Erez Persi - Related publications

Tel Aviv University, Tel Aviv-Yafo, Tel Aviv District, Israel 
Visual System, Heterogeneities in neural networks, Peptide Markers
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Wang B, Jiang L. Principal Component Analysis Applications in COVID-19 Genome Sequence Studies. Cognitive Computation. 1-12. PMID 33456620 DOI: 10.1007/s12559-020-09790-w   
2021 Woodard J, Zhang C, Zhang Y. ADDRESS: A database of disease-associated human variants incorporating protein structure and folding stabilities. Journal of Molecular Biology. 166840. PMID 33539887 DOI: 10.1016/j.jmb.2021.166840   
2021 Zhang C, Zheng W, Cheng M, Omenn GS, Freddolino PL, Zhang Y. Functions of Essential Genes and a Scale-Free Protein Interaction Network Revealed by Structure-Based Function and Interaction Prediction for a Minimal Genome. Journal of Proteome Research. PMID 33393786 DOI: 10.1021/acs.jproteome.0c00359   
2021 Jeong J, Yun K, Mun S, Chung WH, Choi SY, Nam YD, Lim MY, Hong CP, Park C, Ahn Y, Han K. The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology. Scientific Reports. 11: 1727. PMID 33462291 DOI: 10.1038/s41598-020-80826-9   
2021 Maruyama SR, Rogerio LA, Freitas PD, Teixeira MMG, Ribeiro JMC. Total Ortholog Median Matrix as an alternative unsupervised approach for phylogenomics based on evolutionary distance between protein coding genes. Scientific Reports. 11: 3791. PMID 33589693 DOI: 10.1038/s41598-021-81926-w   
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 Zhao P, Zheng X, Yu Y, Hou Z, Diao C, Wang H, Kang H, Ning C, Li J, Feng W, Wang W, Liu GE, Li B, Smith J, Chamba Y, et al. Mining Unknown Porcine Protein Isoforms by Tissue-Based Map of Proteome Enhances the Pig Genome Annotation. Genomics, Proteomics & Bioinformatics. PMID 33631433 DOI: 10.1016/j.gpb.2021.02.002   
2021 Valiente-Mullor C, Beamud B, Ansari I, Francés-Cuesta C, García-González N, Mejía L, Ruiz-Hueso P, González-Candelas F. One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads. Plos Computational Biology. 17: e1008678. PMID 33503026 DOI: 10.1371/journal.pcbi.1008678   
2021 Garg SG, Kapust N, Lin W, Knopp M, Tria FDK, Nelson-Sathi S, Gould SB, Fan L, Zhu R, Zhang C, Martin WF. Anomalous Phylogenetic Behavior of Ribosomal Proteins in Metagenome-Assembled Asgard Archaea. Genome Biology and Evolution. 13. PMID 33462601 DOI: 10.1093/gbe/evaa238   
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 Koonin EV, Makarova KS, Wolf YI. Evolution of Microbial Genomics: Conceptual Shifts over a Quarter Century. Trends in Microbiology. PMID 33541841 DOI: 10.1016/j.tim.2021.01.005   
2021 Shen P, Xu A, Hou Y, Wang H, Gao C, He F, Yang D. Conserved paradoxical relationships among the evolutionary, structural and expressional features of KRAB zinc-finger proteins reveal their special functional characteristics. Bmc Molecular and Cell Biology. 22: 7. PMID 33482715 DOI: 10.1186/s12860-021-00346-w   
2021 Li Y, Liu X, Tang P, Zhang H, Qin Q, Zhang Z. Genome sequence and organization of the Mythimna (formerly Pseudaletia) unipuncta granulovirus Hawaiian strain. Scientific Reports. 11: 414. PMID 33432025 DOI: 10.1038/s41598-020-80117-3   
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 Dang Z, Yang J, Wang L, Tao Q, Zhang F, Zhang Y, Luo Z. Sampling Variation of RAD-Seq Data from Diploid and Tetraploid Potato ( L.). Plants (Basel, Switzerland). 10. PMID 33562246 DOI: 10.3390/plants10020319   
