Manolis Kellis - Related publications

CSAIL Massachusetts Institute of Technology, Cambridge, MA, United States 
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50 most relevant papers in past 60 days:
Year Citation  Score
2020 Picart-Picolo A, Grob S, Picault N, Franek M, Llauro C, Halter T, Maier TR, Jobet E, Descombin J, Zhang P, Paramasivan V, Baum TJ, Navarro L, Dvořáčková M, Mirouze M, et al. Large tandem duplications affect gene expression, 3D organization, and plant-pathogen response. Genome Research. PMID 33033057 DOI: 10.1101/gr.261586.120   
2020 Ko G, Jang I, Koo N, Park SJ, Oh SH, Kim MS, Choi JH, Kim H, Sim YM, Byeon I, Kim PG, Kim KY, Yoon JC, Mun KL, Lee B, et al. Prometheus, an omics portal for interkingdom comparative genomic analyses. Plos One. 15: e0240191. PMID 33112870 DOI: 10.1371/journal.pone.0240191   
2020 Wright BW, Ruan J, Molloy MP, Jaschke PR. Genome Modularization Reveals Overlapped Gene Topology Is Necessary for Efficient Viral Reproduction. Acs Synthetic Biology. PMID 33044064 DOI: 10.1021/acssynbio.0c00323   
2020 Goel N, Singh S, Aseri TC. Global sequence features based translation initiation site prediction in human genomic sequences. Heliyon. 6: e04825. PMID 32964155 DOI: 10.1016/j.heliyon.2020.e04825   
2020 Kuo RI, Cheng Y, Zhang R, Brown JWS, Smith J, Archibald AL, Burt DW. Illuminating the dark side of the human transcriptome with long read transcript sequencing. Bmc Genomics. 21: 751. PMID 33126848 DOI: 10.1186/s12864-020-07123-7   
2020 Zhao S, Luo J, Zeng X, Li K, Yuan R, Zhu L, Li X, Wu G, Yan X. Rolling Circle Amplification (RCA)-Mediated Genome-Wide ihpRNAi Mutant Library Construction in . International Journal of Molecular Sciences. 21. PMID 33008068 DOI: 10.3390/ijms21197243   
2020 Fan G, Liu X, Sun S, Shi C, Du X, Han K, Yang B, Fu Y, Liu M, Seim I, Zhang H, Xu Q, Wang J, Su X, Shao L, et al. The Chromosome Level Genome and Genome-wide Association Study for the Agronomic Traits of . Iscience. 23: 101538. PMID 33083766 DOI: 10.1016/j.isci.2020.101538   
2020 Ntasis VF, Panousis NI, Tektonidou MG, Dermitzakis ET, Boumpas DT, Bertsias GK, Nikolaou C. Extensive fragmentation and re-organization of transcription in Systemic Lupus Erythematosus. Scientific Reports. 10: 16648. PMID 33024230 DOI: 10.1038/s41598-020-73654-4   
2020 Ntasis VF, Panousis NI, Tektonidou MG, Dermitzakis ET, Boumpas DT, Bertsias GK, Nikolaou C. Extensive fragmentation and re-organization of transcription in Systemic Lupus Erythematosus. Scientific Reports. 10: 16648. PMID 33024230 DOI: 10.1038/s41598-020-73654-4   
2020 Calderano SG, Nishiyama Junior MY, Marini M, Nunes NO, Reis MDS, Patané JSL, da Silveira JF, da Cunha JPC, Elias MC. Identification of Novel Interspersed DNA Repetitive Elements in the Genome Associated with the 3'UTRs of Surface Multigenic Families. Genes. 11. PMID 33096822 DOI: 10.3390/genes11101235   
2020 Al Mahdi HB, Edris S, Bahieldin A, Al-Aama JY, Elango R, Jamalalail BA, Sabbagh HJ. Identification of Causative Variants Contributing to Nonsyndromic Orofacial Clefts Using Whole-Exome Sequencing in a Saudi Family. Genetic Testing and Molecular Biomarkers. PMID 33121284 DOI: 10.1089/gtmb.2019.0233   
