases

Luo, J., Song, Z., Yu, S., Cui, D., Wang, B., Ding, F., Song, L., Dai, Y., & Li, N. (2014) · PLoS ONE · doi:10.1371/journal.pone.0095225 · Cited by 104 · see citing works

Dietary innovations spurred the diversification of ruminants during the Caenozoic

Cantalapiedra, J. L., FitzJohn, R. G., Kuhn, T. S., Fernández, M. H., DeMiguel, D., Azanza, B., Morales, J., & Mooers, A. Ø. (2013) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2013.2746 · Cited by 103 · see citing works

The Human Genome

Pennisi, E. (2001) · Science · doi:10.1126/science.291.5507.1177 · Cited by 100 · see citing works

Are There Really Twice as Many Bovid Species as We Thought?

Heller, R., Frandsen, P., Lorenzen, E. D., & SIEGISMUND, H. R. (2013) · Systematic Biology · doi:10.1093/sysbio/syt004 · Cited by 100 · see citing works

Characterization of the bovine pregnancy-associated glycoprotein gene family – analysis of gene sequences, regulatory regions within the promoter and expression of selected genes

Telugu, B. P. V. L., Walker, A. M., & Green, J. A. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-185 · Cited by 97 · see citing works

CytochromebPhylogeny of the Family Bovidae: Resolution within the Alcelaphini, Antilopini, Neotragini, and Tragelaphini

Matthee, C. A., & Robinson, T. J. (1999) · Molecular Phylogenetics and Evolution · doi:10.1006/mpev.1998.0573 · Cited by 93 · see citing works

Isozygous and selectable marker-free MSTN knockout cloned pigs generated by the combined use of CRISPR/Cas9 and Cre/LoxP

Bi, Y., Hua, Z., Liu, X., WenJun, H., Ren, H., Xiao, H., Zhang, L., Li, L., Wang, Z., Laible, G., et al. (2016) · Scientific Reports · doi:10.1038/srep31729 · Cited by 93 · see citing works

A new, early Puercan (earliest Paleocene) species ofPurgatorius(Plesiadapiformes, Primates) from Saskatchewan, Canada

Fox, R. C., & Scott, C. S. (2011) · Journal of Paleontology · doi:10.1666/10-059.1 · Cited by 89 · see citing works

Loss of Singleminded-2s in the Mouse Mammary Gland Induces an Epithelial-Mesenchymal Transition Associated with Up-Regulation of Slug and Matrix Metalloprotease 2

Laffin, B., Wellberg, E. A., Kwak, H., Burghardt, R. C., Metz, R. P., Gustafson, T. L., Schedin, P. S., & Porter, W. W. (2007) · Molecular and Cellular Biology · doi:10.1128/mcb.01701-07 · Cited by 85 · see citing works

Bovids of the World

Castelló, J. (2016) · doi:10.1515/9781400880652 · Cited by 84 · see citing works

New remains of primitive ruminants from Thailand: evidence of the early evolution of the Ruminantia in Asia

Métais, G., Chaimanee, Y., Jaeger, J., & Ducrocq, S. (2001) · Zoologica Scripta · doi:10.1046/j.0300-3256.2001.00071.x · Cited by 78 · see citing works

Ecology of Ungulates

Baskin, L. M., & Danell, K. (2003) · Springer eBooks · doi:10.1007/978-3-662-06820-5 · Cited by 78 · see citing works

CRISPR /Cas9‐mediated MSTN disruption and heritable mutagenesis in goats causes increased body mass

Wang, X., Niu, Y., Zhou, J., Zhu, H., Ma, B., Yu, H., Yan, H., Hua, J., Huang, X., Qu, L., et al. (2018) · Animal Genetics · doi:10.1111/age.12626 · Cited by 78 · see citing works

Systematic relationships of five newly sequenced cervid species

Heckeberg, N. S., Erpenbeck, D., Wörheide, G., & Rössner, G. E. (2016) · PeerJ · doi:10.7717/peerj.2307 · Cited by 76 · see citing works

Fibroblast growth factor signaling in mammalian tooth development

Li, C., Procházka, J., Goodwin, A. F., & Klein, O. D. (2013) · Odontology · doi:10.1007/s10266-013-0142-1 · Cited by 74 · see citing works

Epithelial, metabolic and innate immunity transcriptomic signatures differentiating the rumen from other sheep and mammalian gastrointestinal tract tissues

Xiang, R., Oddy, V. H., Archibald, A. L., Vercoe, P. E., & Dalrymple, B. P. (2016) · PeerJ · doi:10.7717/peerj.1762 · Cited by 71 · see citing works

Draft genome of the reindeer ( Rangifer tarandus )

Li, Z., Lin, Z., Ba, H., Chen, L., Yang, Y. P., Wang, K., Qiu, Q., Wang, W., & Li, G. (2017) · GigaScience · doi:10.1093/gigascience/gix102 · Cited by 69 · see citing works

Grades and clades in hornless ruminant evolution: the reality of the Gelocidae and the systematic position of Lophiomeryx and Bachitherium

Janis, C. M. (1987) · Journal of Vertebrate Paleontology · doi:10.1080/02724634.1987.10011653 · Cited by 68 · see citing works

The oldest bovid from the Siwaliks, Pakistan

Solounias, N., Barry, J. C., Bernor, R. L., Lindsay, E. H., & Raza, S. M. (1995) · Journal of Vertebrate Paleontology · doi:10.1080/02724634.1995.10011263 · Cited by 65 · see citing works

admixturegraph: an R package for admixture graph manipulation and fitting

Leppälä, K., Nielsen, S. V., & Mailund, T. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx048 · Cited by 65 · see citing works

Giraffe genome sequence reveals clues to its unique morphology and physiology

Agaba, M. K., Ishengoma, E., Miller, W., McGrath, B. C., Hudson, C. N., Bedoya-Reina, O. C., Ratan, A., Burhans, R., Chikhi, R., Medvedev, P., et al. (2016) · Nature Communications · doi:10.1038/ncomms11519 · Cited by 64 · see citing works

Generation of biallelic knock-out sheep via gene-editing and somatic cell nuclear transfer

Li, H., Wang, G., Hao, Z., Zhang, G., Qing, Y., Liu, S., Qing, L., Pan, W., Chen, L., Liu, G., et al. (2016) · Scientific Reports · doi:10.1038/srep33675 · Cited by 61 · see citing works

The Organogenesis and early histogenesis of the bovine stomach

Warner, E. D. (1958) · American Journal of Anatomy · doi:10.1002/aja.1001020103 · Cited by 58 · see citing works

