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

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

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

Fast gapped-read alignment with Bowtie 2

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

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

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

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

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

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

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 16,450

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

PAML 4: Phylogenetic Analysis by Maximum Likelihood

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

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

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 13,104

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

APE: analyses of phylogenetics and evolution in R language

Paradis, E., Claude, J., & Strimmer, K. (2004) · Bioinformatics · doi:10.1093/bioinformatics/btg412 · Cited by 11,335

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 11,073

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

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

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 6,454

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

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

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

Quality control and preprocessing of metagenomic datasets

Schmieder, R., & Edwards, R. A. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr026 · Cited by 5,119

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

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 5,073

Wound Healing--Aiming for Perfect Skin Regeneration

Martin, P. B. (1997) · Science · doi:10.1126/science.276.5309.75 · Cited by 4,842

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

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 4,083

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 3,971 · cited 1×

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

Pathogen Recognition and Inflammatory Signaling in Innate Immune Defenses

Mogensen, T. H. (2009) · Clinical Microbiology Reviews · doi:10.1128/cmr.00046-08 · Cited by 3,296

Gene finding in novel genomes

Korf, I. F. (2004) · BMC Bioinformatics · doi:10.1186/1471-2105-5-59 · Cited by 3,228

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 2,942

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

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

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 2,625

Inference of human population history from individual whole-genome sequences

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

GeneWise and genomewise

Birney, E., Clamp, M., & Durbin, R. (2004) · Genome Research · doi:10.1101/gr.1865504 · Cited by 2,542

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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., Milan, D., Megens, H., et al. (2012) · Nature · doi:10.1038/nature11622 · Cited by 1,424

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

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 1,287

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

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 1,168

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

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

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

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 986

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 983

Divergence time and evolutionary rate estimation with multilocus data.

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

Factors That Alter Rumen Microbial Ecology

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

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 868

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 866

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 842

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

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

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

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 746

Animal Genome Size Database

Gregory, T. R. (2002) · Cited by 663

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 652

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 639

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 638

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

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

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 586

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

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

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 556

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

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×

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

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

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

(2010) · CABI eBooks · doi:10.1079/9781845936730.0000 · Cited by 472

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 472

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

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

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 465

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

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

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 409

The Evolution of Artiodactyls

Prothero, D. R. (2007) · Johns Hopkins University Press eBooks · doi:10.56021/9780801887352 · Cited by 384

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 366

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

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

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 331

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 324

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

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

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

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

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 280

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

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

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

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 267

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

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 255

Regulation of bone development and maintenance by Runx2

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

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

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 237

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 235

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 225

The Phusion Assembler

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

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 221

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 215

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

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

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

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

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

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

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 178

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

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 153

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

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

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

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 144

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

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 135

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

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 123

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

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

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 113

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

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

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

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 100

The Human Genome

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

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

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 95

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

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

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

Bovids of the World

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

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 80

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

Ecology of Ungulates

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

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 76

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

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 69

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

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

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 67

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 66

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 64

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 63

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

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

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

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

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

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

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 47

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

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

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

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 40

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 39

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

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

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

Ardipithecus Kadabba

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

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

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 27

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

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

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

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

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

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

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

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

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. F., Janke, A., & Nilsson, M. A. (2015) · Gene · doi:10.1016/j.gene.2015.06.064 · Cited by 10

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

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

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

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

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

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 204

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

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

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 185

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

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 89

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

Ruminant phylogenetics: A reproductive biological perspective

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