Daniel Mende - Related publications

Affiliations: 
Structural and Computational Biology European Molecular Biology Laboratory (EMBL), Heidelberg, Baden-Württemberg, Germany 
Website:
http://www.embl.de/research/units/scb/bork/members/index.php?s_personId=5768
NOTE: We are testing a new system for identifying relevant work based on semantic analysis that identifies similarities between recently published papers and the current author's publications. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches.
50 most relevant papers in past 60 days:
Year Citation  Score
2021 Lee CY, Lee YF, Lai LC, Tsai MH, Lu TP, Chuang EY. MiDSystem: A Comprehensive Online System for De Novo Assembly and Analysis of Microbial Genomes. New Biotechnology. PMID 34411700 DOI: 10.1016/j.nbt.2021.08.002   
2021 Sharon BM, Hulyalkar NV, Nguyen VH, Zimmern PE, Palmer KL, De Nisco NJ. Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies. Journal of Visualized Experiments : Jove. PMID 34487123 DOI: 10.3791/62872   
2021 Saha S, Cooksey AM, Childers AK, Poelchau MF, McCarthy FM. Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes. Insects. 12. PMID 34442314 DOI: 10.3390/insects12080748   
2021 Kang L, Michalak P, Hallerman E, Moncrief ND. A Draft Genome Assembly for the Eastern Fox Squirrel, Sciurus niger. G3 (Bethesda, Md.). PMID 34550334 DOI: 10.1093/g3journal/jkab315   
2021 Shan Y, Pei X, Yong S, Li J, Qin Q, Zeng S, Yu J. Analysis of the complete chloroplast genomes of and (Lamiaceae). Mitochondrial Dna. Part B, Resources. 6: 2672-2680. PMID 34435116 DOI: 10.1080/23802359.2021.1920491   
2021 Woodhouse MR, Cannon EK, Portwood JL, Harper LC, Gardiner JM, Schaeffer ML, Andorf CM. A pan-genomic approach to genome databases using maize as a model system. Bmc Plant Biology. 21: 385. PMID 34416864 DOI: 10.1186/s12870-021-03173-5   
2021 Hodor P, Pope CE, Whitlock KB, Hoffman LR, Limbrick DL, McDonald PJ, Hauptman JS, Ojemann JG, Simon TD. Molecular Characterization of Microbiota in Cerebrospinal Fluid From Patients With CSF Shunt Infections Using Whole Genome Amplification Followed by Shotgun Sequencing. Frontiers in Cellular and Infection Microbiology. 11: 699506. PMID 34490140 DOI: 10.3389/fcimb.2021.699506   
2021 Díaz R, Torres-Miranda A, Orellana G, Garrido D. Comparative Genomic Analysis of Novel subsp. Strains Reveals Functional Divergence in the Human Gut Microbiota. Microorganisms. 9. PMID 34576801 DOI: 10.3390/microorganisms9091906   
2021 Zhang F, Wang N, Cheng G, Shu X, Wang T, Zhuang W, Lu R, Wang Z. Comparative Chloroplast Genomes of Four Species (Amaryllidaceae) Provides New Insight into Interspecific Relationship and Phylogeny. Biology. 10. PMID 34439948 DOI: 10.3390/biology10080715   
2021 Huang Z, Zhou X, Stanton C, Ross RP, Zhao J, Zhang H, Yang B, Chen W. Comparative Genomics and Specific Functional Characteristics Analysis of . Microorganisms. 9. PMID 34576887 DOI: 10.3390/microorganisms9091992   
2021 Tikariha H, Pavagadhi S, Mayalagu S, Poh MCH, Swarup S. Hybrid Genome Assembly for Predicting Functional Potential of a Novel Strain as Plant Biomass Valorisation Agent. Indian Journal of Microbiology. 61: 283-290. PMID 34294994 DOI: 10.1007/s12088-021-00935-5   
