Terrence S. Furey, Ph.D. - Related publications

Affiliations: 
University of California, Santa Cruz, Santa Cruz, CA, United States 
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Kim J, Lee C, Ko BJ, Chaisson M, Gedman GL, Cantin LJ, et al. Towards complete and error-free genome assemblies of all vertebrate species. Nature. 592: 737-746. PMID 33911273 DOI: 10.1038/s41586-021-03451-0   
2021 Wahlster L, Verboon JM, Ludwig LS, Black SC, Luo W, Garg K, Voit RA, Collins RL, Garimella K, Costello M, Chao KR, Goodrich JK, DiTroia SP, O'Donnell-Luria A, Talkowski ME, et al. Familial thrombocytopenia due to a complex structural variant resulting in a WAC-ANKRD26 fusion transcript. The Journal of Experimental Medicine. 218. PMID 33857290 DOI: 10.1084/jem.20210444   
2021 Zhou J, Zhang S, Wang J, Shen H, Ai B, Gao W, Zhang C, Fei Q, Yuan D, Wu Z, Tembrock LR, Li S, Gu C, Liao X. Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution. Scientific Reports. 11: 9471. PMID 33947883 DOI: 10.1038/s41598-021-88160-4   
2021 Kwon SB, Ernst J. Learning a genome-wide score of human-mouse conservation at the functional genomics level. Nature Communications. 12: 2495. PMID 33941776 DOI: 10.1038/s41467-021-22653-8   
2021 Lopes M, Louzada S, Gama-Carvalho M, Chaves R. Genomic Tackling of Human Satellite DNA: Breaking Barriers through Time. International Journal of Molecular Sciences. 22. PMID 33946766 DOI: 10.3390/ijms22094707   
2021 Berná L, Marquez P, Cabrera A, Greif G, Francia ME, Robello C. Reevaluation of the and genomes reveals misassembly, karyotype differences, and chromosomal rearrangements. Genome Research. 31: 823-833. PMID 33906964 DOI: 10.1101/gr.262832.120   
2021 McKinlay A, Fultz D, Wang F, Pikaard CS. Targeted Enrichment of rRNA Gene Tandem Arrays for Ultra-Long Sequencing by Selective Restriction Endonuclease Digestion. Frontiers in Plant Science. 12: 656049. PMID 33995452 DOI: 10.3389/fpls.2021.656049   
2021 Hong J, Gao R, Yang Y. CrepHAN: Cross-species prediction of enhancers by using hierarchical attention networks. Bioinformatics (Oxford, England). PMID 33978703 DOI: 10.1093/bioinformatics/btab349   
2021 Zhao Y, Li Z, Cheng L, Li Y, He F, Wang Y. Characterization of the complete chloroplast genome of a hybrid species × . Mitochondrial Dna. Part B, Resources. 6: 1492-1493. PMID 33969204 DOI: 10.1080/23802359.2020.1848467   
2021 Bhattacharyya T, Sowdhamini R. Genome-wide survey of tyrosine phosphatases in thirty mammalian genomes. Cellular Signalling. 110009. PMID 33848580 DOI: 10.1016/j.cellsig.2021.110009   
2021 Weng YM, Francoeur CB, Currie CR, Kavanaugh DH, Schoville SD. A high-quality carabid genome assembly provides insights into beetle genome evolution and cold adaptation. Molecular Ecology Resources. PMID 33938156 DOI: 10.1111/1755-0998.13409   
2021 Purugganan MD, Jackson SA. Advancing crop genomics from lab to field. Nature Genetics. 53: 595-601. PMID 33958781 DOI: 10.1038/s41588-021-00866-3   