2020 Liu H, Hu H, Zhang S, Jin J, Liang X, Huang B, Wang L. The complete chloroplast genome of the rare species and comparative analysis with related species. Physiology and Molecular Biology of Plants : An International Journal of Functional Plant Biology. 26: 2075-2083. PMID 33088051 DOI: 10.1007/s12298-020-00882-3   
2020 Wang L, Zhu T, Deal KR, Dvorak J, Luo MC. Computational Identification and Comparative Analysis of Conserved miRNAs and Their Putative Target Genes in the and Genomes. Plants (Basel, Switzerland). 9. PMID 33050178 DOI: 10.3390/plants9101330   
2020 Lei Y, Yang L, Jiang H, Chen J, Sun N, Lv W, He S. Recent genome duplications facilitate the phenotypic diversity of Hb repertoire in the Cyprinidae. Science China. Life Sciences. PMID 33051703 DOI: 10.1007/s11427-020-1809-0   
2020 Rossi A, Treu L, Toppo S, Zschach H, Campanaro S, Dutilh BE. Evolutionary Study of the Crassphage Virus at Gene Level. Viruses. 12. PMID 32957679 DOI: 10.3390/v12091035   
2020 Alaei-Mahabadi B, Elliott K, Larsson E. Systematic investigation of promoter substitutions resulting from somatic intrachromosomal structural alterations in diverse human cancers. Scientific Reports. 10: 18176. PMID 33097743 DOI: 10.1038/s41598-020-74420-2   
2020 Jiang K, Miao LY, Wang ZW, Ni ZY, Hu C, Zeng XH, Huang WC. Chloroplast Genome Analysis of Two Medicinal spp. (Orchidaceae) Shed Light on the Genetic Information, Comparative Genomics, and Species Identification. Plants (Basel, Switzerland). 9. PMID 33050285 DOI: 10.3390/plants9101332   
2020 Law JN, Kale SD, Murali TM. Accurate and efficient gene function prediction using a Multi-Bacterial network. Bioinformatics (Oxford, England). PMID 33063084 DOI: 10.1093/bioinformatics/btaa885   
2020 Picard L, Ganivet Q, Allatif O, Cimarelli A, Guéguen L, Etienne L. DGINN, an automated and highly-flexible pipeline for the detection of genetic innovations on protein-coding genes. Nucleic Acids Research. 48: e103. PMID 32941639 DOI: 10.1093/nar/gkaa680   
2020 Yi XG, Yu XQ, Chen J, Zhang M, Liu SW, Zhu H, Li M, Duan YF, Chen L, Wu L, Zhu S, Sun ZS, Liu XH, Wang XR. The genome of Chinese flowering cherry () provides new insights into species. Horticulture Research. 7: 165. PMID 33082971 DOI: 10.1038/s41438-020-00382-1   
2020 Saha P, Sowpati DT, Soujanya M, Srivastava I, Mishra RK. Interplay of pericentromeric genome organization and chromatin landscape regulates the expression of Drosophila melanogaster heterochromatic genes. Epigenetics & Chromatin. 13: 41. PMID 33028366 DOI: 10.1186/s13072-020-00358-4   
2020 Han B, Yi J, Dai J, Zheng T, Gu F, Zhao Q, Zhu F, Song X, Deng H, Wei P, Song C, Liu D, Jiang X, Wang F, Chen Y, et al. A chromosome-level genome assembly of Dendrobium huoshanense using long reads and Hi-C data. Genome Biology and Evolution. PMID 33045048 DOI: 10.1093/gbe/evaa215   
2020 Hong MJ, Kim JB, Seo YW, Kim DY. F-Box Genes in the Wheat Genome and Expression Profiling in Wheat at Different Developmental Stages. Genes. 11. PMID 33007852 DOI: 10.3390/genes11101154   
2020 Psomopoulos FE, van Helden J, Médigue C, Chasapi A, Ouzounis CA. Ancestral state reconstruction of metabolic pathways across pangenome ensembles. Microbial Genomics. PMID 32924924 DOI: 10.1099/mgen.0.000429   