PAX9 regulates squamous cell differentiation and carcinogenesis in the oro‐oesophageal epithelium

Xiong, Z., Ren, S., Chen, H., Liu, Y., Huang, C. D., Zhang, Y. L., Odera, J. O., Chen, T., Kist, R., Peters, H., et al. (2017) · The Journal of Pathology · doi:10.1002/path.4998 · Cited by 57 · see citing works

Systematics and Evolution of the Miocene Three-Horned Palaeomerycid Ruminants (Mammalia, Cetartiodactyla)

Sánchez, I. M., Cantalapiedra, J. L., Ríos, M., Quiralte, V., & Morales, J. (2015) · PLoS ONE · doi:10.1371/journal.pone.0143034 · Cited by 55 · see citing works

Millions of Years Behind: Slow Adaptation of Ruminants to Grasslands

Toljagić, O., Voje, K. L., Matschiner, M., Liow, L. H., & Hansen, T. F. (2017) · Systematic Biology · doi:10.1093/sysbio/syx059 · Cited by 51 · see citing works

Aldo–keto reductases AKR1C1, AKR1C2 and AKR1C3 may enhance progesterone metabolism in ovarian endometriosis

Hevir, N., Vouk, K., Šinkovec, J., Ribič-Pucelj, M., & Lanišnik Rižner, T. (2011) · Chemico-Biological Interactions · doi:10.1016/j.cbi.2011.01.003 · Cited by 48 · see citing works

Genome-Wide Polymorphism and Comparative Analyses in the White-Tailed Deer (Odocoileus virginianus): A Model for Conservation Genomics

Seabury, C. M., Bhattarai, E. K., Taylor, J. F., Viswanathan, G. G., Cooper, S. M., Davis, D. S., Dowd, S. E., Lockwood, M. L., & Seabury, P. M. (2011) · PLoS ONE · doi:10.1371/journal.pone.0015811 · Cited by 48 · see citing works

The genus Hispanomeryx (Mammalia, Ruminantia, Moschidae) and its bearing on musk deer phylogeny and systematics

Sánchez, I. M., Domingo, M. S., & Morales, J. (2010) · Palaeontology · doi:10.1111/j.1475-4983.2010.00992.x · Cited by 46 · see citing works

Old World Ruminant Morphophysiology, Life History, and Fossil Record: Exploring Key Innovations of a Diversification Sequence

Clauß, M., & Rössner, G. E. (2014) · Annales Zoologici Fennici · doi:10.5735/086.051.0210 · Cited by 46 · see citing works

Overexpression of SERPIN B3 promotes epithelial proliferation and lung fibrosis in mice

Lunardi, F., Villano, G., Perissinotto, E., Agostini, C., Rea, F., Gnoato, M., Bradaschia, A., Valente, M., Pontisso, P., & Calabrese, F. (2011) · Laboratory Investigation · doi:10.1038/labinvest.2011.1 · Cited by 45 · see citing works

Human enamel thickness and ENAM polymorphism

Daubert, D. M., Kelley, J. L., Udod, Y. G., Habor, C., Kleist, C. G., Furman, I. K., Tikonov, I. N., Swanson, W. J., & Roberts, F. A. (2016) · International Journal of Oral Science · doi:10.1038/ijos.2016.1 · Cited by 42 · see citing works

Establishment and phenotypic analysis of an Mstn knockout rat

Gu, H., Cao, Y., Qiu, B., Zhou, Z., Deng, R., Chen, Z., Li, R., Li, X., Wei, Q., Xia, X., et al. (2016) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2016.06.030 · Cited by 39 · see citing works

Phylogenetic analyses and improved resolution of the family Bovidae based on complete mitochondrial genomes

Yang, C., Xiang, C., Qi, W., Xia, S., Tu, F., Zhang, X., Moermond, T. C., & Yue, B. (2013) · Biochemical Systematics and Ecology · doi:10.1016/j.bse.2012.12.005 · Cited by 38 · see citing works

Late Pliocene Bovidae from Ledi-Geraru (Lower Awash Valley, Ethiopia) and their implications for Afar paleoecology

Bibi, F., Rowan, J., & Reed, K. E. (2017) · Journal of Vertebrate Paleontology · doi:10.1080/02724634.2017.1337639 · Cited by 36 · see citing works

Dietary niche partitioning among fossil bovids in late Miocene C3 habitats: Consilience of functional morphology and stable isotope analysis

Bibi, F. (2007) · Palaeogeography Palaeoclimatology Palaeoecology · doi:10.1016/j.palaeo.2007.06.014 · Cited by 31 · see citing works

Cranial and postcranial morphological data in ruminant phylogenetics

Janis, C. M., & Theodor, J. M. (2014) · Open access LMU (Ludwid Maxmilian's Universitat Munchen) · doi:10.5282/ubm/epub.22383 · Cited by 29 · see citing works

Ardipithecus Kadabba

Haile-Selassie, Y., & Woldegabriel, G. (2009) · University of California Press eBooks · doi:10.1525/9780520942509 · Cited by 29 · see citing works

Studies on reduction of S-nitrosoglutathione by human carbonyl reductases 1 and 3

Staab-Weijnitz, C. A., Hartmanová, T., El-Hawari, Y., Ebert, B., Kisiela, M., Wsól, V., Martin, H.-J., & Maser, E. (2011) · Chemico-Biological Interactions · doi:10.1016/j.cbi.2011.01.016 · Cited by 27 · see citing works

New hippotragini (Bovidae, Mammalia) from the Late Miocene of Toros-Menalla (Chad)

Geraads, D., Blondel, C., Likius, A., Mackaye, H. T., Vignaud, P., & Brunet, M. (2008) · Journal of Vertebrate Paleontology · doi:10.1671/0272-4634(2008)28[231:nhbmft]2.0.co;2 · Cited by 26 · see citing works

A primitive caprine from the Upper Vallesian of La Roma 2 (Alfambra, Teruel, Aragon, Spain)

Alcalá, L., & Morales, J. (1997) · Comptes Rendus de l Académie des Sciences - Series IIA - Earth and Planetary Science · doi:10.1016/s1251-8050(97)82509-8 · Cited by 25 · see citing works

Draft genome of the Marco Polo Sheep (Ovis ammon polii)

Yang, Y. P., Wang, Y., Zhao, Y., Zhang, X., Li, R., Chen, L., Zhang, G., Jiang, Y., Qiu, Q., Wang, W., et al. (2017) · GigaScience · doi:10.1093/gigascience/gix106 · Cited by 25 · see citing works

