Prashanti Manda, Ph.D. - Related publications

2012 Computer Science and Engineering Mississippi State University, Starkville, MS, United States 
Computer Science
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Wu PI, Ross C, Siegele DA, Hu JC. Insights from the reanalysis of high-throughput chemical genomics data for Escherichia coli K-12. G3 (Bethesda, Md.). 11. PMID 33561236 DOI: 10.1093/g3journal/jkaa035   
2021 O'Meara TR, O'Meara MJ. DeORFanizing Candida albicans Genes using Coexpression. Msphere. 6. PMID 33472984 DOI: 10.1128/mSphere.01245-20   
2021 Karpe SD, Tiwari V, Ramanathan S. InsectOR-Webserver for sensitive identification of insect olfactory receptor genes from non-model genomes. Plos One. 16: e0245324. PMID 33465132 DOI: 10.1371/journal.pone.0245324   
2021 Kranjc N, Crisanti A, Nolan T, Bernardini F. Genome Conservation as a Resource for Rational Gene Drive Target Site Selection. Insects. 12. PMID 33498790 DOI: 10.3390/insects12020097   
2021 Yang P, Wang D, Guo W, Kang L. FAWMine: An integrated database and analysis platform for fall armyworm genomics. Insect Science. PMID 33511767 DOI: 10.1111/1744-7917.12903   
2021 Geissler AS, Anthon C, Alkan F, González-Tortuero E, Poulsen LD, Kallehauge TB, Breüner A, Seemann SE, Vinther J, Gorodkin J. BSGatlas: a unified genome and transcriptome annotation atlas with enhanced information access. Microbial Genomics. PMID 33539279 DOI: 10.1099/mgen.0.000524   
2021 Ruiz-Perez CA, Conrad RE, Konstantinidis KT. MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes. Bmc Bioinformatics. 22: 11. PMID 33407081 DOI: 10.1186/s12859-020-03940-5   
2021 Duan M, Bao H, Bau T. Analyses of transcriptomes and the first complete genome of Leucocalocybe mongolica provide new insights into phylogenetic relationships and conservation. Scientific Reports. 11: 2930. PMID 33536487 DOI: 10.1038/s41598-021-81784-6   
2021 Cui Y, Wu B, Peng A, Song X, Chen X. The Genome of Banana Leaf Blight Pathogen str. FS66 Harbors Widespread Gene Transfer From . Frontiers in Plant Science. 12: 629859. PMID 33613610 DOI: 10.3389/fpls.2021.629859   
2021 Kushwaha B, Pandey M, Das P, Joshi CG, Nagpure NS, Kumar R, Kumar D, Agarwal S, Srivastava S, Singh M, Sahoo L, Jayasankar P, Meher PK, Shah TM, Hinsu AT, et al. The genome of walking catfish Clarias magur (Hamilton, 1822) unveils the genetic basis that may have facilitated the development of environmental and terrestrial adaptation systems in air-breathing catfishes. Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. PMID 33416875 DOI: 10.1093/dnares/dsaa031   
2021 Jadhav K, Kushwaha B, Jadhav I, Shankar P, Geethadevi A, Kumar G, Mittal S, Sharma GP, Parashar M, Parashar D. Genomic analysis of a novel species Halomonas shambharensis isolated from hypersaline lake in Northwest India. Molecular Biology Reports. PMID 33479827 DOI: 10.1007/s11033-020-06131-w   
2021 Guo Y, Xue Z, Yuan R, Li JJ, Pastor WA, Liu W. RAD: a web application to identify region associated differentially expressed genes. Bioinformatics (Oxford, England). PMID 33532827 DOI: 10.1093/bioinformatics/btab075   