2021 Li XD, Pan H, Lu XJ, Wei XY, Shi M, Lu P. Complete chloroplast genome sequencing of Job's tears ( L.): genome structure, comparative analysis, and phylogenetic relationships. Mitochondrial Dna. Part B, Resources. 6: 1399-1405. PMID 33948493 DOI: 10.1080/23802359.2021.1911704   
2021 Ghosh Dasgupta M, Dev SA, Muneera Parveen AB, Sarath P, Sreekumar VB. Draft genome of Korthalsia laciniosa (Griff.) Mart., a climbing rattan elucidates its phylogenetic position. Genomics. 113: 2010-2022. PMID 33862180 DOI: 10.1016/j.ygeno.2021.04.023   
2021 Lui LM, Nielsen TN, Arkin AP. A method for achieving complete microbial genomes and improving bins from metagenomics data. Plos Computational Biology. 17: e1008972. PMID 33961626 DOI: 10.1371/journal.pcbi.1008972   
2021 Yang C, Ma L, Xiao D, Liu X, Jiang X, Ying Z, Lin Y. Chromosome-scale assembly of the Sparassis latifolia genome obtained using long-read and Hi-C sequencing. G3 (Bethesda, Md.). PMID 34021320 DOI: 10.1093/g3journal/jkab173   
2021 Kim K, Kim M, Kim Y, Lee D, Jung I. Hi-C as a molecular rangefinder to examine genomic rearrangements. Seminars in Cell & Developmental Biology. PMID 33992531 DOI: 10.1016/j.semcdb.2021.04.024   
2021 Bernard G, Stephens TG, González-Pech RA, Chan CX. Inferring Phylogenomic Relationship of Microbes Using Scalable Alignment-Free Methods. Methods in Molecular Biology (Clifton, N.J.). 2242: 69-76. PMID 33961218 DOI: 10.1007/978-1-0716-1099-2_5   
2021 Hassan H, Szalat R. Genetic Predictors of Mortality in Patients with Multiple Myeloma. The Application of Clinical Genetics. 14: 241-254. PMID 33953598 DOI: 10.2147/TACG.S262866   
2021 Wang M, Li J, Wang P, Liu F, Liu Z, Zhao G, Xu Z, Pei L, Grover CE, Wendel JF, Wang K, Zhang X. Comparative genome analyses highlight transposon-mediated genome expansion and the evolutionary architecture of 3D genomic folding in cotton. Molecular Biology and Evolution. PMID 33973633 DOI: 10.1093/molbev/msab128   
2021 Banerjee S, Bhandary P, Woodhouse M, Sen TZ, Wise RP, Andorf CM. FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences. Bmc Bioinformatics. 22: 205. PMID 33879057 DOI: 10.1186/s12859-021-04120-9   
2021 Jiang M, Li Y, Chen H, Wang B, Liu C. Comparative and phylogenetic analysis of the complete chloroplast genome sequences of and . Mitochondrial Dna. Part B, Resources. 6: 1498-1506. PMID 33969207 DOI: 10.1080/23802359.2021.1911700   
2021 Agostini F, Zagalak J, Attig J, Ule J, Luscombe NM. Intergenic RNA mainly derives from nascent transcripts of known genes. Genome Biology. 22: 136. PMID 33952325 DOI: 10.1186/s13059-021-02350-x   
2021 Puri A, Bajaj A, Lal S, Singh Y, Lal R. Phylogenomic Framework for Taxonomic Delineation of spp. and Exploration of Core-Pan Genome. Indian Journal of Microbiology. 61: 180-194. PMID 33927459 DOI: 10.1007/s12088-021-00929-3   
2021 Yang LL, Niu JQ, Tang WW. The complete chloroplast genome of pioneering plant L. (Cyperaceae) in ecological restoration. Mitochondrial Dna. Part B, Resources. 6: 1335-1336. PMID 33889743 DOI: 10.1080/23802359.2021.1908865   
2021 Engelbrecht J, Duong TA, Prabhu SA, Seedat M, van den Berg N. Genome of the destructive oomycete Phytophthora cinnamomi provides insights into its pathogenicity and adaptive potential. Bmc Genomics. 22: 302. PMID 33902447 DOI: 10.1186/s12864-021-07552-y   