SOX9 Duplication Linked to Intersex in Deer

Kropatsch, R., Dekomien, G., Akkad, D. A., Gerding, W. M., Petrasch‐Parwez, E., Young, N. D., Altmüller, J., Nürnberg, P., Gasser, R. B., & Epplen, J. T. (2013) · PLoS ONE · doi:10.1371/journal.pone.0073734 · Cited by 24 · see citing works

Draft genome of the milu (Elaphurus davidianus)

Zhang, C., Chen, L., Zhou, Y., Wang, K., Chemnick, L. G., Ryder, O. A., Wang, W., Zhang, G., & Qiu, Q. (2017) · GigaScience · doi:10.1093/gigascience/gix130 · Cited by 24 · see citing works

Fossil Tragelaphini (Artiodactyla: Bovidae) from the Late Pliocene Hadar Formation, Afar Regional State, Ethiopia

Reed, K. E., & Bibi, F. (2010) · Journal of Mammalian Evolution · doi:10.1007/s10914-010-9146-6 · Cited by 17 · see citing works

Bovidae (Mammalia) from the Lower Pliocene of Chad

Geraads, D., Blondel, C., Mackaye, H. T., Likius, A., Vignaud, P., & Brunet, M. (2009) · Journal of Vertebrate Paleontology · doi:10.1671/039.029.0311 · Cited by 17 · see citing works

Assembling the ruminant tree: combining morphology, molecules, extant taxa, and fossils

Bibi, F. (2014) · Open access LMU (Ludwid Maxmilian's Universitat Munchen) · doi:10.5282/ubm/epub.22396 · Cited by 15 · see citing works

Genomic organization and evolution of ruminant lysozyme c genes.

Irwin, D. M. (2015) · Europe PMC (PubMed Central) · doi:10.13918/j.issn.2095-8137.2015.1.1 · Cited by 13 · see citing works

A genome survey sequencing of the Java mouse deer (Tragulus javanicus) adds new aspects to the evolution of lineage specific retrotransposons in Ruminantia (Cetartiodactyla).

Gallus, S., Kumar, V., Bertelsen, M., Janke, A., & Nilsson, M. (2015) · Gene · doi:10.1016/j.gene.2015.06.064 · Cited by 11 · see citing works

Effect of mouse Sim2 gene on the cell cycle of PC12 cells

Meng, X., Shi, J., Peng, B., Zou, X., & Zhang, C. (2006) · Cell Biology International · doi:10.1016/j.cellbi.2005.11.012 · Cited by 6 · see citing works

反すう動物リゾチームC遺伝子のゲノム構成と進化【Powered by NICT】

Irwin David, M. (2015) · Zoological Research · Cited by 3 · see citing works

Relation between the Potential Gradient and the Number of Large Ions in the Atmosphere

Nolan, J. J. (1924) · Nature · doi:10.1038/113493a0 · Cited by 2 · see citing works

Data from: Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits

Chen, L., Qiu, Q., Jiang, Y., Wang, K., Lin, Z., Li, Z., Zhang, G., Heller, R., & Wang, W. (2019) · Data Archiving and Networked Services (DANS) · doi:10.5061/dryad.52213gc · Cited by 1 · see citing works

Dense sampling of bird diversity increases power of comparative genomics

Feng, S., Stiller, J., Deng, Y., Armstrong, J., Fang, Q., Reeve, A. H., Xie, D., Chen, G., Guo, C., Faircloth, B. C., et al. (2020) · Nature · doi:10.1038/s41586-020-2873-9 · Cited by 459 · see citing works

Phylotranscriptomics in Cucurbitaceae Reveal Multiple Whole-Genome Duplications and Key Morphological and Molecular Innovations

Guo, J., Xu, W., Hu, Y., Huang, J., Zhao, Y., Zhang, L., Huang, C., & Mā, H. (2020) · Molecular Plant · doi:10.1016/j.molp.2020.05.011 · Cited by 201 · see citing works

Genetic basis of ruminant headgear and rapid antler regeneration

Wang, Y., Zhang, C., Wang, N., Li, Z., Heller, R., Liu, R., Zhao, Y., Han, J., Pan, X., Zheng, Z., et al. (2019) · Science · doi:10.1126/science.aav6335 · Cited by 186 · see citing works

The origin of domestication genes in goats

Zheng, Z., Wang, X., Li, M., Li, Y., Yang, Z., Wang, X., Pan, X., Gong, M., Zhang, Y., Guo, Y., et al. (2020) · Science Advances · doi:10.1126/sciadv.aaz5216 · Cited by 184 · see citing works

Whole-Genome Resequencing of Worldwide Wild and Domestic Sheep Elucidates Genetic Diversity, Introgression, and Agronomically Important Loci

Lv, F., Cao, Y.-H., Liu, G., Luo, L.-Y., Lu, R., Liu, M., Li, W., Zhou, P., Wang, X., Shen, M., et al. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab353 · Cited by 183 · see citing works

Phylogenomic analyses provide insights into primate evolution

Shao, Y., Zhou, L., Li, F., Zhao, L., Zhang, B.-L., Shao, F., Chen, J., Chen, C., Bi, X., Zhuang, X.-L., et al. (2023) · Science · doi:10.1126/science.abn6919 · Cited by 170 · see citing works

The systematics of the Cervidae: a total evidence approach

Heckeberg, N. S. (2020) · PeerJ · doi:10.7717/peerj.8114 · Cited by 153 · see citing works

The Piroplasmida Babesia, Cytauxzoon, and Theileria in farm and companion animals: species compilation, molecular phylogeny, and evolutionary insights

Schnittger, L., Ganzinelli, S., Bhoora, R. V., Omondi, D., Nijhof, A. M., & Florin‐Christensen, M. (2022) · Parasitology Research · doi:10.1007/s00436-022-07424-8 · Cited by 139 · see citing works

Understanding the role of rumen epithelial host-microbe interactions in cattle feed efficiency

Na, S. W., & Guan, L. L. (2022) · Animal nutrition · doi:10.1016/j.aninu.2022.04.002 · Cited by 122 · see citing works

Chromosome-Level Reference Genome and Population Genomic Analysis Provide Insights into the Evolution and Improvement of Domesticated Mulberry (Morus alba)

Feng, J., Luo, R., Dai, X., Liu, H., Yu, G., Han, S., Lü, X., Su, C., Chen, Q., Song, Q., et al. (2020) · Molecular Plant · doi:10.1016/j.molp.2020.05.005 · Cited by 119 · see citing works

