James W. Thomas - Related publications

Affiliations: 
Emory University Emory University, Atlanta, GA 
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50 most relevant papers in past 60 days:
Year Citation  Score
2019 Rajarajan P, Borrman T, Liao W, Espeso-Gil S, Chandrasekaran S, Jiang Y, Weng Z, Brennand KJ, Akbarian S. Spatial genome exploration in the context of cognitive and neurological disease. Current Opinion in Neurobiology. 59: 112-119. PMID 31255842 DOI: 10.1016/j.conb.2019.05.007   
2019 Le Cam B, Sargent D, Gouzy J, Amselem J, Bellanger MN, Bouchez O, Brown S, Caffier V, De Gracia Coquerel M, Debuchy R, Duvaux L, Payen T, Sannier M, Shiller J, Collemare J, et al. Population Genome Sequencing of the Scab Fungal Species and . G3 (Bethesda, Md.). PMID 31253647 DOI: 10.1534/g3.119.400047   
2019 Amemiya HM, Kundaje A, Boyle AP. The ENCODE Blacklist: Identification of Problematic Regions of the Genome. Scientific Reports. 9: 9354. PMID 31249361 DOI: 10.1038/s41598-019-45839-z   
2019 Bassett KA, Mormile MR, Frank RL. Whole-Genome Identification and Characterization of Bacterial Insertion Sequences Using Bioinformatic Tools. Methods in Molecular Biology (Clifton, N.J.). 2016: 171-180. PMID 31197719 DOI: 10.1007/978-1-4939-9570-7_16   
2019 Moore RJ, Lacey JA. Genomics of the Pathogenic Clostridia. Microbiology Spectrum. 7. PMID 31215504 DOI: 10.1128/microbiolspec.GPP3-0033-2018   
2019 Iourov IY, Vorsanova SG, Yurov YB, Kutsev SI. Ontogenetic and Pathogenetic Views on Somatic Chromosomal Mosaicism. Genes. 10. PMID 31109140 DOI: 10.3390/genes10050379   
2019 Tutaj M, Smith JR, Bolton ER. Rat Genome Assemblies, Annotation, and Variant Repository. Methods in Molecular Biology (Clifton, N.J.). 2018: 43-70. PMID 31228151 DOI: 10.1007/978-1-4939-9581-3_2   
2019 Yang Y, Zhang Y, Ren B, Dixon JR, Ma J. Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF. Cell Systems. PMID 31229558 DOI: 10.1016/j.cels.2019.05.011   
2019 Calonga-Solís V, Malheiros D, Beltrame MH, Vargas LB, Dourado RM, Issler HC, Wassem R, Petzl-Erler ML, Augusto DG. Unveiling the Diversity of Immunoglobulin Heavy Constant Gamma () Gene Segments in Brazilian Populations Reveals 28 Novel Alleles and Evidence of Gene Conversion and Natural Selection. Frontiers in Immunology. 10: 1161. PMID 31214166 DOI: 10.3389/fimmu.2019.01161   
2019 Yang X, Yang Y, Ling J, Guan J, Guo X, Dong D, Jin L, Huang S, Liu J, Li G. A high-throughput BAC-end analysis protocol (BAC-anchor) for profiling genome assembly and physical mapping. Plant Biotechnology Journal. PMID 31254434 DOI: 10.1111/pbi.13203   
2019 Zhou Q, Gao H, Zhang Y, Fan G, Xu H, Zhai J, Xu W, Chen Z, Zhang H, Liu S, Niu Y, Li W, Li W, Lin H, Chen S. A chromosome-level genome assembly of the giant grouper (Epinephelus lanceolatus) provides insights into its innate immunity and rapid growth. Molecular Ecology Resources. PMID 31230418 DOI: 10.1111/1755-0998.13048   
2019 Roberson EDO. A catalog of CasX genome editing sites in common model organisms. Bmc Genomics. 20: 528. PMID 31248380 DOI: 10.1186/s12864-019-5924-6   