2021 Li X, Cheng X, Liao B, Xu J, Han X, Zhang J, Lin Z, Hu L. Spatial protein expression of by in-depth proteomic analysis for ginsenoside biosynthesis and transportation. Journal of Ginseng Research. 45: 58-65. PMID 33437157 DOI: 10.1016/j.jgr.2020.01.009   
2021 Li X, Cheng X, Liao B, Xu J, Han X, Zhang J, Lin Z, Hu L. Spatial protein expression of by in-depth proteomic analysis for ginsenoside biosynthesis and transportation. Journal of Ginseng Research. 45: 58-65. PMID 33437157 DOI: 10.1016/j.jgr.2020.01.009   
2021 James JE, Willis SM, Nelson PG, Weibel C, Kosinski LJ, Masel J. Universal and taxon-specific trends in protein sequences as a function of age. Elife. 10. PMID 33416492 DOI: 10.7554/eLife.57347   
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 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 Girgis HZ, James BT, Luczak BB. : rapid alignment-free prediction of sequence alignment identity scores using self-supervised general linear models. Nar Genomics and Bioinformatics. 3: lqab001. PMID 33554117 DOI: 10.1093/nargab/lqab001   
2021 Hennessey RC, Brown KM. Cancer regulatory variation. Current Opinion in Genetics & Development. 66: 41-49. PMID 33422949 DOI: 10.1016/j.gde.2020.11.010   
2021 Hennessey RC, Brown KM. Cancer regulatory variation. Current Opinion in Genetics & Development. 66: 41-49. PMID 33422949 DOI: 10.1016/j.gde.2020.11.010   
2021 Vitorino R, Guedes S, Amado F, Santos M, Akimitsu N. The role of micropeptides in biology. Cellular and Molecular Life Sciences : Cmls. PMID 33507325 DOI: 10.1007/s00018-020-03740-3   
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 Mandal S, Debnath U, Sarkar J. Structural-Genetic Characterization Of Novel Butaryl co-A Dehydrogenase and Proposition of Butanol Biosynthesis Pathway in Pusillimonas ginsengisoli SBSA. Journal of Molecular Evolution. PMID 33462639 DOI: 10.1007/s00239-020-09989-3   
2021 Shaibu JO, Onwuamah CK, James AB, Okwuraiwe AP, Amoo OS, Salu OB, Ige FA, Liboro G, Odewale E, Okoli LC, Ahmed RA, Achanya D, Adesesan A, Amuda OA, Sokei J, et al. Full length genomic sanger sequencing and phylogenetic analysis of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Nigeria. Plos One. 16: e0243271. PMID 33428634 DOI: 10.1371/journal.pone.0243271   
2021 Karakatsanis LP, Pavlos EG, Tsoulouhas G, Stamokostas GL, Mosbruger T, Duke JL, Pavlos GP, Monos DS. Spatial constrains and information content of sub-genomic regions of the human genome. Iscience. 24: 102048. PMID 33554061 DOI: 10.1016/j.isci.2021.102048   
2021 Zhang G, Wang H, Yin X, Kong W, Wang Q, Chen Y, Wei J, Liu J, Guo X. Characterization of the complete chloroplast genome of N. P. Balakr. (Apiaceae) and its phylogenetic implications. Mitochondrial Dna. Part B, Resources. 6: 447-449. PMID 33628883 DOI: 10.1080/23802359.2020.1870902   
2021 Singh U, Wurtele ES. orfipy: a fast and flexible tool for extracting ORFs. Bioinformatics (Oxford, England). PMID 33576786 DOI: 10.1093/bioinformatics/btab090   
2021 Literman R, Schwartz R. Genome-scale profiling reveals noncoding loci carry higher proportions of concordant data. Molecular Biology and Evolution. PMID 33528497 DOI: 10.1093/molbev/msab026   
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 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 Harkess A, McLoughlin F, Bilkey N, Elliott K, Emenecker R, Mattoon E, Miller K, Czymmek K, Vierstra R, Meyers BC, Michael TP. An improved Spirodela polyrhiza genome and proteomic analyses reveal a conserved chromosomal structure with high abundances of chloroplastic proteins favoring energy production. Journal of Experimental Botany. PMID 33454741 DOI: 10.1093/jxb/erab006   
