| Year |
Citation |
Score |
| 2023 |
Maclary ET, Holt C, Concepcion GT, Sović I, Vickrey AI, Yandell M, Kronenberg Z, Shapiro MD. Assembly and annotation of two high-quality columbid reference genomes from sequencing of a Columba livia x Columba guinea F1 hybrid. G3 (Bethesda, Md.). PMID 38066578 DOI: 10.1093/g3journal/jkad280 |
0.695 |
|
| 2023 |
Maclary ET, Holt C, Concepcion GT, Sović I, Vickrey AI, Yandell M, Kronenberg Z, Shapiro MD. Assembly and annotation of two high-quality columbid reference genomes from sequencing of a x F hybrid. Biorxiv : the Preprint Server For Biology. PMID 37873124 DOI: 10.1101/2023.10.11.561892 |
0.699 |
|
| 2023 |
Amaral P, Carbonell-Sala S, Vega FM, Faial T, Frankish A, Gingeras T, Guigo R, Harrow JL, Hatzigeorgiou AG, Johnson R, Murphy TD, Pertea M, Pruitt KD, Pujar S, Takahashi H, ... ... Yandell M, et al. The status of the human gene catalogue. Arxiv. PMID 36994150 |
0.345 |
|
| 2023 |
Timoshevskaya N, Eşkut KI, Timoshevskiy VA, Robb SMC, Holt C, Hess JE, Parker HJ, Baker CF, Miller AK, Saraceno C, Yandell M, Krumlauf R, Narum SR, Lampman RT, Gemmell NJ, et al. An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes. Cell Reports. 42: 112263. PMID 36930644 DOI: 10.1016/j.celrep.2023.112263 |
0.306 |
|
| 2022 |
Nicholas TJ, Al-Sweel N, Farrell A, Mao R, Bayrak-Toydemir P, Miller CE, Bentley D, Palmquist R, Moore B, Hernandez EJ, Cormier MJ, Fredrickson E, Noble K, Rynearson S, Holt C, ... ... Yandell M, et al. Comprehensive variant calling from whole-genome sequencing identifies a complex inversion that disrupts ZFPM2 in familial congenital diaphragmatic hernia. Molecular Genetics & Genomic Medicine. e1888. PMID 35119225 DOI: 10.1002/mgg3.1888 |
0.302 |
|
| 2021 |
Fouks B, Brand P, Nguyen HN, Herman J, Camara F, Ence D, Hagen D, Hoff KJ, Nachweide S, Romoth L, Walden KK, Guigo R, Stanke M, Narzisi G, Yandell M, et al. The genomic basis of evolutionary differentiation among honey bees. Genome Research. PMID 33947700 DOI: 10.1101/gr.272310.120 |
0.343 |
|
| 2021 |
Tollis M, Ferris E, Campbell MS, Harris VK, Rupp SM, Harrison TM, Kiso WK, Schmitt DL, Garner MM, Athena Aktipis C, Maley CC, Boddy AM, Yandell M, Gregg C, Schiffman JD, et al. Elephant Genomes Reveal Accelerated Evolution in Mechanisms Underlying Disease Defenses. Molecular Biology and Evolution. PMID 33944920 DOI: 10.1093/molbev/msab127 |
0.346 |
|
| 2020 |
Bogenschutz EL, Fox ZD, Farrell A, Wynn J, Moore B, Yu L, Aspelund G, Marth G, Yandell M, Shen Y, Chung WK, Kardon G. Deep whole-genome sequencing of multiple proband tissues and parental blood reveals the complex genetic etiology of congenital diaphragmatic hernias. Hgg Advances. 1. PMID 33263113 DOI: 10.1016/j.xhgg.2020.100008 |
0.358 |
|
| 2020 |
Bruders R, Van Hollebeke H, Osborne EJ, Kronenberg Z, Maclary E, Yandell M, Shapiro MD. A copy number variant is associated with a spectrum of pigmentation patterns in the rock pigeon (Columba livia). Plos Genetics. 16: e1008274. PMID 32433666 DOI: 10.1371/Journal.Pgen.1008274 |
0.718 |
|
| 2020 |
Lu A, Watkins M, Li Q, Robinson SD, Concepcion GP, Yandell M, Weng Z, Olivera BM, Safavi-Hemami H, Fedosov AE. Transcriptomic profiling reveals extraordinary diversity of venom peptides in unexplored predatory gastropods of the genus Clavus. Genome Biology and Evolution. PMID 32333764 DOI: 10.1093/Gbe/Evaa083 |
0.307 |
|
| 2020 |
Gorsi B, Moriwaki M, Moore MB, Rajkovic A, Nelson LM, Yandell M, Welt CK. OR31-06 Candidate Gene Variants in a Large Cohort of Women with Primary Ovarian Insufficiency Journal of the Endocrine Society. 4. DOI: 10.1210/Jendso/Bvaa046.1419 |
0.422 |
|
| 2020 |
Wesolowski S, Nussenzveig R, Santos VS, Esther J, Goel D, Swami U, Gupta S, Maughan BL, Yandell M, Grivas P, Agarwal N. Genomic correlates of response to PD-1 axis inhibitors (IO) in metastatic urothelial cancer (mUC) using explainable artificial intelligence (AI). Journal of Clinical Oncology. 38: 570-570. DOI: 10.1200/Jco.2020.38.6_Suppl.570 |
0.358 |
|
| 2020 |
Lin E, Wesolowski S, Nussenzveig R, McFarland TR, Swami U, Maughan BL, Yandell M, Agarwal N. Identification of genomic alterations in signaling pathways associated with poor survival in newly diagnosed metastatic prostate cancer (mCSPC) using artificial intelligence (AI). Journal of Clinical Oncology. 38: 169-169. DOI: 10.1200/Jco.2020.38.6_Suppl.169 |