Comparative genomics provides insights into the aquatic adaptations of mammals

Yuan, Y., Zhang, Y., Zhang, P., Liu, C., Wang, J., Gao, H., Hoelzel, A. R., Seim, I., Lv, M., Lin, M., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2106080118 · Cited by 119 · see citing works

Whole-genome analysis of giraffe supports four distinct species

Coimbra, R. T. F., Winter, S., Kumar, V., Koepfli, K.-P., Gooley, R. M., Dobrynin, P., Fennessy, J., & Janke, A. (2021) · Current Biology · doi:10.1016/j.cub.2021.04.033 · Cited by 102 · see citing works

Ancient and modern genomes unravel the evolutionary history of the rhinoceros family

Liu, S., Westbury, M. V., Dussex, N., Mitchell, K. J., Sinding, M.-H. S., Heintzman, P. D., Duchêne, D. A., Kapp, J. D., von Seth, J., Heiniger, H., et al. (2021) · Cell · doi:10.1016/j.cell.2021.07.032 · Cited by 101 · see citing works

A review of the pangenome: how it affects our understanding of genomic variation, selection and breeding in domestic animals?

Gong, Y., Li, Y., Liu, X., Ma, Y., & Jiang, L. (2023) · Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology · doi:10.1186/s40104-023-00860-1 · Cited by 101 · see citing works

Genomic insights into the phylogeny and biomass-degrading enzymes of rumen ciliates

Li, Z., Wang, X., Zhang, Y., Yu, Z., Zhang, T., Dai, X., Pan, X., Jing, R., Yan, Y., Liu, Y., et al. (2022) · The ISME Journal · doi:10.1038/s41396-022-01306-8 · Cited by 94 · see citing works

Biological adaptations in the Arctic cervid, the reindeer ( Rangifer tarandus )

Lin, Z., Chen, L., Chen, X., Zhong, Y., Yang, Y., Xia, W., Liu, C., Zhu, W., Wang, H., Yan, B., et al. (2019) · Science · doi:10.1126/science.aav6312 · Cited by 85 · see citing works

Genetics of the phenotypic evolution in sheep: a molecular look at diversity-driving genes

Kalds, P., Zhou, S., Gao, Y., Cai, B., Huang, S., Chen, Y., & Wang, X. (2022) · Genetics Selection Evolution · doi:10.1186/s12711-022-00753-3 · Cited by 85 · see citing works

Worldwide Late Pleistocene and Early Holocene population declines in extant megafauna are associated with Homo sapiens expansion rather than climate change

Bergman, J., Pedersen, R. Ø., Lundgren, E. J., Lemoine, R. T., Monsarrat, S., Pearce, E. A., Schierup, M. H., & Svenning, J. (2023) · Nature Communications · doi:10.1038/s41467-023-43426-5 · Cited by 86 · see citing works

A towering genome: Experimentally validated adaptations to high blood pressure and extreme stature in the giraffe

Liu, C., Gao, J., Cui, X., Li, Z., Chen, L., Yuan, Y., Zhang, Y., Mei, L., Zhao, L., Cai, D., et al. (2021) · Science Advances · doi:10.1126/sciadv.abe9459 · Cited by 82 · see citing works

Taxonomy, phylogeny and identification of Chaetomiaceae with emphasis on thermophilic species

Wang, X. W., Han, P. J., Bai, F., Luo, A., Bensch, K., Meijer, M., Kraak, B., Han, D.-Y., Sun, B. D., Crous, P. W., et al. (2022) · Studies in Mycology · doi:10.3114/sim.2022.101.03 · Cited by 81 · see citing works

Parallel pathways for recruiting effector proteins determine centromere drive and suppression

Kumon, T., Ma, J., Akins, R. B., Stefanik, D. J., Nordgren, E. C., Kim, J., Levine, M. T., & Lampson, M. A. (2021) · Cell · doi:10.1016/j.cell.2021.07.037 · Cited by 76 · see citing works

LRScaf: improving draft genomes using long noisy reads

Mao, Q., Wu, S., Li, A., Zhao, F., Hu, F., Ding, L., Chang, Y., & Ruan, J. (2019) · BMC Genomics · doi:10.1186/s12864-019-6337-2 · Cited by 74 · see citing works

Ancient Demographics Determine the Effectiveness of Genetic Purging in Endangered Lizards

Xie, H., Liang, X., Chen, Z., Li, W.-M., Mi, C., Li, M., Wu, Z., Zhou, X., & Du, W. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab359 · Cited by 66 · see citing works

Distinguishing African bovids using Zooarchaeology by Mass Spectrometry (ZooMS): New peptide markers and insights into Iron Age economies in Zambia

Janzen, A., Richter, K. K., Mwebi, O., Brown, S., Onduso, V., Gatwiri, F., Ndiema, E., Katongo, M., Goldstein, S. T., Douka, K., et al. (2021) · PLoS ONE · doi:10.1371/journal.pone.0251061 · Cited by 67 · see citing works

Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer

Yin, Y., Fan, H.-Z., Zhou, B., Hu, Y.-B., Fan, G., Wang, J.-H., Zhou, F., Nie, W.-H., Zhang, C.-Z., Liu, L., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-27091-0 · Cited by 51 · see citing works

Chromosome-level genome assembly of grass carp (Ctenopharyngodon idella) provides insights into its genome evolution

Wu, C., Ma, Z., Zheng, G.-D., Zou, S.-M., Zhang, X.-J., & Zhang, Y. (2022) · BMC Genomics · doi:10.1186/s12864-022-08503-x · Cited by 60 · see citing works

Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere

Lopes, F., de Oliveira, L. R., Kessler, A., Beux, Y., Crespo, E. A., Cárdenas‐Alayza, S., Majluf, P., Sepúlveda, M., Brownell, R. L., Franco‐Trecu, V., et al. (2020) · Systematic Biology · doi:10.1093/sysbio/syaa099 · Cited by 62 · see citing works

RGD v2.0: a major update of the ruminant functional and evolutionary genomics database

Fu, W., Wang, R., Nanaei, H. A., Wang, J., Hu, D., & Jiang, Y. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab887 · Cited by 65 · see citing works

Cross-tissue single-cell transcriptomic landscape reveals the key cell subtypes and their potential roles in the nutrient absorption and metabolism in dairy cattle

Wu, J., Zhu, S., Gu, F., Valencak, T. G., Liu, J., & Sun, H. (2021) · Journal of Advanced Research · doi:10.1016/j.jare.2021.11.009 · Cited by 63 · see citing works

Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution

Mudd, A. B., Bredeson, J. V., Baum, R., Hockemeyer, D. F., & Rokhsar, D. S. (2020) · Communications Biology · doi:10.1038/s42003-020-1096-9 · Cited by 61 · see citing works

