| MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes BL Cantarel, I Korf, SMC Robb, G Parra, E Ross, B Moore, C Holt, ... Genome research 18 (1), 188-196, 2008 | 1787 | 2008 |
| MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects C Holt, M Yandell BMC bioinformatics 12, 1-14, 2011 | 1770 | 2011 |
| Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution JJ Smith, S Kuraku, C Holt, T Sauka-Spengler, N Jiang, MS Campbell, ... Nature genetics 45 (4), 415-421, 2013 | 697 | 2013 |
| Genome annotation and curation using MAKER and MAKER‐P MS Campbell, C Holt, B Moore, M Yandell Current protocols in bioinformatics 48 (1), 4.11. 1-4.11. 39, 2014 | 618 | 2014 |
| Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies DB Neale, JL Wegrzyn, KA Stevens, AV Zimin, D Puiu, MW Crepeau, ... Genome biology 15, 1-13, 2014 | 544 | 2014 |
| Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire CA Lévesque, H Brouwer, L Cano, JP Hamilton, C Holt, E Huitema, ... Genome biology 11, 1-22, 2010 | 422 | 2010 |
| MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations MS Campbell, MY Law, C Holt, JC Stein, GD Moghe, DE Hufnagel, J Lei, ... Plant physiology 164 (2), 513-524, 2014 | 408 | 2014 |
| Genomic signatures of evolutionary transitions from solitary to group living KM Kapheim, H Pan, C Li, SL Salzberg, D Puiu, T Magoc, HM Robertson, ... Science 348 (6239), 1139-1143, 2015 | 386 | 2015 |
| Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile) CD Smith, A Zimin, C Holt, E Abouheif, R Benton, E Cash, V Croset, ... Proceedings of the National Academy of Sciences 108 (14), 5673-5678, 2011 | 329 | 2011 |
| Draft genome of the red harvester ant Pogonomyrmex barbatus CR Smith, CD Smith, HM Robertson, M Helmkampf, A Zimin, M Yandell, ... Proceedings of the National Academy of Sciences 108 (14), 5667-5672, 2011 | 299 | 2011 |
| The Genome Sequence of the Leaf-Cutter Ant Atta cephalotes Reveals Insights into Its Obligate Symbiotic Lifestyle G Suen, C Teiling, L Li, C Holt, E Abouheif, E Bornberg-Bauer, P Bouffard, ... PLoS genetics 7 (2), e1002007, 2011 | 288 | 2011 |
| The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution JJ Smith, N Timoshevskaya, C Ye, C Holt, MC Keinath, HJ Parker, ... Nature genetics 50 (2), 270-277, 2018 | 276 | 2018 |
| Unique Features of the Loblolly Pine (Pinus taeda L.) Megagenome Revealed Through Sequence Annotation JL Wegrzyn, JD Liechty, KA Stevens, LS Wu, CA Loopstra, ... Genetics 196 (3), 891-909, 2014 | 246 | 2014 |
| The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences A Kovach, JL Wegrzyn, G Parra, C Holt, GE Bruening, CA Loopstra, ... BMC genomics 11, 1-14, 2010 | 170 | 2010 |
| Amyloid-β 11C-PiB-PET imaging results from 2 randomized bapineuzumab phase 3 AD trials E Liu, ME Schmidt, R Margolin, R Sperling, R Koeppe, NS Mason, ... Neurology 85 (8), 692-700, 2015 | 164 | 2015 |
| Quantitative measures for the management and comparison of annotated genomes K Eilbeck, B Moore, C Holt, M Yandell BMC bioinformatics 10, 1-15, 2009 | 153 | 2009 |
| The Douglas-fir genome sequence reveals specialization of the photosynthetic apparatus in Pinaceae DB Neale, PE McGuire, NC Wheeler, KA Stevens, MW Crepeau, ... G3: Genes, Genomes, Genetics 7 (9), 3157-3167, 2017 | 104 | 2017 |
| First fungal genome sequence from Africa: a preliminary analysis BD Wingfield, ET Steenkamp, QC Santana, MPA Coetzee, S Bam, ... South African Journal of Science 108 (1), 1-9, 2012 | 62 | 2012 |
| Improved Genome Assembly and Annotation for the Rock Pigeon (Columba livia) C Holt, M Campbell, DA Keays, N Edelman, A Kapusta, E Maclary, ... G3: Genes, Genomes, Genetics 8 (5), 1391-1398, 2018 | 56 | 2018 |
| Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes MY Law, KL Childs, MS Campbell, JC Stein, AJ Olson, C Holt, N Panchy, ... Plant physiology 167 (1), 25-39, 2015 | 55 | 2015 |