0.364 |
|
| 2020 |
Lin E, Hahn AW, Nussenzveig R, Wesolowski S, Maughan BL, McFarland TR, Rathi N, Sartor AO, Sonpavde G, Swami U, Kohli M, Rich TA, Yandell M, Agarwal N. Genomic alterations associated with the progression from castration-sensitive to castration-resistant metastatic prostate cancer based on machine learning analysis of cell-free DNA genomic profile. Journal of Clinical Oncology. 38: e17596-e17596. DOI: 10.1200/Jco.2020.38.15_Suppl.E17596 |
0.316 |
|
| 2019 |
Watkins WS, Hernandez EJ, Wesolowski S, Bisgrove BW, Sunderland RT, Lin E, Lemmon G, Demarest BL, Miller TA, Bernstein D, Brueckner M, Chung WK, Gelb BD, Goldmuntz E, Newburger JW, ... ... Yandell M, et al. De novo and recessive forms of congenital heart disease have distinct genetic and phenotypic landscapes. Nature Communications. 10: 4722. PMID 31624253 DOI: 10.1038/S41467-019-12582-Y |
0.406 |
|
| 2019 |
Berauer JP, Mezina AI, Okou DT, Sabo A, Muzny DM, Gibbs RA, Hegde MR, Chopra P, Cutler DJ, Perlmutter DH, Bull LN, Thompson RJ, Loomes KM, Spinner NB, Rajagopalan R, ... ... Yandell M, et al. Identification of PKD1L1 Gene Variants in Children with the Biliary Atresia Splenic Malformation Syndrome. Hepatology (Baltimore, Md.). PMID 30664273 DOI: 10.1002/Hep.30515 |
0.335 |
|
| 2019 |
Lin E, Hahn AW, Sonpavde G, Lilly MB, Nussenzveig R, Ledet E, Pal SK, Grivas P, Rich TA, Raymond VM, Sartor AO, Yandell M, Agarwal N. Discovery of targetable mutational signatures in advanced prostate cancer (aPC) using machine learning and next-generation sequencing (NGS) of circulating tumor DNA (ctDNA). Journal of Clinical Oncology. 37: 226-226. DOI: 10.1200/Jco.2019.37.7_Suppl.226 |
0.359 |
|
| 2019 |
Lin E, Hahn AW, Sonpavde G, Lilly MB, Nussenzveig R, Ledet E, Pal SK, Grivas P, Rich TA, Raymond VM, Sartor AO, Yandell M, Agarwal N. Profiling of genomic alterations in MAPK/ERK signaling in a large cohort of metastatic prostate cancer (mPC) patients. Journal of Clinical Oncology. 37: 5032-5032. DOI: 10.1200/Jco.2019.37.15_Suppl.5032 |
0.387 |
|
| 2018 |
Li Q, Watkins M, Robinson SD, Safavi-Hemami H, Yandell M. Discovery of Novel Conotoxin Candidates Using Machine Learning. Toxins. 10. PMID 30513724 DOI: 10.3390/Toxins10120503 |
0.318 |
|
| 2018 |
Smith JJ, Timoshevskaya N, Ye C, Holt C, Keinath MC, Parker HJ, Cook ME, Hess JE, Narum SR, Lamanna F, Kaessmann H, Timoshevskiy VA, Waterbury CKM, Saraceno C, Wiedemann LM, ... ... Yandell M, et al. Publisher Correction: The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution. Nature Genetics. PMID 30224652 DOI: 10.1038/S41588-018-0199-4 |
0.321 |
|
| 2018 |
Vickrey AI, Bruders R, Kronenberg Z, Mackey E, Bohlender RJ, Maclary ET, Maynez R, Osborne EJ, Johnson KP, Huff CD, Yandell M, Shapiro MD. Introgression of regulatory alleles and a missense coding mutation drive plumage pattern diversity in the rock pigeon. Elife. 7. PMID 30014848 DOI: 10.7554/Elife.34803 |
0.725 |
|
| 2018 |
Peterson KA, Yoshigi M, Hazel MW, Delker DA, Lin E, Krishnamurthy C, Consiglio N, Robson J, Yandell M, Clayton F. RNA sequencing confirms similarities between PPI-responsive oesophageal eosinophilia and eosinophilic oesophagitis. Alimentary Pharmacology & Therapeutics. PMID 29863285 DOI: 10.1111/Apt.14825 |
0.304 |
|
| 2018 |
Liu MJ, Sugimoto K, Uygun S, Panchy N, Campbell MS, Yandell M, Howe GA, Shiu SH. Regulatory Divergence in Wound-Responsive Gene Expression between Domesticated and Wild Tomato. The Plant Cell. PMID 29743197 DOI: 10.1105/Tpc.18.00194 |
0.329 |
|
| 2018 |
Majoros WH, Holt C, Campbell MS, Ware D, Yandell M, Reddy TE. Predicting Gene Structure Changes Resulting from Genetic Variants via Exon Definition Features. Bioinformatics (Oxford, England). PMID 29701825 DOI: 10.1093/Bioinformatics/Bty324 |
0.399 |
|
| 2018 |
Smith JJ, Timoshevskaya N, Ye C, Holt C, Keinath MC, Parker HJ, Cook ME, Hess JE, Narum SR, Lamanna F, Kaessmann H, Timoshevskiy VA, Waterbury CKM, Saraceno C, Wiedemann LM, ... ... Yandell M, et al. Publisher Correction: The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution. Nature Genetics. PMID 29674745 DOI: 10.1038/S41588-018-0075-2 |
0.334 |
|
| 2018 |