2021 Selberg AGA, Gaucher EA, Liberles DA. Ancestral Sequence Reconstruction: From Chemical Paleogenetics to Maximum Likelihood Algorithms and Beyond. Journal of Molecular Evolution. PMID 33486547 DOI: 10.1007/s00239-021-09993-1   
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 Niehus S, Jónsson H, Schönberger J, Björnsson E, Beyter D, Eggertsson HP, Sulem P, Stefánsson K, Halldórsson BV, Kehr B. PopDel identifies medium-size deletions simultaneously in tens of thousands of genomes. Nature Communications. 12: 730. PMID 33526789 DOI: 10.1038/s41467-020-20850-5   
2021 Macey JR, Pabinger S, Barbieri CG, Buring ES, Gonzalez VL, Mulcahy DG, DeMeo DP, Urban L, Hime PM, Prost S, Elliott AN, Gemmell NJ. Evidence of two deeply divergent co-existing mitochondrial genomes in the Tuatara reveals an extremely complex genomic organization. Communications Biology. 4: 116. PMID 33514857 DOI: 10.1038/s42003-020-01639-0   
2021 Weigand MR, Peng Y, Pouseele H, Kania D, Bowden KE, Williams MM, Tondella ML. Genomic surveillance and improved molecular typing of using wgMLST. Journal of Clinical Microbiology. PMID 33627319 DOI: 10.1128/JCM.02726-20   
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 Smith CH. A high-quality reference genome for a parasitic bivalve with doubly uniparental inheritance (Bivalvia: Unionida). Genome Biology and Evolution. PMID 33570560 DOI: 10.1093/gbe/evab029   
2021 Xu P, Chen Y, Gao M, Chong Z. ClipSV: improving structural variation detection by read extension, spliced alignment and tree-based decision rules. Nar Genomics and Bioinformatics. 3: lqab003. PMID 33554118 DOI: 10.1093/nargab/lqab003   
2021 Hendling M, Conzemius R, Barišić I. ResiDB: An automated database manager for sequence data. Computational and Structural Biotechnology Journal. 19: 847-851. PMID 33495705 DOI: 10.1016/j.csbj.2021.01.024   
2021 Seabolt MH, Konstantinidis KT, Roellig DM. Hidden Diversity within Common Protozoan Parasites Revealed by a Novel Genomotyping Scheme. Applied and Environmental Microbiology. PMID 33397705 DOI: 10.1128/AEM.02275-20   
2021 Cao C, Greenberg M, Long Q. WgLink: reconstructing whole-genome viral haplotypes using  L0+L1-regularization. Bioinformatics (Oxford, England). PMID 33532820 DOI: 10.1093/bioinformatics/btab076   
2021 Dong Y, Li C, Kim K, Cui L, Liu X. Genome annotation of disease-causing microorganisms. Briefings in Bioinformatics. PMID 33537706 DOI: 10.1093/bib/bbab004   
2021 Strijk JS, Hinsinger DD, Roeder MM, Chatrou LW, Couvreur TLP, Erkens RHJ, Sauquet H, Pirie MD, Thomas DC, Cao K. Chromosome-level reference genome of the soursop (Annona muricata): a new resource for Magnoliid research and tropical pomology. Molecular Ecology Resources. PMID 33569882 DOI: 10.1111/1755-0998.13353   
2021 Santiago JC, Goldman JD, Zhao H, Pankow AP, Okuku F, Schmitt MW, Chen LH, Hill CA, Casper C, Phipps WT, Mullins JI. Intra-host changes in Kaposi sarcoma-associated herpesvirus genomes in Ugandan adults with Kaposi sarcoma. Plos Pathogens. 17: e1008594. PMID 33465147 DOI: 10.1371/journal.ppat.1008594   
2021 Bohutínská M, Handrick V, Yant L, Schmickl R, Kolář F, Bomblies K, Paajanen P. De-novo mutation and rapid protein (co-)evolution during meiotic adaptation in Arabidopsis arenosa. Molecular Biology and Evolution. PMID 33502506 DOI: 10.1093/molbev/msab001   
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