2021 Wang Z, Zhang F, Liang Y, Zheng K, Gu C, Zhang W, Liu Y, Zhang X, Shao H, Jiang Y, Guo C, He H, Wang H, Sung YY, Mok WJ, et al. Genome and Ecology of a Novel Podovirus, ZP6, Representing a New Viral Genus, . Microbiology Spectrum. e0046321. PMID 34643440 DOI: 10.1128/Spectrum.00463-21   
2021 Yuan XL, Zhang CS, Kong FY, Zhang ZF, Wang FL. Genome Analysis of JM01 Provides Insights into Its Pathogenicity Mechanisms. Plants (Basel, Switzerland). 10. PMID 34451665 DOI: 10.3390/plants10081620   
2021 Manni M, Berkeley MR, Seppey M, Simão FA, Zdobnov EM. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Molecular Biology and Evolution. PMID 34320186 DOI: 10.1093/molbev/msab199   
2021 Basher ARMA, Mclaughlin RJ, Hallam SJ. Metabolic Pathway Prediction Using Non-Negative Matrix Factorization with Improved Precision. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 34520674 DOI: 10.1089/cmb.2021.0258   
2021 Paterson GK. Genomic epidemiology of the opportunistic pathogen from companion dogs. Journal of Medical Microbiology. 70. PMID 34431760 DOI: 10.1099/jmm.0.001407   
2021 Girard L, Lood C, Höfte M, Vandamme P, Rokni-Zadeh H, van Noort V, Lavigne R, De Mot R. The Ever-Expanding Genus: Description of 43 New Species and Partition of the Group. Microorganisms. 9. PMID 34442845 DOI: 10.3390/microorganisms9081766   
2021 Ma X, Olsen JL, Reusch TBH, Procaccini G, Kudrna D, Williams M, Grimwood J, Rajasekar S, Jenkins J, Schmutz J, Van de Peer Y. Improved chromosome-level genome assembly and annotation of the seagrass, (eelgrass). F1000research. 10: 289. PMID 34621505 DOI: 10.12688/f1000research.38156.1   
2021 Chen W, Ren ZH, Tang N, Chai G, Zhang H, Zhang Y, Ma J, Wu Z, Shen X, Huang X, Luo GZ, Ji Q. Targeted genetic screening in bacteria with a Cas12k-guided transposase. Cell Reports. 36: 109635. PMID 34469724 DOI: 10.1016/j.celrep.2021.109635   
2021 Wijayasekara D, Ali A. Evolutionary study of maize dwarf mosaic virus using nearly complete genome sequences acquired by next-generation sequencing. Scientific Reports. 11: 18786. PMID 34552152 DOI: 10.1038/s41598-021-98299-9   
2021 Zhang L, Wang S, Su C, Harris AJ, Zhao L, Su N, Wang JR, Duan L, Chang ZY. Comparative Chloroplast Genomics and Phylogenetic Analysis of (Zygophyllaceae) of China. Frontiers in Plant Science. 12: 723622. PMID 34630471 DOI: 10.3389/fpls.2021.723622   
2021 Wright BW, Molloy MP, Jaschke PR. Overlapping genes in natural and engineered genomes. Nature Reviews. Genetics. PMID 34611352 DOI: 10.1038/s41576-021-00417-w   
2021 Galvez LC, Koh RBL, Barbosa CFC, Asunto JC, Catalla JL, Atienza RG, Costales KT, Aquino VM, Zhang D. Sequencing and de Novo Assembly of Abaca ( Née) var. Abuab Genome. Genes. 12. PMID 34440376 DOI: 10.3390/genes12081202   
2021 Zeng Q, Liu J, Wang C, Wang H, Zhang L, Hu J, Bao L, Wang S. High-quality reannotation of the king scallop genome reveals no 'gene-rich' feature and evolution of toxin resistance. Computational and Structural Biotechnology Journal. 19: 4954-4960. PMID 34527199 DOI: 10.1016/j.csbj.2021.08.038   
2021 Lee G, Kim MJ, Shin JH. Data on complete genome sequence and annotation of LMG 24727. Data in Brief. 38: 107271. PMID 34430681 DOI: 10.1016/j.dib.2021.107271   