2021 Domingo-Sananes MR, McInerney JO. Mechanisms That Shape Microbial Pangenomes. Trends in Microbiology. PMID 33423895 DOI: 10.1016/j.tim.2020.12.004   
2021 Wang W, Peng D, Baptista RP, Li Y, Kissinger JC, Tarleton RL. Strain-specific genome evolution in Trypanosoma cruzi, the agent of Chagas disease. Plos Pathogens. 17: e1009254. PMID 33508020 DOI: 10.1371/journal.ppat.1009254   
2021 Sharma V, Gupta P, Priscilla K, SharanKumar, Hangargi B, Veershetty A, Ramrao DP, Suresh S, Narasanna R, Naik GR, Kumar A, Guo B, Zhuang W, Varshney RK, Pandey MK, et al. Metabolomics Intervention Towards Better Understanding of Plant Traits. Cells. 10. PMID 33562333 DOI: 10.3390/cells10020346   
2021 Yin M, Zhang S, Du X, Mateo RG, Guo W, Li A, Wang Z, Wu S, Chen J, Liu J, Ren G. Genomic analysis of Medicago ruthenica provides insights into its tolerance to abiotic stress and demographic history. Molecular Ecology Resources. PMID 33615703 DOI: 10.1111/1755-0998.13363   
2021 Lee K, Kim DW, Cha CJ. Overview of bioinformatic methods for analysis of antibiotic resistome from genome and metagenome data. Journal of Microbiology (Seoul, Korea). 59: 270-280. PMID 33624264 DOI: 10.1007/s12275-021-0652-4   
2021 Friis G, Vizueta J, Smith EG, Nelson DR, Khraiwesh B, Qudeimat E, Salehi-Ashtiani K, Ortega A, Marshell A, Duarte CM, Burt JA. A high-quality genome assembly and annotation of the gray mangrove, Avicennia marina. G3 (Bethesda, Md.). 11. PMID 33561229 DOI: 10.1093/g3journal/jkaa025   
2021 Chen J, Huang J, Yan T, Peng X, Lin J. [Progress in the construction and screening of random mutation library]. Sheng Wu Gong Cheng Xue Bao = Chinese Journal of Biotechnology. 37: 163-177. PMID 33501798 DOI: 10.13345/j.cjb.200261   
2021 Paige B, Bell J, Bellet A, Gascón A, Ezer D. Reconstructing Genotypes in Private Genomic Databases from Genetic Risk Scores. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 33400590 DOI: 10.1089/cmb.2020.0445   
2021 Pachganov S, Murtazalieva K, Zarubin A, Taran T, Chartier D, Tatarinova TV. Prediction of Rice Transcription Start Sites Using TransPrise: A Novel Machine Learning Approach. Methods in Molecular Biology (Clifton, N.J.). 2238: 261-274. PMID 33471337 DOI: 10.1007/978-1-0716-1068-8_17   
2021 Kim E, Hart T. Improved analysis of CRISPR fitness screens and reduced off-target effects with the BAGEL2 gene essentiality classifier. Genome Medicine. 13: 2. PMID 33407829 DOI: 10.1186/s13073-020-00809-3   
2021 Cho SH, Jeong Y, Lee E, Ko SR, Ahn CY, Oh HM, Cho BK, Cho S. Assessment of species diversity through pan-genome analysis with newly isolated sp. 3-20A1M. Journal of Microbiology and Biotechnology. PMID 33526758 DOI: 10.4014/jmb.2012.12054   
2021 McNair K, Ecale Zhou CL, Souza B, Malfatti S, Edwards RA. Utilizing Amino Acid Composition and Entropy of Potential Open Reading Frames to Identify Protein-Coding Genes. Microorganisms. 9. PMID 33429904 DOI: 10.3390/microorganisms9010129   
2021 Jiang Z, Tu L, Yang W, Zhang Y, Hu T, Ma B, Lu Y, Cui X, Gao J, Wu X, Tong Y, Zhou J, Song Y, Liu Y, Liu N, et al. The chromosome-level reference genome assembly for and insights into ginsenoside biosynthesis. Plant Communications. 2: 100113. PMID 33511345 DOI: 10.1016/j.xplc.2020.100113   