An atlas of CNV maps in cattle, goat and sheep

Huang, Y., Li, Y., Wang, X., Yu, J., Cai, Y., Zheng, Z., Li, R., Zhang, S., Chen, N., Nanaei, H. A., et al. (2021) · Science China Life Sciences · doi:10.1007/s11427-020-1850-x · Cited by 61 · see citing works

Genomic patterns in the widespread Eurasian lynx shaped by Late Quaternary climatic fluctuations and anthropogenic impacts

Lucena-Pérez, M., Marmesat, E., Kleinman‐Ruiz, D., Martínez‐Cruz, B., Wȩcek, K., Saveljev, A. P., Seryodkin, I. V., Okhlopkov, I. M., Dvornikov, M. G., Ozoliņš, J., et al. (2020) · Molecular Ecology · doi:10.1111/mec.15366 · Cited by 60 · see citing works

Chromosome‐level genome assembly of Lethenteron reissneri provides insights into lamprey evolution

Zhu, T., Li, Y., Pang, Y., Han, Y.-L., Li, J., Wang, Z., Liu, X., Li, H., Hua, Y., Jiang, H., et al. (2020) · Molecular Ecology Resources · doi:10.1111/1755-0998.13279 · Cited by 43 · see citing works

A Hu sheep genome with the first ovine Y chromosome reveal introgression history after sheep domestication

Li, R., Yang, P., Li, M., Fang, W., Yue, X., Nanaei, H. A., Gan, S., Du, D., Cai, Y., Dai, X., et al. (2020) · Science China Life Sciences · doi:10.1007/s11427-020-1807-0 · Cited by 56 · see citing works

Niche construction and the transition to herbivory: Phenotype switching and the organization of new nutritional modes

Chiu, L., & Gilbert, S. F. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-817996-3.00015-3 · Cited by 55 · see citing works

Phylogeny and evolution of the genus Cervus (Cervidae, Mammalia) as revealed by complete mitochondrial genomes

Mackiewicz, P., Matosiuk, M., Świsłocka, M., Zachos, F. E., Hajji, G. M., Saveljev, A. P., Seryodkin, I. V., Farahvash, T., Rezaei, H. R., Torshizi, R. V., et al. (2022) · Scientific Reports · doi:10.1038/s41598-022-20763-x · Cited by 54 · see citing works

Symbiotic organs: the nexus of host–microbe evolution

Fronk, D. C., & Sachs, J. L. (2022) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2022.02.014 · Cited by 53 · see citing works

Evolutionary Conservation Genomics Reveals Recent Speciation and Local Adaptation in Threatened Takins

Yang, L., Wei, F., Zhan, X., Fan, H., Zhao, P., Huang, G., Chang, J., Lei, Y., & Hu, Y. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac111 · Cited by 53 · see citing works

CASTER: Direct species tree inference from whole-genome alignments

Zhang, C., Nielsen, R., & Mirarab, S. (2025) · Science · doi:10.1126/science.adk9688 · Cited by 51 · see citing works

Hyena paleogenomes reveal a complex evolutionary history of cross-continental gene flow between spotted and cave hyena

Westbury, M. V., Hartmann, S. A., Barlow, A., Preick, M., Ridush, B., Nagel, D., Rathgeber, T., Ziegler, R., Baryshnikov, G., Sheng, G., et al. (2020) · Science Advances · doi:10.1126/sciadv.aay0456 · Cited by 52 · see citing works

Evolutionary Constraint on Visual and Nonvisual Mammalian Opsins

Upton, B. A., Díaz, N. M., Gordon, S. A., Gelder, R. N. V., Buhr, E. D., & Lang, R. A. (2021) · Journal of Biological Rhythms · doi:10.1177/0748730421999870 · Cited by 52 · see citing works

Molecular phylogeny and historical biogeography of the cave fish genusSinocyclocheilus(Cypriniformes: Cyprinidae) in southwest China

Wen, H., Luo, T., Yali, W. A. N. G., Wang, S., Tao, L. I. U., Xiao, N., & Zhou, J. (2021) · Integrative Zoology · doi:10.1111/1749-4877.12624 · Cited by 49 · see citing works

Genome sequence and comparative analysis of reindeer (Rangifer tarandus) in northern Eurasia

Weldenegodguad, M., Pokharel, K., Ming, Y., Honkatukia, M., Peippo, J., Reilas, T., Røed, K. H., & Kantanen, J. (2020) · Scientific Reports · doi:10.1038/s41598-020-65487-y · Cited by 48 · see citing works

New physiological insights into the phenomena of deer antler: A unique model for skeletal tissue regeneration

Feleke, M., Bennett, S., Chen, J., Hu, X., Williams, D., & Xu, J. (2020) · Journal of Orthopaedic Translation · doi:10.1016/j.jot.2020.10.012 · Cited by 48 · see citing works

Multiple genome alignment in the telomere-to-telomere assembly era

Kille, B., Balaji, A., Sedlazeck, F. J., Nute, M., & Treangen, T. J. (2022) · Genome Biology · doi:10.1186/s13059-022-02735-6 · Cited by 47 · see citing works

Metabolic Enabling and Detoxification by Mammalian Gut Microbes

Dearing, M. D., & Weinstein, S. B. (2022) · Annual Review of Microbiology · doi:10.1146/annurev-micro-111121-085333 · Cited by 47 · see citing works

Phylogenetics and phylogeography of red deer mtDNA lineages during the last 50 000 years in Eurasia

Doan, K., Niedziałkowska, M., Stefaniak, K., Sykut, M. T., Jędrzejewska, B., Ratajczak‐Skrzatek, U., Piotrowska, N., Ridush, B., Zachos, F. E., Popović, D., et al. (2021) · Zoological Journal of the Linnean Society · doi:10.1093/zoolinnean/zlab025 · Cited by 47 · see citing works

Species-specific traits mediate avian demographic responses under past climate change

Germain, R. R., Feng, S., Chen, G., Graves, G. R., Tobias, J. A., Rahbek, C., Lei, F., Fjeldså, J., Hosner, P. A., Gilbert, M. T. P., et al. (2023) · Nature Ecology & Evolution · doi:10.1038/s41559-023-02055-3 · Cited by 44 · see citing works

Large-scale snake genome analyses provide insights into vertebrate development

Peng, C., Wu, D., Ren, J., Peng, Z., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., et al. (2023) · Cell · doi:10.1016/j.cell.2023.05.030 · Cited by 43 · see citing works

Joint identification of sex and sex‐linked scaffolds in non‐model organisms using low depth sequencing data