2019 Saitou M, Gokcumen O. Resolving the Insertion Sites of Polymorphic Duplications Reveals a HERC2 Haplotype under Selection. Genome Biology and Evolution. 11: 1679-1690. PMID 31124564 DOI: 10.1093/gbe/evz107   
2019 Mosca E, Cruz F, Gómez-Garrido J, Bianco L, Rellstab C, Brodbeck S, Csilléry K, Fady B, Fladung M, Fussi B, Gömöry D, González-Martínez SC, Grivet D, Gut M, Hansen OK, et al. A Reference Genome Sequence for the European Silver Fir ( Mill.): A Community-Generated Genomic Resource. G3 (Bethesda, Md.). PMID 31217262 DOI: 10.1534/g3.119.400083   
2019 García-Angulo A, Merlo MA, Rodríguez ME, Portela-Bens S, Liehr T, Rebordinos L. Genome and Phylogenetic Analysis of Genes Involved in the Immune System of - Potential Applications in Aquaculture. Frontiers in Genetics. 10: 529. PMID 31244883 DOI: 10.3389/fgene.2019.00529   
2019 Xu S, Zhao L, Xiao S, Gao T. Whole genome resequencing data for three rockfish species of Sebastes. Scientific Data. 6: 97. PMID 31222011 DOI: 10.1038/s41597-019-0100-z   
2019 Almeida OAC, Moreira GCM, Rezende FM, Boschiero C, de Oliveira Peixoto J, Ibelli AMG, Ledur MC, de Novais FJ, Coutinho LL. Identification of selection signatures involved in performance traits in a paternal broiler line. Bmc Genomics. 20: 449. PMID 31159736 DOI: 10.1186/s12864-019-5811-1   
2019 Wojcik MH, Thiele K, Grant CF, Chao K, Goodrich J, O'Donnell-Luria A, Lacro RV, Tan WH, Agrawal PB. Genome Sequencing Identifies the Pathogenic Variant Missed by Prior Testing in an Infant with Marfan Syndrome. The Journal of Pediatrics. PMID 31235381 DOI: 10.1016/j.jpeds.2019.05.029   
2019 Levesque S, de Melo AG, Labrie SJ, Moineau S. Mobilome of Sheds Light on Its Genetic Diversity and Its Adaptation to Smear-Ripened Cheeses. Frontiers in Microbiology. 10: 1270. PMID 31244798 DOI: 10.3389/fmicb.2019.01270   
2019 Chowdhary S, Kainth AS, Gross DS. Chromosome Conformation Capture That Detects Novel Cis- and Trans-Interactions in Budding Yeast. Methods (San Diego, Calif.). PMID 31252061 DOI: 10.1016/j.ymeth.2019.06.023   
2019 Zhang B, Zhu W, Diao S, Wu X, Lu J, Ding C, Su X. The poplar pangenome provides insights into the evolutionary history of the genus. Communications Biology. 2: 215. PMID 31240253 DOI: 10.1038/s42003-019-0474-7   
2019 Renaud G, Hanghøj K, Korneliussen TS, Willerslev E, Orlando L. Joint Estimates of Heterozygosity and Runs of Homozygosity for Modern and Ancient Samples. Genetics. 212: 587-614. PMID 31088861 DOI: 10.1534/genetics.119.302057   
2019 Chen Z, Omori Y, Koren S, Shirokiya T, Kuroda T, Miyamoto A, Wada H, Fujiyama A, Toyoda A, Zhang S, Wolfsberg TG, Kawakami K, Phillippy AM, , Mullikin JC, et al. De novo assembly of the goldfish () genome and the evolution of genes after whole-genome duplication. Science Advances. 5: eaav0547. PMID 31249862 DOI: 10.1126/sciadv.aav0547   
2019 Langley SA, Miga KH, Karpen GH, Langley CH. Haplotypes spanning centromeric regions reveal persistence of large blocks of archaic DNA. Elife. 8. PMID 31237235 DOI: 10.7554/eLife.42989   