2021 Alabi N, Wu Y, Bossdorf O, Rieseberg LH, Colautti RI. Genome Report: A draft genome of Alliaria petiolata (garlic mustard) as a model system for invasion genetics. G3 (Bethesda, Md.). PMID 34599816 DOI: 10.1093/g3journal/jkab339   
2021 Qin X, Wang H, Miao C, Yang X, Zhang Y, Feng J, Forsythe SJ, Man C, Jiang Y. Comparative genomics reveals environmental adaptation differences between Cronobacter species. Food Research International (Ottawa, Ont.). 147: 110541. PMID 34399518 DOI: 10.1016/j.foodres.2021.110541   
2021 Whitmore L, Yetsko K, Farrell JA, Page-Karjian A, Daniel W, Shaver DJ, Frandsen HR, Walker JS, Crowder W, Bovery C, Rollinson Ramia D, Burkhalter B, Ryan E, Duffy DJ. Evolutionary Comparisons of Chelonid Alphaherpesvirus 5 (ChHV5) Genomes from Fibropapillomatosis-Afflicted Green (), Olive Ridley () and Kemp's Ridley () Sea Turtles. Animals : An Open Access Journal From Mdpi. 11. PMID 34573455 DOI: 10.3390/ani11092489   
2021 Vega-Estévez S, Armitage A, Bates HJ, Harrison RJ, Buscaino A. The Genome of the CTG(Ser1) Yeast Is Plastic. Mbio. e0187121. PMID 34488452 DOI: 10.1128/mBio.01871-21   
2021 Jiang X, Xu Z, Zhang T, Li Y, Li W, Tan H. Whole-Genome-Based Geographic Surveillance: A Visualized and Expandable Webtool. Frontiers in Microbiology. 12: 687259. PMID 34408729 DOI: 10.3389/fmicb.2021.687259   
2021 Martínez-Cárdenas A, Cruz-Zamora Y, Fajardo-Hernández CA, Villanueva-Silva R, Cruz-García F, Raja HA, Figueroa M. Genome Mining and Molecular Networking-Based Metabolomics of the Marine Facultative sp. MEXU 27854. Molecules (Basel, Switzerland). 26. PMID 34500798 DOI: 10.3390/molecules26175362   
2021 Zhu J, Tian L, Chen P, Han M, Song L, Tong X, Sun X, Yang F, Lin Z, Liu X, Liu C, Wang X, Lin Y, Cai K, Hou Y, et al. Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa. Genomics, Proteomics & Bioinformatics. PMID 34492339 DOI: 10.1016/j.gpb.2021.05.001   
2021 Deng A, Sun Z, Wang T, Cui D, Li L, Liu S, Huang F, Wen T. Simultaneous Multiplex Genome Engineering Accelerated Natural Transformation in . Frontiers in Microbiology. 12: 714449. PMID 34484154 DOI: 10.3389/fmicb.2021.714449   
2021 Ulaszewski B, Meger J, Mishra B, Thines M, Burczyk J. Complete Chloroplast Genomes of L. Reveal Sequence Conservation in the Inverted Repeat and the Presence of Allelic Variation in NUPTs. Genes. 12. PMID 34573338 DOI: 10.3390/genes12091357   
2021 Lee JH, Siddique MI, Kwon JK, Kang BC. Comparative Genomic Analysis Reveals Genetic Variation and Adaptive Evolution in the Pathogenicity-Related Genes of . Frontiers in Microbiology. 12: 694136. PMID 34484141 DOI: 10.3389/fmicb.2021.694136   
2021 Hutter CR, Cobb KA, Portik DM, Travers SL, Wood PL, Brown RM. FrogCap: A modular sequence capture probe-set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales. Molecular Ecology Resources. PMID 34569723 DOI: 10.1111/1755-0998.13517   
2021 Wold J, Koepfli KP, Galla SJ, Eccles D, Hogg CJ, Le Lec MF, Guhlin J, Santure AW, Steeves TE. Expanding the conservation genomics toolbox: incorporating structural variants to enhance genomic studies for species of conservation concern. Molecular Ecology. PMID 34424587 DOI: 10.1111/mec.16141   
2021 Park J, Wang HH. Systematic dissection of σ sequence diversity and function in bacteria. Cell Reports. 36: 109590. PMID 34433066 DOI: 10.1016/j.celrep.2021.109590   