2021 Patumcharoenpol P, Nakphaichit M, Panagiotou G, Senavonge A, Suratannon N, Vongsangnak W. MetGEMs Toolbox: Metagenome-scale models as integrative toolbox for uncovering metabolic functions and routes of human gut microbiome. Plos Computational Biology. 17: e1008487. PMID 33406089 DOI: 10.1371/journal.pcbi.1008487   
2021 Kuo MW, Tsai HH, Wang SH, Chen YY, Yu AL, Yu J. Yulink, predicted from evolutionary analysis, is involved in cardiac function. Journal of Biomedical Science. 28: 7. PMID 33423678 DOI: 10.1186/s12929-020-00701-7   
2021 Hasan MM, Shoombuatong W, Kurata H, Manavalan B. Critical evaluation of web-based DNA N6-methyladenine site prediction tools. Briefings in Functional Genomics. PMID 33491072 DOI: 10.1093/bfgp/elaa028   
2021 Ramadan M, Alariqi M, Ma Y, Li Y, Liu Z, Zhang R, Jin S, Min L, Zhang X. Efficient CRISPR/Cas9 mediated Pooled-sgRNAs assembly accelerates targeting multiple genes related to male sterility in cotton. Plant Methods. 17: 16. PMID 33557889 DOI: 10.1186/s13007-021-00712-x   
2021 Wang H, Dong Y, Liao W, Zhang X, Wang Q, Li G, Xu JR, Liu H. High-Quality Genome Resource of strain CanS41 by Oxford Nanopore Long-Read Sequencing. Plant Disease. PMID 33529071 DOI: 10.1094/PDIS-12-20-2615-A   
2021 Gemović B, Perović V, Davidović R, Drljača T, Veljkovic N. Alignment-free method for functional annotation of amino acid substitutions: Application on epigenetic factors involved in hematologic malignancies. Plos One. 16: e0244948. PMID 33395407 DOI: 10.1371/journal.pone.0244948   
2021 Camiolo S, Suárez NM, Chalka A, Venturini C, Breuer J, Davison AJ. GRACy: A tool for analysing human cytomegalovirus sequence data. Virus Evolution. 7: veaa099. PMID 33505707 DOI: 10.1093/ve/veaa099   
2021 Otero M, Sarno SN, Acebedo SL, Ramírez JA. Tracing Molecular Properties Throughout Evolution: A Chemoinformatic Approach. Journal of Theoretical Biology. 110601. PMID 33508327 DOI: 10.1016/j.jtbi.2021.110601   
2021 Dumas G, Malesys S, Bourgeron T. Systematic detection of brain protein-coding genes under positive selection during primate evolution and their roles in cognition. Genome Research. PMID 33441416 DOI: 10.1101/gr.262113.120   
2021 Zhang YJ, Lan Y, Chen B. ASDB: A comprehensive omics database for Anopheles sinensis. Genomics. PMID 33588073 DOI: 10.1016/j.ygeno.2021.02.005   
2021 Lin W, Shi Y, Jia G, Sun H, Sun T, Hou D. Genome sequencing and annotation and phylogenomic analysis of the medicinal mushroom , a traditional medicinal species in the family Ganodermataceae. Mycologia. 1-10. PMID 33555992 DOI: 10.1080/00275514.2020.1851135   
2021 Gan W, Chung-Davidson YW, Chen Z, Song S, Cui W, He W, Zhang Q, Li W, Li M, Ren J. Global tissue transcriptomic analysis to improve genome annotation and unravel skin pigmentation in goldfish. Scientific Reports. 11: 1815. PMID 33469041 DOI: 10.1038/s41598-020-80168-6   
2021 Michel S, Wagner C, Nosenko T, Steiner B, Samad-Zamini M, Buerstmayr M, Mayer K, Buerstmayr H. Merging Genomics and Transcriptomics for Predicting Fusarium Head Blight Resistance in Wheat. Genes. 12. PMID 33477759 DOI: 10.3390/genes12010114   