Holt C, Campbell M, Keays DA, Edelman N, Kapusta A, Maclary E, Domyan E, Suh A, Warren WC, Yandell M, Gilbert MTP, Shapiro MD. Improved Genome Assembly and Annotation for the Rock Pigeon (). G3 (Bethesda, Md.). PMID 29519939 DOI: 10.1534/G3.117.300443 |
0.437 |
|
| 2018 |
Flygare S, Hernandez EJ, Phan L, Moore B, Li M, Fejes A, Hu H, Eilbeck K, Huff C, Jorde L, G Reese M, Yandell M. The VAAST Variant Prioritizer (VVP): ultrafast, easy to use whole genome variant prioritization tool. Bmc Bioinformatics. 19: 57. PMID 29463208 DOI: 10.1186/S12859-018-2056-Y |
0.412 |
|
| 2018 |
Smith JJ, Timoshevskaya N, Ye C, Holt C, Keinath MC, Parker HJ, Cook ME, Hess JE, Narum SR, Lamanna F, Kaessmann H, Timoshevskiy VA, Waterbury CKM, Saraceno C, Wiedemann LM, ... ... Yandell M, et al. The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution. Nature Genetics. PMID 29358652 DOI: 10.1038/S41588-017-0036-1 |
0.412 |
|
| 2018 |
Vickrey AI, Bruders R, Kronenberg Z, Mackey E, Bohlender RJ, Maclary ET, Maynez R, Osborne EJ, Johnson KP, Huff CD, Yandell M, Shapiro MD. Author response: Introgression of regulatory alleles and a missense coding mutation drive plumage pattern diversity in the rock pigeon Elife. DOI: 10.7554/Elife.34803.037 |
0.675 |
|
| 2017 |
Yu Y, Hu H, Bohlender RJ, Hu F, Chen JS, Holt C, Fowler J, Guthery SL, Scheet P, Hildebrandt MA, Yandell M, Huff CD. XPAT: a toolkit to conduct cross-platform association studies with heterogeneous sequencing datasets. Nucleic Acids Research. PMID 29294048 DOI: 10.1093/Nar/Gkx1280 |
0.374 |
|
| 2017 |
Jin SC, Homsy J, Zaidi S, Lu Q, Morton S, DePalma SR, Zeng X, Qi H, Chang W, Sierant MC, Hung WC, Haider S, Zhang J, Knight J, Bjornson RD, ... ... Yandell M, et al. Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands. Nature Genetics. PMID 28991257 DOI: 10.1038/Ng.3970 |
0.396 |
|
| 2017 |
Li Q, Barghi N, Lu A, Fedosov AE, Bandyopadhyay PK, Lluisma AO, Concepcion GP, Yandell M, Olivera BM, Safavi-Hemami H. Divergence of the Venom Exogene Repertoire in Two Sister Species of Turriconus. Genome Biology and Evolution. 9: 2211-2225. PMID 28922871 DOI: 10.1093/Gbe/Evx157 |
0.366 |
|
| 2017 |
Eilbeck K, Quinlan A, Yandell M. Settling the score: variant prioritization and Mendelian disease. Nature Reviews. Genetics. PMID 28804138 DOI: 10.1038/Nrg.2017.52 |
0.418 |
|
| 2017 |
Neale DB, McGuire PE, Wheeler NC, Stevens KA, Crepeau MW, Cardeno C, Zimin AV, Puiu D, Pertea GM, Sezen UU, Casola C, Koralewski TE, Paul R, Gonzalez-Ibeas D, Zaman S, ... ... Yandell M, et al. The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae. G3 (Bethesda, Md.). PMID 28751502 DOI: 10.1534/G3.117.300078 |
0.444 |
|
| 2017 |
Young EL, Maese L, Robinson R, Pflieger L, Moore B, Rynearson S, Fowler T, Tavtigian SV, Yandell M, Mason CC, Hawkins DS, Lupo PJ, Schiffman JD. Abstract 2704: Pathogenic mutations and variants of unknown significance (VUS) in cancer predisposition genes are associated with over 10% of pediatric rhabdomyosarcoma: a report from the Children’s Oncology Group Cancer Research. 77: 2704-2704. DOI: 10.1158/1538-7445.Am2017-2704 |
0.36 |
|
| 2016 |
Majoros WH, Campbell MS, Holt C, DeNardo E, Ware D, Allen AS, Yandell M, Reddy TE. High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE. Bioinformatics (Oxford, England). PMID 28011790 DOI: 10.1093/Bioinformatics/Btw799 |
0.445 |
|
| 2016 |
Cone KR, Kronenberg ZN, Yandell M, Elde NC. Emergence of a viral RNA polymerase variant during gene copy number amplification promotes rapid evolution of vaccinia virus. Journal of Virology. PMID 27928012 DOI: 10.1128/Jvi.01428-16 |
0.702 |
|
| 2016 |
Hu H, Coon H, Li M, Yandell M, Huff CD. VARPRISM: incorporating variant prioritization in tests of de novo mutation association. Genome Medicine. 8: 91. PMID 27562213 DOI: 10.1186/S13073-016-0341-9 |
0.375 |
|
| 2016 |
Campbell M, Oakeson KF, Yandell M, Halpert JR, Dearing D. The draft genome sequence and annotation of the desert woodrat Neotoma lepida. Genomics Data. 9: 58-9. PMID 27408812 DOI: 10.1016/J.Gdata.2016.06.008 |
0.401 |
|
| 2016 |
Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, Berlin AM, Campbell MS, Barrell D, Martin KJ, Mulley JF, ... ... Yandell M, et al. Corrigendum: The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nature Genetics. 48: 700. PMID 27230688 DOI: 10.1038/Ng0616-700C |