Nursyifa, C., Brüniche–Olsen, A., Garcia‐Erill, G., Heller, R., & Albrechtsen, A. (2021) · Molecular Ecology Resources · doi:10.1111/1755-0998.13491 · Cited by 43 · see citing works

Sexual selection promotes giraffoid head-neck evolution and ecological adaptation

Wang, S., Ye, J., Meng, J., Li, C., Costeur, L., Mennecart, B., Zhang, C., Zhang, J., Aiglstorfer, M., Wang, Y., et al. (2022) · Science · doi:10.1126/science.abl8316 · Cited by 41 · see citing works

Comparative genomics reveals the hybrid origin of a macaque group

Zhang, B.-L., Chen, W., Wang, Z., Pang, W. K., Luo, M., Wang, S., Shao, Y., He, W.-Q., Deng, Y., Zhou, L., et al. (2023) · Science Advances · doi:10.1126/sciadv.add3580 · Cited by 41 · see citing works

Single-cell transcriptomic landscape of the sheep rumen provides insights into physiological programming development and adaptation of digestive strategies

Yuan, Y., 西北工业大学生态环境学院, 陕. 西. 7., Sun, D., Qin, T., Mao, S., Zhu, W., Yin, Y., Huang, J., Heller, R., Li, Z., et al. (2022) · 动物学研究 · doi:10.24272/j.issn.2095-8137.2022.086 · Cited by 41 · see citing works

Evolutionary causes and consequences of ungulate migration

Abraham, J. O., Upham, N. S., Damian‐Serrano, A., & Jesmer, B. R. (2022) · Nature Ecology & Evolution · doi:10.1038/s41559-022-01749-4 · Cited by 45 · see citing works

Modes of genetic adaptations underlying functional innovations in the rumen

Pan, X., Cai, Y., Li, Z., Chen, X., Heller, R., Wang, N., Wang, Y., Zhao, C., Wang, Y., Xu, H., et al. (2020) · Science China Life Sciences · doi:10.1007/s11427-020-1828-8 · Cited by 41 · see citing works

Phylogenomics and Biogeography of Populus Based on Comprehensive Sampling Reveal Deep-Level Relationships and Multiple Intercontinental Dispersals

Wang, Y., Huang, J., Li, E., Xu, S., Zhan, Z., Zhang, X., Yang, Z., Guo, F., Liu, K., Liu, D., et al. (2022) · Frontiers in Plant Science · doi:10.3389/fpls.2022.813177 · Cited by 40 · see citing works

Adaptations to a cold climate promoted social evolution in Asian colobine primates

Qi, X., Wu, J., Zhao, L., Wang, L., Guang, X., Garber, P. A., Opie, C., Yuan, Y., Diao, R., Li, G., et al. (2023) · Science · doi:10.1126/science.abl8621 · Cited by 39 · see citing works

Multi-Omics Reveals the Impact of Exogenous Short-Chain Fatty Acid Infusion on Rumen Homeostasis: Insights into Crosstalk between the Microbiome and the Epithelium in a Goat Model

Zhen, Y., Xi, Z., Abdu, S. M. N., He, F., Han, M., Yin, J., Ge, L., Chen, Y., Wang, Y., Wei, W., et al. (2023) · Microbiology Spectrum · doi:10.1128/spectrum.05343-22 · Cited by 39 · see citing works

Genome Sequencing and Transcriptome Analysis Reveal Recent Species-Specific Gene Duplications in the Plastic Gilthead Sea Bream (Sparus aurata)

Pérez‐Sánchez, J., Naya-Català, F., Soriano, B., Piazzon, M. C., Hafez, A. I., Gabaldón, T., Lloréns, C., Sitjà‐Bobadilla, A., & Calduch-Giner, J. À. (2019) · Frontiers in Marine Science · doi:10.3389/fmars.2019.00760 · Cited by 39 · see citing works

A compendium of ruminant gastrointestinal phage genomes revealed a higher proportion of lytic phages than in any other environments

Wu, Y., Gao, N., Sun, C., Feng, T., Liu, Q., & Chen, W. (2024) · Microbiome · doi:10.1186/s40168-024-01784-2 · Cited by 38 · see citing works

Island area, body size and demographic history shape genomic diversity in Darwin's finches and related tanagers

Brüniche–Olsen, A., Kellner, K. F., & DeWoody, J. A. (2019) · Molecular Ecology · doi:10.1111/mec.15266 · Cited by 38 · see citing works

ILS-Aware Analysis of Low-Homoplasy Retroelement Insertions: Inference of Species Trees and Introgression Using Quartets.

Springer, M., Molloy, E., Sloan, D. B., Simmons, M. P., & Gatesy, J. (2019) · Journal of Heredity · doi:10.1093/jhered/esz076 · Cited by 35 · see citing works

Ruminant inner ear shape records 35 million years of neutral evolution

Mennecart, B., Dziomber, L., Aiglstorfer, M., Bibi, F., DeMiguel, D., Fujita, M., Kubo, M. O., Laurens, F., Meng, J., Métais, G., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-34656-0 · Cited by 36 · see citing works

A multi-tissue single-cell expression atlas in cattle

Han, B., Li, H., Zheng, W., Zhang, Q., Chen, A., Zhu, S., Shi, T., Wang, F., Zou, D., Yu, S., et al. (2025) · Nature Genetics · doi:10.1038/s41588-025-02329-5 · Cited by 36 · see citing works

Opportunistic sampling of wild native and invasive birds reveals a rich diversity of adenoviruses in Australia

Vaz, F. F., Raso, T. D. F., Agius, J. E., Hunt, T., Leishman, A., Eden, J., & Phalen, D. N. (2020) · Virus Evolution · doi:10.1093/ve/veaa024 · Cited by 36 · see citing works

Deer antlers: the fastest growing tissue with least cancer occurrence

Li, C., Li, Y., Wang, W., Scimeca, M., Melino, G., Du, R., & Shi, Y. (2023) · Cell Death and Differentiation · doi:10.1038/s41418-023-01231-z · Cited by 35 · see citing works

The First High-Quality Reference Genome of Sika Deer Provides Insights into High-Tannin Adaptation

Xing, X., Ai, C., Wang, T., Li, Y., Liu, H., Hu, P., Wang, G., Liu, H., Wang, H., Zhang, R., et al. (2022) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2022.05.008 · Cited by 35 · see citing works

Phylogeny and evolution of Cupressaceae: Updates on intergeneric relationships and new insights on ancient intergeneric hybridization

Liu, X.-Q., Xia, X., Chen, L., & Wang, X. (2022) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2022.107606 · Cited by 34 · see citing works