2021 Kim MS, Lee T, Baek J, Kim JH, Kim C, Jeong SC. Genome assembly of the popular Korean soybean cultivar Hwangkeum. G3 (Bethesda, Md.). 11. PMID 34568925 DOI: 10.1093/g3journal/jkab272   
2021 Chen Z, Shen M, Mao C, Wang C, Yuan P, Wang T, Sun D. A Type I Restriction Modification System Influences Genomic Evolution Driven by Horizontal Gene Transfer in . Frontiers in Microbiology. 12: 709571. PMID 34413842 DOI: 10.3389/fmicb.2021.709571   
2021 Liu Y, Huang L, Hu H, Cai M, Liang X, Li X, Zhang Z, Xie Y, Xiao C, Chen S, Chen D, Yong T, Pan H, Gao X, Wu Q. Whole-genome assembly of Ganoderma leucocontextum (Ganodermataceae, Fungi) discovered from the Tibetan Plateau of China. G3 (Bethesda, Md.). PMID 34586388 DOI: 10.1093/g3journal/jkab337   
2021 Trujillo-Montenegro JH, Rodríguez Cubillos MJ, Loaiza CD, Quintero M, Espitia-Navarro HF, Salazar Villareal FA, Viveros Valens CA, González Barrios AF, De Vega J, Duitama J, Riascos JJ. Unraveling the Genome of a High Yielding Colombian Sugarcane Hybrid. Frontiers in Plant Science. 12: 694859. PMID 34484261 DOI: 10.3389/fpls.2021.694859   
2021 Ren F, Wang L, Zhuo W, Lu S, Zhu X, Liu C, Yang M. First complete chloroplast genome of the rare medicinal plant . Mitochondrial Dna. Part B, Resources. 6: 2993-2994. PMID 34568558 DOI: 10.1080/23802359.2021.1975507   
2021 Murphy CL, Yang R, Decker T, Cavalliere C, Andreev V, Bircher N, Cornell J, Dohmen R, Pratt CJ, Grinnell A, Higgs J, Jett C, Gillett E, Khadka R, Mares S, et al. Genomes of novel Myxococcota reveal severely curtailed machineries for predation and cellular differentiation. Applied and Environmental Microbiology. AEM0170621. PMID 34524899 DOI: 10.1128/AEM.01706-21   
2021 Lupande-Mwenebitu D, Khedher MB, Khabthani S, Rym L, Phoba MF, Nabti LZ, Lunguya-Metila O, Pantel A, Lavigne JP, Rolain JM, Diene SM. First Genome Description of Isolate Bearing NDM-1 from Blood Culture. Microorganisms. 9. PMID 34442831 DOI: 10.3390/microorganisms9081751   
2021 Patino LH, Castillo-Castañeda A, Muñoz M, Muskus C, Rivero-Rodríguez M, Pérez-Doria A, Bejarano EE, Ramírez JD. Revisiting the heterogeneous global genomic population structure of . Microbial Genomics. 7. PMID 34491157 DOI: 10.1099/mgen.0.000640   
2021 Chattopadhyay B, Forcina G, Garg KM, Irestedt M, Guerrini M, Barbanera F, Rheindt FE. Novel genome reveals susceptibility of popular gamebird, the red-legged partridge (Alectoris rufa, Phasianidae), to climate change. Genomics. 113: 3430-3438. PMID 34400239 DOI: 10.1016/j.ygeno.2021.08.010   
2021 Al-Qurainy F, Gaafar AZ, Khan S, Nadeem M, Alshameri AM, Tarroum M, Alansi S, Almarri NB, Alfarraj NS. Estimation of Genome Size in the Endemic Species and the Locally Rare Species Using comparative Analyses of Flow Cytometry and K-Mer Approaches. Plants (Basel, Switzerland). 10. PMID 34371565 DOI: 10.3390/plants10071362   
2021 Lewis S, Nash A, Li Q, Ahn TH. Comparison of 16S and whole genome dog microbiomes using machine learning. Biodata Mining. 14: 41. PMID 34419136 DOI: 10.1186/s13040-021-00270-x   
2021 Li Y, Liu H, Zou J. Complete chloroplast genome of : a species endemic to Guizhou, China. Mitochondrial Dna. Part B, Resources. 6: 2596-2598. PMID 34395889 DOI: 10.1080/23802359.2021.1961625