0.39 |
|
| 2016 |
Barber MF, Kronenberg Z, Yandell M, Elde NC. Antimicrobial Functions of Lactoferrin Promote Genetic Conflicts in Ancient Primates and Modern Humans. Plos Genetics. 12: e1006063. PMID 27203426 DOI: 10.1371/Journal.Pgen.1006063 |
0.672 |
|
| 2016 |
Domyan ET, Kronenberg Z, Infante CR, Vickrey AI, Stringham SA, Bruders R, Guernsey MW, Park S, Payne J, Beckstead RB, Kardon G, Menke DB, Yandell M, Shapiro MD. Molecular shifts in limb identity underlie development of feathered feet in two domestic avian species. Elife. 5. PMID 26977633 DOI: 10.7554/Elife.12115 |
0.687 |
|
| 2016 |
Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, Berlin AM, Campbell MS, Barrell D, Martin KJ, Mulley JF, ... ... Yandell M, et al. The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nature Genetics. 48: 427-37. PMID 26950095 DOI: 10.1038/Ng.3526 |
0.455 |
|
| 2016 |
Graf EH, Simmon KE, Tardif KD, Hymas W, Flygare S, Eilbeck K, Yandell M, Schlaberg R. Unbiased Detection of Respiratory Viruses Using RNA-seq-Based Metagenomics: A Systematic Comparison to A Commercial PCR Panel. Journal of Clinical Microbiology. PMID 26818672 DOI: 10.1128/Jcm.03060-15 |
0.349 |
|
| 2016 |
Domyan ET, Kronenberg Z, Infante CR, Vickrey AI, Stringham SA, Bruders R, Guernsey MW, Park S, Payne J, Beckstead RB, Kardon G, Menke DB, Yandell M, Shapiro MD. Author response: Molecular shifts in limb identity underlie development of feathered feet in two domestic avian species Elife. DOI: 10.7554/Elife.12115.028 |
0.648 |
|
| 2015 |
Campbell MS, Yandell M. An Introduction to Genome Annotation. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. 52: 4.1.1-4.1.17. PMID 26678385 DOI: 10.1002/0471250953.Bi0401S52 |
0.421 |
|
| 2015 |
Mason CC, Khorashad JS, Tantravahi SK, Kelley TW, Zabriskie MS, Yan D, Pomicter AD, Reynolds KR, Eiring AM, Kronenberg Z, Sherman RL, Tyner JW, Dalley BK, Dao KH, Yandell M, et al. Age-related mutations and chronic myelomonocytic leukemia. Leukemia. PMID 26648538 DOI: 10.1038/Leu.2015.337 |
0.688 |
|
| 2015 |
Kronenberg ZN, Osborne EJ, Cone KR, Kennedy BJ, Domyan ET, Shapiro MD, Elde NC, Yandell M. Wham: Identifying Structural Variants of Biological Consequence. Plos Computational Biology. 11: e1004572. PMID 26625158 DOI: 10.1371/Journal.Pcbi.1004572 |
0.71 |
|
| 2015 |
Boothby TC, Tenlen JR, Smith FW, Wang JR, Patanella KA, Osborne Nishimura E, Tintori SC, Li Q, Jones CD, Yandell M, Messina DN, Glasscock J, Goldstein B. Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. Proceedings of the National Academy of Sciences of the United States of America. PMID 26598659 DOI: 10.1073/Pnas.1510461112 |
0.437 |
|
| 2015 |
Bowles NE, Jou CJ, Arrington CB, Kennedy BJ, Earl A, Matsunami N, Meyers LL, Etheridge SP, Saarel EV, Bleyl SB, Yost HJ, Yandell M, Leppert MF, Tristani-Firouzi M, Gruber PJ, et al. Exome analysis of a family with Wolff-Parkinson-White syndrome identifies a novel disease locus. American Journal of Medical Genetics. Part A. PMID 26284702 DOI: 10.1002/Ajmg.A.37297 |
0.396 |
|
| 2015 |
Nash D, Arrington CB, Kennedy BJ, Yandell M, Wu W, Zhang W, Ware S, Jorde LB, Gruber PJ, Yost HJ, Bowles NE, Bleyl SB. Shared Segment Analysis and Next-Generation Sequencing Implicates the Retinoic Acid Signaling Pathway in Total Anomalous Pulmonary Venous Return (TAPVR). Plos One. 10: e0131514. PMID 26121141 DOI: 10.1371/Journal.Pone.0131514 |
0.43 |
|
| 2015 |
Kapheim KM, Pan H, Li C, Salzberg SL, Puiu D, Magoc T, Robertson HM, Hudson ME, Venkat A, Fischman BJ, Hernandez A, Yandell M, Ence D, Holt C, Yocum GD, et al. Social evolution. Genomic signatures of evolutionary transitions from solitary to group living. Science (New York, N.Y.). 348: 1139-43. PMID 25977371 DOI: 10.1126/Science.Aaa4788 |
0.356 |
|
| 2015 |
Law M, Childs KL, Campbell MS, Stein JC, Olson AJ, Holt C, Panchy N, Lei J, Jiao D, Andorf CM, Lawrence CJ, Ware D, Shiu SH, Sun Y, Jiang N, ... Yandell M, et al. 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. Plant Physiology. 167: 25-39. PMID 25384563 DOI: 10.1104/Pp.114.245027 |
0.406 |
|
| 2014 |
Galati DF, Bonney S, Kronenberg Z, Clarissa C, Yandell M, Elde NC, Jerka-Dziadosz M, Giddings TH, Frankel J, Pearson CG. DisAp-dependent striated fiber elongation is required to organize ciliary arrays. The Journal of Cell Biology. 207: 705-15. PMID 25533842 DOI: 10.1083/Jcb.201409123 |