2019 Ye X, Tang X, Wang X, Che J, Wu M, Liang J, Ye L, Qian Q, Li J, You Z, Zhang Y, Wang S, Zhong B. Improving silkworm genome annotation using a proteogenomics approach. Journal of Proteome Research. PMID 31250652 DOI: 10.1021/acs.jproteome.8b00965   
2019 Vadakkemukadiyil Chellappan B, Pr S, Vijayan S, Rajan VS, Sasi A, Nair AS. High Quality Draft Genome of Arogyapacha ), an Important Medicinal Plant Endemic to Western Ghats of India. G3 (Bethesda, Md.). PMID 31189529 DOI: 10.1534/g3.119.400164   
2019 Nagasaki M, Kuroki Y, Shibata TF, Katsuoka F, Mimori T, Kawai Y, Minegishi N, Hozawa A, Kuriyama S, Suzuki Y, Kawame H, Nagami F, Takai-Igarashi T, Ogishima S, Kojima K, et al. Construction of JRG (Japanese reference genome) with single-molecule real-time sequencing. Human Genome Variation. 6: 27. PMID 31231536 DOI: 10.1038/s41439-019-0057-7   
2019 Chen H, Lin L, Xie M, Zhong Y, Zhang G, Su W. Survey of the Transcriptome Using PacBio Single-Molecule Long-Read Sequencing. Genes. 10. PMID 31242713 DOI: 10.3390/genes10060481   
2019 Nelson J, Hauser D, Gudiño JA, Guadalupe YA, Meeks JC, Salazar N, Villarreal JC, Li FW. Complete genomes of symbiotic cyanobacteria clarify the evolution of Vanadium-nitrogenase. Genome Biology and Evolution. PMID 31243438 DOI: 10.1093/gbe/evz137   
2019 Savic DJ, Nguyen SV, McCullor K, McShan WM. Biological Impact of a Large Scale Genomic Inversion that Grossly Disrupts the Relative Positions of the Origin and Terminus Loci of the Chromosome. Journal of Bacteriology. PMID 31235514 DOI: 10.1128/JB.00090-19   
2019 Mirny LA, Imakaev M, Abdennur N. Two major mechanisms of chromosome organization. Current Opinion in Cell Biology. 58: 142-152. PMID 31228682 DOI: 10.1016/j.ceb.2019.05.001   
2019 Yan Y, Zhu J, Xie C, Liu C. [Regulatory framework of genome-edited products - a review]. Sheng Wu Gong Cheng Xue Bao = Chinese Journal of Biotechnology. 35: 921-930. PMID 31231990 DOI: 10.13345/j.cjb.180418   
2019 Ayalew S, Confer AW, Couger MB. Genome Sequence of a Bovine Isolate of Pasteurella multocida Strain 232. Microbiology Resource Announcements. 8. PMID 31097504 DOI: 10.1128/MRA.00333-19   
2019 Helmkampf M, Bellinger MR, Geib SM, Sim SB, Takabayashi M. Draft genome of the rice coral Montipora capitata obtained from linked-read sequencing. Genome Biology and Evolution. PMID 31243452 DOI: 10.1093/gbe/evz135   
2019 Tu SL, Upton C. Bioinformatics for Analysis of Poxvirus Genomes. Methods in Molecular Biology (Clifton, N.J.). 2023: 29-62. PMID 31240669 DOI: 10.1007/978-1-4939-9593-6_2   
2019 Arthur RA, Nicholson AC, Humrighouse BW, McQuiston JR, Lasker BA. Draft Genome Sequence of Kroppenstedtia sanguinis X0209, a Clinical Isolate Recovered from Human Blood. Microbiology Resource Announcements. 8. PMID 31196918 DOI: 10.1128/MRA.00354-19   
2019 Zhao J, Hao W, Tang C, Yao H, Li B, Zheng Q, Li Z, Zhang X. Plasticity in Triticeae centromere DNA sequences: a wheat × tall wheatgrass (decaploid) model. The Plant Journal : For Cell and Molecular Biology. PMID 31259444 DOI: 10.1111/tpj.14444   
