Citations for GeneMarkS (717 citations)


1.         Henne, A., et al. (2004). "The genome sequence of the extreme thermophile Thermus thermophilus." Nat Biotechnol 22(5): 547-553.

2.         Philippe, N., et al. (2013). "Pandoraviruses: Amoeba Viruses with Genomes Up to 2.5 Mb Reaching That of Parasitic Eukaryotes." Science 341(6143): 281-286.

3.         O'Leary, N. A., et al (2015). "Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation." Nucleic acids research, gkv1189.


Citations for GeneMark.hmm (1310 citations)


1.         Frost, L. S., et al. (2005). "Mobile genetic elements: The agents of open source evolution." Nature Reviews Microbiology 3(9): 722-732.

2.         La Scola, B., et al. (2008). "The virophage as a unique parasite of the giant mimivirus." Nature 455(7209): 100-U165.

3.         Mavromatis, K., et al. (2007). "Use of simulated data sets to evaluate the fidelity of metagenomics processing methods." Nature Methods 4(6): 495-500.

4.         Oliynyk, M., et al. (2007). "Complete genome sequence of the erythromycin-producing bacterium Saccharopolyspora erythraea NRRL23338." Nat Biotechnol 25(4): 447-453.

5.         Perna, N. T., et al. (2001). "Genome sequence of enterohaemorrhagic Escherichia coli O157: H7 (vol 409, pg 529, 2001)." Nature 410(6825): 240-240.

6.         Stover, C. K., et al. (2000). "Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen." Nature 406(6799): 959-964.

7.         Theologis, A., et al. (2000). "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana." Nature 408(6814): 816-820.

8.         Venter, J. C., et al. (2003). "Massive parallelism, randomness and genomic advances." Nature Genetics 33: 219-227.

9.         Wang, J., et al. (2003). "Vertebrate gene predictions and the problem of large genes." Nature Reviews Genetics 4(9): 741-749.

10.     Wang, R. H., et al. (2009). "PEP1 regulates perennial flowering in Arabis alpina." Nature 459(7245): 423-U138.

11.     Yandell, M. and D. Ence (2012). "A beginner's guide to eukaryotic genome annotation." Nature Reviews Genetics 13(5): 329-342.

12.     Boyer, M., et al. (2009). "Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms." Proceedings of the National Academy of Sciences of the United States of America 106(51): 21848-21853.


Citations for GeneMark (725 citations)


1.         Beaumont, M. A. and B. Rannala (2004). "The Bayesian revolution in genetics." Nature Reviews Genetics 5(4): 251-261.

2.         Griffiths, S., et al. (2006). "Molecular characterization of Ph1 as a major chromosome pairing locus in polyploid wheat." Nature 439(7077): 749-752.

3.         Nakamura, Y., et al. (2004). "Biased biological functions of horizontally transferred genes in prokaryotic genomes." Nature Genetics 36(7): 760-766.

4.         O'Connell, R. J., et al. (2012). "Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses." Nature Genetics 44(9): 1060

5.         Sharan, R. and T. Ideker (2006). "Modeling cellular machinery through biological network comparison." Nat Biotechnol 24(4): 427-433.

6.         Audic, S. and J. M. Claverie (1998). "Self-identification of protein-coding regions in microbial genomes." Proceedings of the National Academy of Sciences of the United States of America 95(17): 10026-10031.

7.         Fitz-Gibbon, S. T., et al. (2002). "Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum." Proceedings of the National Academy of Sciences of the United States of America 99(2): 984-989.

8.         J A Noble, M A Innis, E V Koonin, K E Rudd, F Banuett, and I Herskowitz "The Escherichia coli hflA locus encodes a putative GTP-binding protein and two membrane proteins, one of which contains a protease-like domain", PNAS 1993 90 (22) 10866-10870

9.         Fleischmann, R. D., et al. (1995). "Whole-genome random sequencing and assembly of Haemophilus influenzae Rd." Science 269(5223): 496-512.

10.     Blattner, F. R., et al. (1997). "The complete genome sequence of Escherichia coli K-12." Science 277(5331): 1453

11.     Bult, C. J., et al. (1996). "Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii." Science 273(5278): 1058-1073.


Citations for Heuristic Models (293 citations)


1.         Stein, L. (2001). "Genome annotation: From sequence to biology." Nature Reviews Genetics 2(7): 493-503.

2.         Martinez-Garcia, et al. (2014). "Unveiling viral-host interactions within the microbial dark matter". Nature communications, 5.


Citations for GeneMark Web Server (323 citations)


1.         Iverson, V., et al. (2012). "Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota." Science 335(6068): 587-590.