0.656 |
|
| 2014 |
Schrader L, Kim JW, Ence D, Zimin A, Klein A, Wyschetzki K, Weichselgartner T, Kemena C, Stökl J, Schultner E, Wurm Y, Smith CD, Yandell M, Heinze J, Gadau J, et al. Transposable element islands facilitate adaptation to novel environments in an invasive species. Nature Communications. 5: 5495. PMID 25510865 DOI: 10.1038/Ncomms6495 |
0.46 |
|
| 2014 |
Campbell MS, Holt C, Moore B, Yandell M. Genome Annotation and Curation Using MAKER and MAKER-P. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. 48: 4.11.1-4.11.39. PMID 25501943 DOI: 10.1002/0471250953.Bi0411S48 |
0.397 |
|
| 2014 |
Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B, Anaclerio F, Archidiacono N, Baker C, Barrell D, Batzer MA, ... ... Yandell M, et al. Gibbon genome and the fast karyotype evolution of small apes. Nature. 513: 195-201. PMID 25209798 DOI: 10.1038/Nature13679 |
0.411 |
|
| 2014 |
Hu H, Roach JC, Coon H, Guthery SL, Voelkerding KV, Margraf RL, Durtschi JD, Tavtigian SV, Shankaracharya, Wu W, Scheet P, Wang S, Xing J, Glusman G, Hubley R, ... ... Yandell M, et al. A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data. Nature Biotechnology. 32: 663-9. PMID 24837662 DOI: 10.1038/Nbt.2895 |
0.453 |
|
| 2014 |
Tang H, Krishnakumar V, Bidwell S, Rosen B, Chan A, Zhou S, Gentzbittel L, Childs KL, Yandell M, Gundlach H, Mayer KF, Schwartz DC, Town CD. An improved genome release (version Mt4.0) for the model legume Medicago truncatula. Bmc Genomics. 15: 312. PMID 24767513 DOI: 10.1186/1471-2164-15-312 |
0.398 |
|
| 2014 |
Kennedy B, Kronenberg Z, Hu H, Moore B, Flygare S, Reese MG, Jorde LB, Yandell M, Huff C. Using VAAST to Identify Disease-Associated Variants in Next-Generation Sequencing Data. Current Protocols in Human Genetics / Editorial Board, Jonathan L. Haines ... [Et Al.]. 81: 6.14.1-6.14.25. PMID 24763993 DOI: 10.1002/0471142905.Hg0614S81 |
0.685 |
|
| 2014 |
Singleton MV, Guthery SL, Voelkerding KV, Chen K, Kennedy B, Margraf RL, Durtschi J, Eilbeck K, Reese MG, Jorde LB, Huff CD, Yandell M. Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families. American Journal of Human Genetics. 94: 599-610. PMID 24702956 DOI: 10.1016/J.Ajhg.2014.03.010 |
0.371 |
|
| 2014 |
Kumar P P, Franklin S, Emechebe U, Hu H, Moore B, Lehman C, Yandell M, Moon AM. TBX3 regulates splicing in vivo: a novel molecular mechanism for Ulnar-mammary syndrome. Plos Genetics. 10: e1004247. PMID 24675841 DOI: 10.1371/Journal.Pgen.1004247 |
0.304 |
|
| 2014 |
Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, DeChene ET, Towne MC, Savage SK, Price EN, Holm IA, Luquette LJ, Lyon E, Majzoub J, Neupert P, ... ... Yandell M, et al. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. Genome Biology. 15: R53. PMID 24667040 DOI: 10.1186/Gb-2014-15-3-R53 |
0.404 |
|
| 2014 |
Wegrzyn JL, Liechty JD, Stevens KA, Wu LS, Loopstra CA, Vasquez-Gross HA, Dougherty WM, Lin BY, Zieve JJ, Martínez-García PJ, Holt C, Yandell M, Zimin AV, Yorke JA, Crepeau MW, et al. Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation. Genetics. 196: 891-909. PMID 24653211 DOI: 10.1534/Genetics.113.159996 |
0.431 |
|
| 2014 |
Neale DB, Wegrzyn JL, Stevens KA, Zimin AV, Puiu D, Crepeau MW, Cardeno C, Koriabine M, Holtz-Morris AE, Liechty JD, MartÃnez-GarcÃa PJ, Vasquez-Gross HA, Lin BY, Zieve JJ, Dougherty WM, ... ... Yandell M, et al. Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Genome Biology. 15: R59. PMID 24647006 DOI: 10.1186/Gb-2014-15-3-R59 |
0.437 |
|
| 2014 |
Domyan ET, Guernsey MW, Kronenberg Z, Krishnan S, Boissy RE, Vickrey AI, Rodgers C, Cassidy P, Leachman SA, Fondon JW, Yandell M, Shapiro MD. Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon. Current Biology : Cb. 24: 459-64. PMID 24508169 DOI: 10.1016/J.Cub.2014.01.020 |
0.716 |
|
| 2014 |
Safavi-Hemami H, Hu H, Gorasia DG, Bandyopadhyay PK, Veith PD, Young ND, Reynolds EC, Yandell M, Olivera BM, Purcell AW. Combined proteomic and transcriptomic interrogation of the venom gland of Conus geographus uncovers novel components and functional compartmentalization. Molecular & Cellular Proteomics : McP. 13: 938-53. PMID 24478445 DOI: 10.1074/Mcp.M113.031351 |
0.365 |
|
| 2014 |