2020 Doré H, Farrant GK, Guyet U, Haguait J, Humily F, Ratin M, Pitt FD, Ostrowski M, Six C, Brillet-Guéguen L, Hoebeke M, Bisch A, Le Corguillé G, Corre E, Labadie K, et al. Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria. Frontiers in Microbiology. 11: 567431. PMID 33042072 DOI: 10.3389/fmicb.2020.567431   
2020 Wu ZC, Feng HX, Wu L, Zhang M, Zhou WL. Quorum Sensing System in Strain Identified by Genome Sequence Analysis. Acs Omega. 5: 27502-27513. PMID 33134713 DOI: 10.1021/acsomega.0c03986   
2020 Roy AS, Woehle C, LaRoche J. The Transfer of the Ferredoxin Gene From the Chloroplast to the Nuclear Genome Is Ancient Within the Paraphyletic Genus . Frontiers in Microbiology. 11: 523689. PMID 33123095 DOI: 10.3389/fmicb.2020.523689   
2020 Wong KHY, Ma W, Wei CY, Yeh EC, Lin WJ, Wang EHF, Su JP, Hsieh FJ, Kao HJ, Chen HH, Chow SK, Young E, Chu C, Poon A, Yang CF, et al. Towards a reference genome that captures global genetic diversity. Nature Communications. 11: 5482. PMID 33127893 DOI: 10.1038/s41467-020-19311-w   
2020 Nawae W, Yundaeng C, Naktang C, Kongkachana W, Yoocha T, Sonthirod C, Narong N, Somta P, Laosatit K, Tangphatsornruang S, Pootakham W. The Genome and Transcriptome Analysis of the Chloroplast. Plants (Basel, Switzerland). 9. PMID 32967378 DOI: 10.3390/plants9091247   
2020 Li Y, Nong W, Baril T, Yip HY, Swale T, Hayward A, Ferrier DEK, Hui JHL. Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster (Magallana hongkongensis) genome. Bmc Genomics. 21: 713. PMID 33059600 DOI: 10.1186/s12864-020-07027-6   
2020 Eshkiki EM, Hajiahmadi Z, Abedi A, Kordrostami M, Jacquard C. In Silico Analyses of Autophagy-Related Genes in Rapeseed ( L.) under Different Abiotic Stresses and in Various Tissues. Plants (Basel, Switzerland). 9. PMID 33092180 DOI: 10.3390/plants9101393   
2020 Zhao Q, Wu J, Zhang L, Yan C, Jiang S, Li Z, Sun D, Lai Y, Gong Z. Genome-scale analyses and characteristics of putative pathogenicity genes of Stagonosporopsis cucurbitacearum, a pumpkin gummy stem blight fungus. Scientific Reports. 10: 18065. PMID 33093634 DOI: 10.1038/s41598-020-75235-x   
2020 Levin M, Scheibe M, Butter F. Proteotranscriptomics assisted gene annotation and spatial proteomics of Bombyx mori BmN4 cell line. Bmc Genomics. 21: 690. PMID 33023468 DOI: 10.1186/s12864-020-07088-7   
2020 Zhao M, Peng X, Chen N, Shen S. Genome-Wide Identification of the Gene Family in and Functional Analysis of , and in Shoot Branching. Plants (Basel, Switzerland). 9. PMID 33019650 DOI: 10.3390/plants9101301   
2020 Groß C, Bortoluzzi C, de Ridder D, Megens HJ, Groenen MAM, Reinders M, Bosse M. Prioritizing sequence variants in conserved non-coding elements in the chicken genome using chCADD. Plos Genetics. 16: e1009027. PMID 32966296 DOI: 10.1371/journal.pgen.1009027   
2020 Cao LJ, Song W, Yue L, Guo SK, Chen JC, Gong YJ, Hoffmann AA, Wei SJ. Chromosome-level genome of the peach fruit moth Carposina sasakii (Lepidoptera: Carposinidae) provides a resource for evolutionary studies on moths. Molecular Ecology Resources. PMID 33098233 DOI: 10.1111/1755-0998.13288   
2020 Rellstab C, Zoller S, Sailer C, Tedder A, Gugerli F, Shimizu KK, Holderegger R, Widmer A, Fischer MC. Genomic signatures of convergent adaptation to Alpine environments in three Brassicaceae species. Molecular Ecology. PMID 32969558 DOI: 10.1111/mec.15648   