2019 Hakimi H, Ishizaki T, Kegawa Y, Kaneko O, Kawazu SI, Asada M. Genome Editing of Using the CRISPR/Cas9 System. Msphere. 4. PMID 31189559 DOI: 10.1128/mSphere.00109-19   
2019 Nie D, Cao P, Wang F, Zhang J, Liu M, Zhang W, Liu L, Zhao H, Teng W, Tian W, Chen X, Zhang Y, Nan H, Wei Z, Wang T, et al. Analysis of overlapping heterozygous novel submicroscopic CNVs and FANCA-VPS9D1 fusion transcripts in a Fanconi anemia patient. Journal of Human Genetics. PMID 31239491 DOI: 10.1038/s10038-019-0629-x   
2019 Jeske T, Huypens P, Stirm L, Höckele S, Wurmser CM, Böhm A, Weigert C, Staiger H, Klein C, Beckers J, Hastreiter M. DEUS: an R package for accurate small RNA profiling based on differential expression of unique sequences. Bioinformatics (Oxford, England). PMID 31228198 DOI: 10.1093/bioinformatics/btz495   
2019 Minato Y, Gohl DM, Thiede JM, Chacón JM, Harcombe WR, Maruyama F, Baughn AD. Genomewide Assessment of Mycobacterium tuberculosis Conditionally Essential Metabolic Pathways. Msystems. 4. PMID 31239393 DOI: 10.1128/mSystems.00070-19   
2019 Cuomo CA, Fanning S, Gujja S, Zeng Q, Naglik JR, Filler SG, Mitchell AP. Genome Sequence for Candida albicans Clinical Oral Isolate 529L. Microbiology Resource Announcements. 8. PMID 31221654 DOI: 10.1128/MRA.00554-19   
2019 Roos A, Byron SA. Genomics-Enabled Precision Medicine for Cancer. Cancer Treatment and Research. 178: 137-169. PMID 31209844 DOI: 10.1007/978-3-030-16391-4_5   
2019 Tramontano A, Jarc L, Jankowicz-Cieslak J, Hofinger BJ, Gajek K, Szurman-Zubrzycka M, Szarejko I, Ingelbrecht I, Till BJ. Fragmentation of Pooled PCR Products for Highly Multiplexed TILLING. G3 (Bethesda, Md.). PMID 31213514 DOI: 10.1534/g3.119.400301   
2019 Thomas A, Barriere S, Broseus L, Brooke J, Lorenzi C, Villemin JP, Beurier G, Sabatier R, Reynes C, Mancheron A, Ritchie W. GECKO is a genetic algorithm to classify and explore high throughput sequencing data. Communications Biology. 2: 222. PMID 31240260 DOI: 10.1038/s42003-019-0456-9   
2019 Savelli B, Li Q, Webber M, Jemmat AM, Robitaille A, Zamocky M, Mathé C, Dunand C. RedoxiBase: A database for ROS homeostasis regulated proteins. Redox Biology. 26: 101247. PMID 31228650 DOI: 10.1016/j.redox.2019.101247   
2019 Kommadath A, Grant JR, Krivushin K, Butty AM, Baes CF, Carthy TR, Berry DP, Stothard P. A large interactive visual database of copy number variants discovered in taurine cattle. Gigascience. 8. PMID 31241156 DOI: 10.1093/gigascience/giz073   
2019 Bromfield ESP, Cloutier S, Nguyen HDT. Description and complete genome sequence of Bradyrhizobium amphicarpaeae sp. nov., harbouring photosystem and nitrogen-fixation genes. International Journal of Systematic and Evolutionary Microbiology. PMID 31251718 DOI: 10.1099/ijsem.0.003569   
2019 Hua K, Zhang J, Botella JR, Ma C, Kong F, Liu B, Zhu JK. Perspectives on the application of genome editing technologies in crop breeding. Molecular Plant. PMID 31260812 DOI: 10.1016/j.molp.2019.06.009   
2019 Nan H, Gao LZ. Genome-Wide Analysis of Genes and Their Response to Hormone and Mechanic Stresses in Carrot. Frontiers in Genetics. 10: 363. PMID 31191596 DOI: 10.3389/fgene.2019.00363