Chen K, Wu W, Mathew D, Zhang Y, Browne SK, Rosen LB, McManus MP, Pulsipher MA, Yandell M, Bohnsack JF, Jorde LB, Notarangelo LD, Walter JE. Autoimmunity due to RAG deficiency and estimated disease incidence in RAG1/2 mutations. The Journal of Allergy and Clinical Immunology. 133: 880-2.e10. PMID 24472623 DOI: 10.1016/J.Jaci.2013.11.038 |
0.369 |
|
| 2014 |
Chapin A, Hu H, Rynearson SG, Hollien J, Yandell M, Metzstein MM. In vivo determination of direct targets of the nonsense-mediated decay pathway in Drosophila. G3 (Bethesda, Md.). 4: 485-96. PMID 24429422 DOI: 10.1534/G3.113.009357 |
0.309 |
|
| 2014 |
Campbell MS, Law M, Holt C, Stein JC, Moghe GD, Hufnagel DE, Lei J, Achawanantakun R, Jiao D, Lawrence CJ, Ware D, Shiu SH, Childs KL, Sun Y, Jiang N, ... Yandell M, et al. MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations. Plant Physiology. 164: 513-24. PMID 24306534 DOI: 10.1104/Pp.113.230144 |
0.364 |
|
| 2014 |
Mason CC, Khorashad JS, Tantravahi SK, Kelley TW, Pomicter AD, Iovino AJ, Reynolds KR, Eiring AM, Zabriskie MS, Kronenberg Z, Tyner JW, Dalley B, Dao KT, O'Hare T, Yandell M, et al. Next Generation Sequencing to Delineate the Mutational Landscape of Chronic Myelomonocytic Leukemia (CMML): Novel Disease Genes and Correlations with Survival Blood. 124: 4637-4637. DOI: 10.1182/Blood.V124.21.4637.4637 |
0.692 |
|
| 2014 |
Castoe TA, De Koning APJ, Hall KT, Card DC, Schield DR, Fujita MK, Ruggiero RP, Degner JF, Daza JM, Gu W, Reyes-Velasco J, Shaney KJ, Castoe JM, Fox SE, Poole AW, ... ... Yandell M, et al. The Burmese python genome reveals the molecular basis for extreme adaptation in snakes (Proceedings of the National Academy of Sciences of the United States of America (2013) 110, 51, (20645-20650) DOI: 10.1073/pnas. 1314475110) Proceedings of the National Academy of Sciences of the United States of America. 111: 3194. DOI: 10.1073/Pnas.1324133111 |
0.329 |
|
| 2013 |
Castoe TA, de Koning AP, Hall KT, Card DC, Schield DR, Fujita MK, Ruggiero RP, Degner JF, Daza JM, Gu W, Reyes-Velasco J, Shaney KJ, Castoe JM, Fox SE, Poole AW, ... ... Yandell M, et al. The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. Proceedings of the National Academy of Sciences of the United States of America. 110: 20645-50. PMID 24297902 DOI: 10.1073/Pnas.1314475110 |
0.444 |
|
| 2013 |
Vonk FJ, Casewell NR, Henkel CV, Heimberg AM, Jansen HJ, McCleary RJ, Kerkkamp HM, Vos RA, Guerreiro I, Calvete JJ, Wüster W, Woods AE, Logan JM, Harrison RA, Castoe TA, ... ... Yandell M, et al. The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system. Proceedings of the National Academy of Sciences of the United States of America. 110: 20651-6. PMID 24297900 DOI: 10.1073/Pnas.1314702110 |
0.485 |
|
| 2013 |
Hu H, Huff CD, Moore B, Flygare S, Reese MG, Yandell M. VAAST 2.0: improved variant classification and disease-gene identification using a conservation-controlled amino acid substitution matrix. Genetic Epidemiology. 37: 622-34. PMID 23836555 DOI: 10.1002/Gepi.21743 |
0.369 |
|
| 2013 |
Kapusta A, Kronenberg Z, Lynch VJ, Zhuo X, Ramsay L, Bourque G, Yandell M, Feschotte C. Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. Plos Genetics. 9: e1003470. PMID 23637635 DOI: 10.1371/Journal.Pgen.1003470 |
0.709 |
|
| 2013 |
Amemiya CT, Alföldi J, Lee AP, Fan S, Philippe H, Maccallum I, Braasch I, Manousaki T, Schneider I, Rohner N, Organ C, Chalopin D, Smith JJ, Robinson M, Dorrington RA, ... ... Yandell M, et al. The African coelacanth genome provides insights into tetrapod evolution. Nature. 496: 311-6. PMID 23598338 DOI: 10.1038/Nature12027 |
0.448 |
|
| 2013 |
Smith JJ, Kuraku S, Holt C, Sauka-Spengler T, Jiang N, Campbell MS, Yandell MD, Manousaki T, Meyer A, Bloom OE, Morgan JR, Buxbaum JD, Sachidanandam R, Sims C, Garruss AS, et al. Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nature Genetics. 45: 415-21, 421e1-2. PMID 23435085 DOI: 10.1038/Ng.2568 |
0.324 |
|
| 2013 |
Shapiro MD, Kronenberg Z, Li C, Domyan ET, Pan H, Campbell M, Tan H, Huff CD, Hu H, Vickrey AI, Nielsen SC, Stringham SA, Hu H, Willerslev E, Gilbert MT, ... Yandell M, et al. Genomic diversity and evolution of the head crest in the rock pigeon. Science (New York, N.Y.). 339: 1063-7. PMID 23371554 DOI: 10.1126/Science.1230422 |
0.724 |