2020 Qin S, Wei K, Cui Z, Liang Y, Li M, Gu L, Yang C, Zhou X, Li L, Xu W, Liu C, Miao J, Zhang Z. Comparative Genomics of and Insight Into Flavonoid Biosynthesis. Frontiers in Plant Science. 11: 528108. PMID 33013959 DOI: 10.3389/fpls.2020.528108   
2020 Zhang W, Yang M, Zhou M, Wang Y, Wu X, Zhang X, Ding Y, Zhao G, Yin Z, Wang C. Identification of Signatures of Selection by Whole-Genome Resequencing of a Chinese Native Pig. Frontiers in Genetics. 11: 566255. PMID 33093844 DOI: 10.3389/fgene.2020.566255   
2020 Misteli T. The Self-Organizing Genome: Principles of Genome Architecture and Function. Cell. 183: 28-45. PMID 32976797 DOI: 10.1016/j.cell.2020.09.014   
2020 De Oliveira R, Rimbert H, Balfourier F, Kitt J, Dynomant E, Vrána J, Doležel J, Cattonaro F, Paux E, Choulet F. Structural Variations Affecting Genes and Transposable Elements of Chromosome 3B in Wheats. Frontiers in Genetics. 11: 891. PMID 33014014 DOI: 10.3389/fgene.2020.00891   
2020 Jungreis I, Sealfon R, Kellis M. SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Research Square. PMID 33024961 DOI: 10.21203/   
2020 Hölzer M, Barf LM, Lamkiewicz K, Vorimore F, Lataretu M, Favaroni A, Schnee C, Laroucau K, Marz M, Sachse K. Comparative Genome Analysis of 33 Strains Reveals Characteristic Features of and Closely Related Species. Pathogens (Basel, Switzerland). 9. PMID 33126635 DOI: 10.3390/pathogens9110899   
2020 Zachariadis V, Cheng H, Andrews N, Enge M. A Highly Scalable Method for Joint Whole-Genome Sequencing and Gene-Expression Profiling of Single Cells. Molecular Cell. PMID 33068522 DOI: 10.1016/j.molcel.2020.09.025   
2020 Weiner AKM, Cerón-Romero MA, Yan Y, Katz LA. Phylogenomics of the epigenetic toolkit reveals punctate retention of genes across eukaryotes. Genome Biology and Evolution. PMID 33049043 DOI: 10.1093/gbe/evaa198   
2020 De la Rosa C, Lozano L, Castillo-Ramírez S, Covarrubias AA, Reyes JL. Origin and evolutionary dynamics of the miR2119 and ADH1 regulatory module in Legumes. Genome Biology and Evolution. PMID 33045056 DOI: 10.1093/gbe/evaa205   
2020 Brown BP, Chopera D, Havyarimana E, Wendoh J, Jaumdally S, Nyangahu DD, Gray CM, Martin DP, Varsani A, Jaspan HB. crAssphage genomes identified in fecal samples of an adult and infants with evidence of positive genomic selective pressure within tail protein genes. Virus Research. 198219. PMID 33137401 DOI: 10.1016/j.virusres.2020.198219   
2020 Bevan S, Schoenfelder S, Young RJ, Zhang L, Andrews S, Fraser P, O'Callaghan PM. High-resolution three-dimensional chromatin profiling of the Chinese hamster ovary cell genome. Biotechnology and Bioengineering. PMID 33095445 DOI: 10.1002/bit.27607   
2020 Peng F, Zhao Z, Xu B, Han J, Yang Q, Lei Y, Tian B, Liu ZL. Characteristics of Organellar Genomes and Nuclear Internal Transcribed Spacers in the Tertiary Relict Genus and Their Phylogenomic Implications. Frontiers in Genetics. 11: 573226. PMID 33101393 DOI: 10.3389/fgene.2020.573226   
2020 Trigui-Lahiani H, Abdeljalil S, Sassi AH, Skouri-Gargouri H, Gargouri A. Molecular characterization and modeling study of the Podr1 gene and genome-scale identification of whole ATP-binding cassette (ABC) transporters in Penicillium occitanis. Genomics. PMID 33069827 DOI: 10.1016/j.ygeno.2020.10.011