A high-quality Bougainvillea genome provides new insights into evolutionary history and pigment biosynthetic pathways in the Caryophyllales

Lan, L., Zhao, H., Xu, S., Kan, S., Zhang, X., Liu, W., Liao, X., Tembrock, L. R., Ren, Y., Reeve, W. G., et al. (2023) · Horticulture Research · doi:10.1093/hr/uhad124 · Cited by 35 · see citing works

Exploring Conflicts in Whole Genome Phylogenetics: A Case Study Within Manakins (Aves: Pipridae)

Zhao, M., Kurtis, S. M., White, N. D., Moncrieff, A. E., Leite, R. N., Brumfield, R. T., Braun, E. L., & Kimball, R. T. (2022) · Systematic Biology · doi:10.1093/sysbio/syac062 · Cited by 33 · see citing works

Chromosomal‐level genome assembly of the scimitar‐horned oryx: Insights into diversity and demography of a species extinct in the wild

Humble, E., Dobrynin, P. V., Senn, H., Chuven, J., Scott, A. F., Mohr, D. W., Dudchenko, O., Omer, A. D., Colaric, Z., Aiden, E. L., et al. (2020) · Molecular Ecology Resources · doi:10.1111/1755-0998.13181 · Cited by 32 · see citing works

Comparative Genomics Sheds Light on the Convergent Evolution of Miniaturized Wasps

Xu, H.-X., Ye, X.-H., Yang, Y.-J., Yang, Y., Sun, Y. H., Mei, Y., Xiong, S.-J., He, K., Xu, L., Fang, Q., et al. (2021) · Molecular biology and evolution · doi:10.1093/molbev/msab273 · Cited by 28 · see citing works

Current sika deer effective population size is near to reaching its historically highest level in the Japanese archipelago by release from hunting rather than climate change and top predator extinction

Iijima, H., Nagata, J., Izuno, A., Uchiyama, K., Akashi, N., Fujiki, D., & Kuriyama, T. (2023) · The Holocene · doi:10.1177/09596836231157063 · Cited by 32 · see citing works

The Ruminant Telomere-to-Telomere (RT2T) Consortium

Kalbfleisch, T., McKay, S., Murdoch, B. M., Adelson, D. L., Almansa-Villa, D., Becker, G. M., Beckett, L. M., Benítez-Galeano, M. J., Biase, F. H., Casey, T., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01835-2 · Cited by 32 · see citing works

Admixture in Mammals and How to Understand Its Functional Implications

Fontsere, C., de Manuel, M., Marquès‐Bonet, T., & Kuhlwilm, M. (2019) · BioEssays · doi:10.1002/bies.201900123 · Cited by 32 · see citing works

Characterization of intestinal microbiota and fecal cortisol, T3, and IgA in forest musk deer ( Moschus berezovskii ) from birth to weaning

Li, Y., Zhang, T., Shi, M., Zhang, B., Hu, X., Xu, S., Ding, J., Liu, S., Hu, D., & Rubenstein, D. I. (2021) · Integrative Zoology · doi:10.1111/1749-4877.12522 · Cited by 32 · see citing works

Population dynamics of caribou shaped by glacial cycles before the last glacial maximum

Taylor, R. S., Manseau, M., Klütsch, C. F. C., Polfus, J. L., Steedman, A. E., Hervieux, D., Kelly, A., Larter, N. C., Gamberg, M., Schwantje, H. M., et al. (2021) · Molecular Ecology · doi:10.1111/mec.16166 · Cited by 32 · see citing works

Warthog Genomes Resolve an Evolutionary Conundrum and Reveal Introgression of Disease Resistance Genes

Garcia‐Erill, G., Jørgensen, C. H. F., Muwanika, V. B., Wang, X., Rasmussen, M. S., de Jong, Y. A., Gaubert, P., Olayemi, A., Salmona, J., Butynski, T. M., et al. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac134 · Cited by 31 · see citing works

Giraffe lineages are shaped by major ancient admixture events

Bertola, L. D., Quinn, L. J. E., Hanghøj, K., Garcia‐Erill, G., Rasmussen, M. S., Balboa, R. F., Meisner, J., Bøggild, T., Wang, X., Lin, L., et al. (2024) · Current Biology · doi:10.1016/j.cub.2024.02.051 · Cited by 31 · see citing works

Moose genomes reveal past glacial demography and the origin of modern lineages

Dussex, N., Alberti, F., Heino, M. T., Olsen, R., van der Valk, T., Ryman, N., Laikre, L., Ahlgren, H., Askeyev, I., Askeyev, O., et al. (2020) · BMC Genomics · doi:10.1186/s12864-020-07208-3 · Cited by 27 · see citing works

Population Genomics of Wall Lizards Reflects the Dynamic History of the Mediterranean Basin

Yang, W., Feiner, N., Salvi, D., Laakkonen, H. M., Jablonski, D., Pinho, C., Carretero, M. Á., Sacchi, R., Zuffi, M. A. L., Scali, S., et al. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab311 · Cited by 30 · see citing works

Genetic advancements and future directions in ruminant livestock breeding: from reference genomes to multiomics innovations

Xu, S., Akhatayeva, Z., Liu, J., Feng, X., Yu, Y., Badaoui, B., Esmailizadeh, A., Kantanen, J., Amills, M., Lenstra, J. A., et al. (2024) · Science China Life Sciences · doi:10.1007/s11427-024-2744-4 · Cited by 29 · see citing works

Chromosome‐level genome assembly of Paralithodes platypus provides insights into evolution and adaptation of king crabs

Tang, B., Wang, Z., Liu, Q.-N., Wang, Z.-F., Ren, Y., Guo, H.-Y., Qi, T., Li, Y.-T., Zhang, H.-B., Jiang, S., et al. (2020) · Molecular Ecology Resources · doi:10.1111/1755-0998.13266 · Cited by 23 · see citing works

Genome-Wide Analysis of Nubian Ibex Reveals Candidate Positively Selected Genes That Contribute to Its Adaptation to the Desert Environment

Chebii, V. J., Oyola, S. O., Kotzé, A., Entfellner, J.-B. D., Mutuku, J. M., & Agaba, M. K. (2020) · Animals · doi:10.3390/ani10112181 · Cited by 28 · see citing works

Genome-wide identification of cyclin-dependent kinase (CDK) genes affecting adipocyte differentiation in cattle

Pan, C., Lei, Z., Wang, S., Wang, X., Wei, D., Cai, X., Luoreng, Z., Wang, L., & Ma, Y. (2021) · BMC Genomics · doi:10.1186/s12864-021-07653-8 · Cited by 28 · see citing works