|
| 2012 |
Vieler A, Wu G, Tsai CH, Bullard B, Cornish AJ, Harvey C, Reca IB, Thornburg C, Achawanantakun R, Buehl CJ, Campbell MS, Cavalier D, Childs KL, Clark TJ, Deshpande R, ... ... Yandell M, et al. Genome, functional gene annotation, and nuclear transformation of the heterokont oleaginous alga Nannochloropsis oceanica CCMP1779. Plos Genetics. 8: e1003064. PMID 23166516 DOI: 10.1371/Journal.Pgen.1003064 |
0.438 |
|
| 2012 |
Hu H, Bandyopadhyay PK, Olivera BM, Yandell M. Elucidation of the molecular envenomation strategy of the cone snail Conus geographus through transcriptome sequencing of its venom duct. Bmc Genomics. 13: 284. PMID 22742208 DOI: 10.1186/1471-2164-13-284 |
0.304 |
|
| 2012 |
Yandell M, Ence D. A beginner's guide to eukaryotic genome annotation. Nature Reviews. Genetics. 13: 329-42. PMID 22510764 DOI: 10.1038/Nrg3174 |
0.404 |
|
| 2012 |
Lyon G, Jiang T, Wijk RV, Wang W, Bodily P, Xing J, Tian L, Robison R, Clement M, Yang L, Zhang P, Liu Y, Moore B, Solinge Wv, Yandell M, et al. Whole exome sequencing reveals the genetic basis of a case of idiopathic hemolytic anemia and suggests candidate rare variants for ADHD in a Utah pedigree F1000research. 3. DOI: 10.7490/F1000Research.1089758.1 |
0.342 |
|
| 2012 |
Wingfield BD, Steenkamp ET, Santana QC, Coetzee MP, Bam S, Barnes I, Beukes CW, Chan WY, De Vos L, Fourie G, Friend M, Gordon TR, Herron DA, Holt C, Korf I, ... ... Yandell M, et al. First fungal genome sequence from Africa: A preliminary analysis South African Journal of Science. 108. DOI: 10.4102/Sajs.V108I1/2.537 |
0.438 |
|
| 2011 |
Holt C, Yandell M. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. Bmc Bioinformatics. 12: 491. PMID 22192575 DOI: 10.1186/1471-2105-12-491 |
0.409 |
|
| 2011 |
Yandell M, Huff C, Hu H, Singleton M, Moore B, Xing J, Jorde LB, Reese MG. A probabilistic disease-gene finder for personal genomes. Genome Research. 21: 1529-42. PMID 21700766 DOI: 10.1101/Gr.123158.111 |
0.428 |
|
| 2011 |
Rope AF, Wang K, Evjenth R, Xing J, Johnston JJ, Swensen JJ, Johnson WE, Moore B, Huff CD, Bird LM, Carey JC, Opitz JM, Stevens CA, Jiang T, Schank C, ... ... Yandell M, et al. Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency. American Journal of Human Genetics. 89: 28-43. PMID 21700266 DOI: 10.1016/J.Ajhg.2011.05.017 |
0.341 |
|
| 2011 |
Suen G, Teiling C, Li L, Holt C, Abouheif E, Bornberg-Bauer E, Bouffard P, Caldera EJ, Cash E, Cavanaugh A, Denas O, Elhaik E, Favé MJ, Gadau J, Gibson JD, ... ... Yandell MD, et al. The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle. Plos Genetics. 7: e1002007. PMID 21347285 DOI: 10.1371/Journal.Pgen.1002007 |
0.342 |
|
| 2011 |
Moore B, Hu H, Singleton M, De La Vega FM, Reese MG, Yandell M. Global analysis of disease-related DNA sequence variation in 10 healthy individuals: implications for whole genome-based clinical diagnostics. Genetics in Medicine : Official Journal of the American College of Medical Genetics. 13: 210-7. PMID 21325948 DOI: 10.1097/Gim.0B013E31820Ed321 |
0.441 |
|
| 2011 |
Smith CR, Smith CD, Robertson HM, Helmkampf M, Zimin A, Yandell M, Holt C, Hu H, Abouheif E, Benton R, Cash E, Croset V, Currie CR, Elhaik E, Elsik CG, et al. Draft genome of the red harvester ant Pogonomyrmex barbatus. Proceedings of the National Academy of Sciences of the United States of America. 108: 5667-72. PMID 21282651 DOI: 10.1073/Pnas.1007901108 |
0.457 |
|
| 2011 |
Smith CD, Zimin A, Holt C, Abouheif E, Benton R, Cash E, Croset V, Currie CR, Elhaik E, Elsik CG, Fave MJ, Fernandes V, Gadau J, Gibson JD, Graur D, ... ... Yandell M, et al. Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile). Proceedings of the National Academy of Sciences of the United States of America. 108: 5673-8. PMID 21282631 DOI: 10.1073/Pnas.1008617108 |
0.469 |
|
| 2011 |
Hu H, Bandyopadhyay PK, Olivera BM, Yandell M. Characterization of the Conus bullatus genome and its venom-duct transcriptome. Bmc Genomics. 12: 60. PMID 21266071 DOI: 10.1186/1471-2164-12-60 |
0.423 |
|
| 2010 |
Reese MG, Moore B, Batchelor C, Salas F, Cunningham F, Marth GT, Stein L, Flicek P, Yandell M, Eilbeck K. A standard variation file format for human genome sequences. Genome Biology. 11: R88. PMID 20796305 DOI: 10.1186/Gb-2010-11-8-R88 |
0.414 |
|
| 2010 |