Citations for GeneMark-ES, version 1 (229 citations)


1.         Peyretaillade, E., et al. (2012). "Annotation of microsporidian genomes using transcriptional signals." Nat Commun 3.

2.         Shulaev, V., et al. (2011). "The genome of woodland strawberry (Fragaria vesca)." Nature Genetics 43(2): 109-116.

3.         Zheng, H., et al. (2013). "The genome of the hydatid tapeworm Echinococcus granulosus." Nature Genetics 45: 1168-1175

4.         Suga, H., et al. (2013). "The Capsaspora genome reveals a complex unicellular prehistory of animals." Nat Commun 4.

5.         Yang, E., et al. (2012). "Origin and evolution of carnivorism in the Ascomycota (fungi)." Proc Natl Acad Sci USA 109(27): 10960-10965.

6.         Ming, R., et al. (2015). The pineapple genome and the evolution of CAM photosynthesis. Nature genetics, 47(12), 1435-1442.


Citations for GeneMark-ES, version 2 (185 citations)


1.         Berka, R. M., et al. (2011). "Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris." Nat Biotechnol 29(10): 922-U222.

2.         De Schutter, K., et al. (2009). "Genome sequence of the recombinant protein production host Pichia pastoris." Nat Biotechnol 27(6): 561-U104.

3.         Neafsey, D. E., et al. (2012). "The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum." Nature Genetics 44(9): 1046-+.

4.         Yandell, M. and D. Ence (2012). "A beginner's guide to eukaryotic genome annotation." Nature Reviews Genetics 13(5): 329-342.

5.         Zheng, A. P., et al. (2013). "The evolution and pathogenic mechanisms of the rice sheath blight pathogen." Nat Commun 4.

6.         Kapheim, K. M., et al. (2015). Genomic signatures of evolutionary transitions from solitary to group living. Science, 348(6239), 1139-1143.

7.         Zhang, Y., et al. (2014). Specific adaptation of Ustilaginoidea virens in occupying host florets revealed by comparative and functional genomics. Nature communications, 5.

8.         Foth, B. J., et al. (2014). Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction. Nature genetics, 46(7), 693-700

9.         Ye, N., et al. (2015). Saccharina genomes provide novel insight into kelp biology. Nature communications, 6.

10.     Kupper, C., et al. (2015). A supergene determines highly divergent male reproductive morphs in the ruff. Nature genetics.

11.     Olsen, J. L., et al. (2016). The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea. Nature.


Citations for MetaGeneMark (201 citations)


1.         Karlsson, F. H., et al. (2012). "Symptomatic atherosclerosis is associated with an altered gut metagenome." Nat Commun 3.

2.         Karlsson, F. H., et al. (2013). "Gut metagenome in European women with normal, impaired and diabetic glucose control." Nature 498(7452): 99-+.

3.         Tyakht, A. V., et al. (2013). "Human gut microbiota community structures in urban and rural populations in Russia." Nat Commun 4: 2469.

4.         Roth, Adam, et al. (2014). "A widespread self-cleaving ribozyme class is revealed by bioinformatics" Nature chemical biology 10.1: 56-60

5.         Nielsen, H. B., et al. (2014). Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nature biotechnology, 32(8), 822-828.

6.         Li, J., Jia, et al. (2014). An integrated catalog of reference genes in the human gut microbiome. Nature biotechnology, 32(8), 834-841

7.         Oh, J., Byrd, et al. (2014). Biogeography and individuality shape function in the human skin metagenome. Nature, 514(7520), 59-64

8.         Forsberg, K. J., et al. (2014). Bacterial phylogeny structures soil resistomes across habitats. Nature, 509(7502), 612.

9.         Zhou, X., et al. (2014). Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history. Nature genetics, 46(12), 1303-1310.

10.     Ivanova, Natalia N., et al. (2014). "Stop codon reassignments in the wild." Science 344.6186: 909-913.

11.     Roth, Adam, et al. (2014). A widespread self-cleaving ribozyme class is revealed by bioinformatics." Nature chemical biology 10.1: 56-60.

12.     Buchfink, et al (2015). "Fast and sensitive protein alignment using DIAMOND." Nature methods 12.1: 59-60.

13.     Weinberg, Zasha, et al (2015). "New classes of self-cleaving ribozymes revealed by comparative genomics analysis." Nature chemical biology 11.8: 606-610.

14.     Sunagawa, Shinichi, et al. (2015). "Structure and function of the global ocean microbiome." Science 348.6237: 1261359.

15.     Ofek-Lalzar, Maya, et al. (2014). "Niche and host-associated functional signatures of the root surface microbiome." Nature communications 5.

16.     Kuleshov, Volodymyr, et al. (2016). "Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome." Nature biotechnology 34.1: 64-69.


Last time updated: Feb. 2016