High diversity, inbreeding and a dynamic Pleistocene demographic history revealed by African buffalo genomes

de Jager, D., Glanzmann, B., Möller, M., Hoal, E. G., van Helden, P. D., Harper, C. K., & Bloomer, P. (2021) · Scientific Reports · doi:10.1038/s41598-021-83823-8 · Cited by 26 · see citing works

Comparative epigenomics reveals the impact of ruminant-specific regulatory elements on complex traits

Chen, S., Liu, S., Shi, S., Jiang, Y., Cao, M., Tang, Y., Li, W., Liu, J., Fang, L., Yu, Y., et al. (2022) · BMC Biology · doi:10.1186/s12915-022-01459-0 · Cited by 27 · see citing works

Increasing Information Content and Diagnosability in Family-Level Classifications

Kuntner, M., Čandek, K., Gregorič, M., Turk, E., Hamilton, C. A., Chamberland, L., Starrett, J., Cheng, R., Coddington, J. A., Agnarsson, I., et al. (2023) · Systematic Biology · doi:10.1093/sysbio/syad021 · Cited by 25 · see citing works

Genetic adaptations of sea anemone to hydrothermal environment

Zhou, Y., Liu, H.-L., Feng, C.-G., Lu, Z.-Q., Liu, J., Huang, Y.-N., Tang, H., Xu, Z.-H., Pu, Y.-J., & Zhang, H.-B. (2023) · Science Advances · doi:10.1126/sciadv.adh0474 · Cited by 27 · see citing works

Telomere-to-telomere genome assembly of a male goat reveals variants associated with cashmere traits

Wu, H., Luo, L.-Y., Zhang, Y.-H., Zhang, C.-Y., Huang, J.-H., Mo, D., Zhao, L.-M., Wang, Z.-X., Wang, Y.-C., He-Hua, E., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-54188-z · Cited by 33 · see citing works

Early concentrate starter introduction induces rumen epithelial parakeratosis by blocking keratinocyte differentiation with excessive ruminal butyrate accumulation

Zhang, K., Zhang, Y., Qin, J., Zhu, H., Liu, N., Sun, D., Yin, Y., Mao, S., Zhu, W., Huang, Z., et al. (2023) · Journal of Advanced Research · doi:10.1016/j.jare.2023.12.016 · Cited by 26 · see citing works

Novel biosensor for sarcosine detection in prostate cancer: Combining molecular imprinted polymer and aptamer strategies

Hamdi, F., Roushani, M., & Hoseini, S. J. (2024) · Microchemical Journal · doi:10.1016/j.microc.2024.112429 · Cited by 25 · see citing works

An integrated chromosome-scale genome assembly of the Masai giraffe ( Giraffa camelopardalis tippelskirchi )

Farré, M., Li, Q., Darolti, I., Zhou, Y., Damas, J., Proskuryakova, A. A., Kulemzina, A. I., Chemnick, L. G., Kim, J., Ryder, O. A., et al. (2019) · GigaScience · doi:10.1093/gigascience/giz090 · Cited by 24 · see citing works

Genomic insights into ruminant evolution: from past to future prospects

Wang, B., Chen, L., & Wang, W. (2019) · 动物学研究 · doi:10.24272/j.issn.2095-8137.2019.061 · Cited by 25 · see citing works

Plio-Pleistocene African megaherbivore losses associated with community biomass restructuring

Bibi, F., & Cantalapiedra, J. L. (2023) · Science · doi:10.1126/science.add8366 · Cited by 25 · see citing works

Selection and Introgression Facilitated the Adaptation of Chinese Native Endangered Cattle in Extreme Environments

Liu, X., Li, Z., Yan, Y., Li, Y., Wu, H., Pei, J., Yan, P., Yang, R., Guo, X., & Lan, X. (2021) · Evolutionary Applications · doi:10.1111/eva.13168 · Cited by 23 · see citing works

Horizontal transfer and subsequent explosive expansion of a DNA transposon in sea kraits ( Laticauda )

Galbraith, J. D., Ludington, A. J., Sanders, K. L., Suh, A., & Adelson, D. L. (2021) · Biology Letters · doi:10.1098/rsbl.2021.0342 · Cited by 24 · see citing works

Genetic diversity and selection signatures in Hainan black goats revealed by whole-genome sequencing data

An, Z. X., Shi, L., Hou, G., Zhou, H., & Xun, W. (2024) · animal · doi:10.1016/j.animal.2024.101147 · Cited by 24 · see citing works

Comparative Microbiome Analysis Reveals the Ecological Relationships Between Rumen Methanogens, Acetogens, and Their Hosts

Li, Z., Wang, X., Alberdi, A., Deng, J., Zhong, Z., Si, H., Zheng, C., Zhou, H., Wang, J., Yang, Y., et al. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.01311 · Cited by 23 · see citing works

Augmin-dependent microtubule self-organization drives kinetochore fiber maturation in mammals

Almeida, A. C., Soares-de-Oliveira, J., Drpic, D., Cheeseman, L. P., Damas, J., Lewin, H. A., Larkin, D. M., Aguiar, P., Pereira, A. J., & Maiato, H. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.110610 · Cited by 23 · see citing works

Phylogeny and characteristics of ruminants

Zahn, L. M. (2019) · Science · doi:10.1126/science.364.6446.1146-j

Genetic basis of ruminant headgear and rapid antler regeneration

Wang, Y., Zhang, C., Wang, N., Li, Z., Heller, R., Liu, R., Zhao, Y., Han, J., Pan, X., Zheng, Z., et al. (2019) · Science · doi:10.1126/science.aav6335 · Cited by 186 · see citing works

Biological adaptations in the Arctic cervid, the reindeer ( Rangifer tarandus )

Lin, Z., Chen, L., Chen, X., Zhong, Y., Yang, Y., Xia, W., Liu, C., Zhu, W., Wang, H., Yan, B., et al. (2019) · Science · doi:10.1126/science.aav6312 · Cited by 85 · see citing works

Data from: Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits

Chen, L., Qiu, Q., Jiang, Y., Wang, K., Lin, Z., Li, Z., Zhang, G., Heller, R., & Wang, W. (2019) · Data Archiving and Networked Services (DANS) · doi:10.5061/dryad.52213gc · Cited by 1 · see citing works

Ruminant phylogenetics: A reproductive biological perspective

Silvia, W. J. (2019) · Bioscientifica Proceedings · doi:10.1530/biosciprocs.8.001 · Cited by 2 · see citing works