Lévesque CA, Brouwer H, Cano L, Hamilton JP, Holt C, Huitema E, Raffaele S, Robideau GP, Thines M, Win J, Zerillo MM, Beakes GW, Boore JL, Busam D, Dumas B, ... ... Yandell M, et al. Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. Genome Biology. 11: R73. PMID 20626842 DOI: 10.1186/Gb-2010-11-7-R73 |
0.45 |
|
| 2010 |
Kovach A, Wegrzyn JL, Parra G, Holt C, Bruening GE, Loopstra CA, Hartigan J, Yandell M, Langley CH, Korf I, Neale DB. The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences. Bmc Genomics. 11: 420. PMID 20609256 DOI: 10.1186/1471-2164-11-420 |
0.445 |
|
| 2009 |
Eilbeck K, Moore B, Holt C, Yandell M. Quantitative measures for the management and comparison of annotated genomes. Bmc Bioinformatics. 10: 67. PMID 19236712 DOI: 10.1186/1471-2105-10-67 |
0.395 |
|
| 2008 |
Yandell M, Moore B, Salas F, Mungall C, MacBride A, White C, Reese MG. Genome-wide analysis of human disease alleles reveals that their locations are correlated in paralogous proteins. Plos Computational Biology. 4: e1000218. PMID 18989397 DOI: 10.1371/Journal.Pcbi.1000218 |
0.419 |
|
| 2008 |
Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, Holt C, Sánchez Alvarado A, Yandell M. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Research. 18: 188-96. PMID 18025269 DOI: 10.1101/Gr.6743907 |
0.431 |
|
| 2007 |
Smith CD, Edgar RC, Yandell MD, Smith DR, Celniker SE, Myers EW, Karpen GH. Improved repeat identification and masking in Dipterans. Gene. 389: 1-9. PMID 17137733 DOI: 10.1016/J.Gene.2006.09.011 |
0.342 |
|
| 2006 |
Yandell M, Mungall CJ, Smith C, Prochnik S, Kaminker J, Hartzell G, Lewis S, Rubin GM. Large-scale trends in the evolution of gene structures within 11 animal genomes. Plos Computational Biology. 2: e15. PMID 16518452 DOI: 10.1371/Journal.Pcbi.0020015 |
0.443 |
|
| 2005 |
Yandell M, Bailey AM, Misra S, Shu S, Wiel C, Evans-Holm M, Celniker SE, Rubin GM. A computational and experimental approach to validating annotations and gene predictions in the Drosophila melanogaster genome. Proceedings of the National Academy of Sciences of the United States of America. 102: 1566-71. PMID 15668397 DOI: 10.1073/Pnas.0409421102 |
0.406 |
|
| 2002 |
Zdobnov EM, von Mering C, Letunic I, Torrents D, Suyama M, Copley RR, Christophides GK, Thomasova D, Holt RA, Subramanian GM, Mueller HM, Dimopoulos G, Law JH, Wells MA, Birney E, ... ... Yandell M, et al. Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science (New York, N.Y.). 298: 149-59. PMID 12364792 DOI: 10.1126/Science.1077061 |
0.454 |
|
| 2002 |
Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JM, Wides R, Salzberg SL, Loftus B, Yandell M, Majoros WH, Rusch DB, et al. The genome sequence of the malaria mosquito Anopheles gambiae. Science (New York, N.Y.). 298: 129-49. PMID 12364791 DOI: 10.1126/Science.1076181 |
0.435 |
|
| 2002 |
Mural RJ, Adams MD, Myers EW, Smith HO, Miklos GL, Wides R, Halpern A, Li PW, Sutton GG, Nadeau J, Salzberg SL, Holt RA, Kodira CD, Lu F, Chen L, ... ... Yandell M, et al. A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science (New York, N.Y.). 296: 1661-71. PMID 12040188 DOI: 10.1126/Science.1069193 |
0.418 |
|
| 2002 |
Kerlavage A, Bonazzi V, di Tommaso M, Lawrence C, Li P, Mayberry F, Mural R, Nodell M, Yandell M, Zhang J, Thomas P. The Celera Discovery System. Nucleic Acids Research. 30: 129-36. PMID 11752274 DOI: 10.1093/Nar/30.1.129 |
0.386 |
|
| 2001 |
Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, et al. The sequence of the human genome. Science (New York, N.Y.). 291: 1304-51. PMID 11181995 DOI: 10.1126/Science.1058040 |
0.439 |
|
| 2000 |
Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, Hariharan IK, Fortini ME, Li PW, Apweiler R, Fleischmann W, Cherry JM, Henikoff S, Skupski MP, Misra S, Ashburner M, et al. Comparative genomics of the eukaryotes. Science (New York, N.Y.). 287: 2204-15. PMID 10731134 DOI: 10.1126/Science.287.5461.2204 |
0.31 |
|
| 2000 |
Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, George RA, Lewis SE, Richards S, Ashburner M, Henderson SN, ... ... Yandell MD, et al. The genome sequence of Drosophila melanogaster. Science (New York, N.Y.). 287: 2185-95. PMID 10731132 DOI: 10.1126/Science.287.5461.2185 |
0.342 |
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