2021 Cheng J, Siejka-Zielińska P, Liu Y, Chandran A, Kriaucionis S, Song CX. Endonuclease enrichment TAPS for cost-effective genome-wide base-resolution DNA methylation detection. Nucleic Acids Research. PMID 33905495 DOI: 10.1093/nar/gkab291   
2021 Wang M, Zhang L, Wang Z. Chromosomal-level reference genome of the neotropical tree Jacaranda mimosifolia D. Don. Genome Biology and Evolution. PMID 33944940 DOI: 10.1093/gbe/evab094   
2021 Zhang H, Ye L, Liu Q, Huang X. Genome assembly of Scorias spongiosa and comparative genomics provide insights into ecological adaptation of honeydew-dependent sooty mould fungi. Genomics. PMID 34022339 DOI: 10.1016/j.ygeno.2021.05.020   
2021 Ciobanu D, Clum A, Ahrendt S, Andreopoulos WB, Salamov A, Chan S, Quandt CA, Foster B, Meier-Kolthoff JP, Tang YT, Schwientek P, Benny GL, Smith ME, Bauer D, Deshpande S, et al. A single-cell genomics pipeline for environmental microbial eukaryotes. Iscience. 24: 102290. PMID 33870123 DOI: 10.1016/j.isci.2021.102290   
2021 Vogan AA, Ament-Velásquez SL, Bastiaans E, Wallerman O, Saupe SJ, Suh A, Johannesson H. The , a massive transposon carrying meiotic drive genes. Genome Research. PMID 33875482 DOI: 10.1101/gr.267609.120   
2021 Roco ÁS, Liehr T, Ruiz-García A, Guzmán K, Bullejos M. Comparative Distribution of Repetitive Sequences in the Karyotypes of and (Anura, Pipidae). Genes. 12. PMID 33919402 DOI: 10.3390/genes12050617   
2021 Shen CY, Wang PZ, Xue W, Liu ZH, Zhao JY, Tong XB, Liu C, Wu XF, Mao X, Tian S, Fu C. The complete mitochondrial genome of soft coral Ofwegen and Benayahu, 2012 (Octocorallia: Alcyonacea): the analysis of mitogenome organization and phylogeny. Mitochondrial Dna. Part B, Resources. 6: 1348-1350. PMID 33889745 DOI: 10.1080/23802359.2021.1906174   
2021 Atak ZK, Taskiran II, Demeulemeester J, Flerin C, Mauduit D, Minnoye L, Hulselmans G, Christiaens V, Ghanem GE, Wouters J, Aerts S. Interpretation of allele-specific chromatin accessibility using cell state-aware deep learning. Genome Research. PMID 33832990 DOI: 10.1101/gr.260851.120   
2021 Chen L, Jiang B, Miao Y, Liu Z, Xie S, Ling P, Zhu J. The complete chloroplast genome sequence of (L.). Mitochondrial Dna. Part B, Resources. 6: 1346-1347. PMID 33889744 DOI: 10.1080/23802359.2021.1878950   
2021 Zhang D, Lam J, Blobel GA. Engineering three-dimensional genome folding. Nature Genetics. PMID 33958782 DOI: 10.1038/s41588-021-00860-9   
2021 Zhu T, Wang L, Rimbert H, Rodriguez JC, Deal KR, De Oliveira R, Choulet F, Keeble-Gagnère G, Tibbits J, Rogers J, Eversole K, Appels R, Gu YQ, Mascher M, Dvorak J, et al. Optical maps refine the bread wheat Triticum aestivum cv Chinese Spring genome assembly. The Plant Journal : For Cell and Molecular Biology. PMID 33893684 DOI: 10.1111/tpj.15289   
2021 Yu X, Wang P, Li J, Zhao Q, Ji C, Zhu Z, Zhai Y, Qin X, Zhou J, Yu H, Cheng X, Isshiki S, Jahn M, Doyle JJ, Ottosen CO, et al. Whole-Genome Sequence of Synthesized Allopolyploids in Reveals Insights into the Genome Evolution of Allopolyploidization. Advanced Science (Weinheim, Baden-Wurttemberg, Germany). 8: 2004222. PMID 33977063 DOI: 10.1002/advs.202004222   