2021 Liu K, Wang R, Guo XX, Zhang XJ, Qu XJ, Fan SJ. Comparative and Phylogenetic Analysis of Complete Chloroplast Genomes in Eragrostideae (Chloridoideae, Poaceae). Plants (Basel, Switzerland). 10. PMID 33419221 DOI: 10.3390/plants10010109   
2021 Jung YL, Kirli K, Alver BH, Park PJ. Resources and challenges for integrative analysis of nuclear architecture data. Current Opinion in Genetics & Development. 67: 103-110. PMID 33450522 DOI: 10.1016/j.gde.2020.12.009   
2021 Kim DH, Choi BS, Kang HM, Park JC, Kim MS, Hagiwara A, Lee JS. The genome of the marine water flea Diaphanosoma celebensis: Identification of phase I, II, and III detoxification genes and potential applications in marine molecular ecotoxicology. Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics. 37: 100787. PMID 33454556 DOI: 10.1016/j.cbd.2020.100787   
2021 Conti A, Corte L, Casagrande Pierantoni D, Robert V, Cardinali G. What Is the Best Lens? Comparing the Resolution Power of Genome-Derived Markers and Standard Barcodes. Microorganisms. 9. PMID 33540579 DOI: 10.3390/microorganisms9020299   
2021 Jing G, Zhang Y, Cui W, Liu L, Xu J, Su X. Meta-Apo improves accuracy of 16S-amplicon-based prediction of microbiome function. Bmc Genomics. 22: 9. PMID 33407112 DOI: 10.1186/s12864-020-07307-1   
2021 Labarre A, López-Escardó D, Latorre F, Leonard G, Bucchini F, Obiol A, Cruaud C, Sieracki ME, Jaillon O, Wincker P, Vandepoele K, Logares R, Massana R. Comparative genomics reveals new functional insights in uncultured MAST species. The Isme Journal. PMID 33452482 DOI: 10.1038/s41396-020-00885-8   
2021 Li X, Li Z, Shen Q, Pan Y, Dong X, Xu Z, Duan S, Li Y, Du Y, Chen S, Ma Z, Dong Y. HGFDB: a collective database of helmeted guinea fowl genomics. Database : the Journal of Biological Databases and Curation. 2021. PMID 33417691 DOI: 10.1093/database/baaa116   
2021 Fernandez-Pozo N, Metz T, Chandler JO, Gramzow L, Mérai Z, Maumus F, Scheid OM, Theißen G, Schranz ME, Leubner-Metzger G, Rensing SA. Aethionema arabicum genome annotation using PacBio full-length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research. The Plant Journal : For Cell and Molecular Biology. PMID 33453123 DOI: 10.1111/tpj.15161   
2021 Tiwari JK, Rawat S, Luthra SK, Zinta R, Sahu S, Varshney S, Kumar V, Dalamu D, Mandadi N, Kumar M, Chakrabarti SK, Rao AR, Rai A. Genome sequence analysis provides insights on genomic variation and late blight resistance genes in potato somatic hybrid (parents and progeny). Molecular Biology Reports. PMID 33442830 DOI: 10.1007/s11033-020-06106-x   
2021 Kapili BJ, Dekas AE. PPIT: an R package for inferring microbial taxonomy from nifH sequences. Bioinformatics (Oxford, England). PMID 33580675 DOI: 10.1093/bioinformatics/btab100   
2021 Goh YJ, Barrangou R. A portable CRISPR-Cas9 system for flexible genome engineering in , and . Applied and Environmental Microbiology. PMID 33397707 DOI: 10.1128/AEM.02669-20   
2021 Assaf R, Xia F, Stevens R. Detecting operons in bacterial genomes via visual representation learning. Scientific Reports. 11: 2124. PMID 33483546 DOI: 10.1038/s41598-021-81169-9