2021 Ghiselli F, Gomes-Dos-Santos A, Adema CM, Lopes-Lima M, Sharbrough J, Boore JL. Molluscan mitochondrial genomes break the rules. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 376: 20200159. PMID 33813887 DOI: 10.1098/rstb.2020.0159   
2021 Yang F, Zhang J, Wang S, Sun Z, Zhou J, Li F, Liu Y, Ding L, Liu Y, Chi W, Liu T, He Y, Xiang P, Bao Z, Olszewski MA, et al. Genomic population structure of Shanghai isolates and identification of genomic features uniquely linked with pathogenicity. Virulence. 12: 1258-1270. PMID 33904371 DOI: 10.1080/21505594.2021.1920762   
2021 Yan H, Liu Y, Wu Z, Yi Y, Huang X. Phylogenetic relationships and characterization of the complete chloroplast genome of . Mitochondrial Dna. Part B, Resources. 6: 1544-1546. PMID 33969214 DOI: 10.1080/23802359.2021.1915200   
2021 Zhao J. Characterization of the complete chloroplast genome of . Mitochondrial Dna. Part B, Resources. 6: 252-253. PMID 33553637 DOI: 10.1080/23802359.2020.1861566   
2021 Crysnanto D, Leonard AS, Fang ZH, Pausch H. Novel functional sequences uncovered through a bovine multiassembly graph. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33972446 DOI: 10.1073/pnas.2101056118   
2021 Gu H, Zhang P, Xu M, Liang D. Amplicon genome fishing (AGF): a rapid and efficient method for sequencing target cis-regulatory regions in nonmodel organisms. Molecular Genetics and Genomics : Mgg. PMID 33797587 DOI: 10.1007/s00438-021-01775-0   
2021 Xiang L, Zhang L, Hu J. The complete chloroplast genome of , an important economic and medicinal plant endemic in China. Mitochondrial Dna. Part B, Resources. 6: 1025-1027. PMID 33796726 DOI: 10.1080/23802359.2021.1895691   
2021 Zheng H, Xu J, Wang Y, Lin Y, Hu Q, Li X, Chu J, Sun C, Chai Y, Pang X. Identification and Characterization of a Cryptic Genomic Deletion-Insertion in Associated with Branchio-Otic Syndrome. Neural Plasticity. 2021: 5524381. PMID 33880118 DOI: 10.1155/2021/5524381   
2021 Yang C, Zhou Y, Marcus S, Formenti G, Bergeron LA, Song Z, Bi X, Bergman J, Rousselle MMC, Zhou C, Zhou L, Deng Y, Fang M, Xie D, Zhu Y, et al. Evolutionary and biomedical insights from a marmoset diploid genome assembly. Nature. PMID 33910227 DOI: 10.1038/s41586-021-03535-x   
2021 Brancaccio RN, Robitaille A, Dutta S, Rollison DE, Tommasino M, Gheit T. MinION nanopore sequencing and assembly of a complete human papillomavirus genome. Journal of Virological Methods. 294: 114180. PMID 33965458 DOI: 10.1016/j.jviromet.2021.114180   
2021 Fan S, Wang Q, Dai J, Jiang J, Hu X, Subbarao KV. The Whole Genome Sequence of Fusarium redolens strain YP04, a Pathogen that Causes Root Rot of American Ginseng. Phytopathology. PMID 33970029 DOI: 10.1094/PHYTO-03-21-0084-A   
2021 Wu P, Xu C, Chen H, Yang J, Zhang X, Zhou S. NOVOWrap: An automated solution for plastid genome assembly and structure standardization. Molecular Ecology Resources. PMID 33934526 DOI: 10.1111/1755-0998.13410