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Mark B. Gerstein - Related publications

Molecular Biophysics and Biochemistry Yale University, New Haven, CT 
Computational Biology and Bioinformatics
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 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 Zhou P, Wang L, Liu H, Li C, Li Z, Wang J, Tan X. CyanoOmicsDB: an integrated omics database for functional genomic analysis of cyanobacteria. Nucleic Acids Research. PMID 34614159 DOI: 10.1093/nar/gkab891   
2021 Jiang S, Du Q, Feng C, Ma L, Zhang Z. CompoDynamics: a comprehensive database for characterizing sequence composition dynamics. Nucleic Acids Research. PMID 34718745 DOI: 10.1093/nar/gkab979   
2021 Acs-Szabo L, Papp LA, Sipiczki M, Miklos I. Genome Comparisons of the Fission Yeasts Reveal Ancient Collinear Loci Maintained by Natural Selection. Journal of Fungi (Basel, Switzerland). 7. PMID 34682285 DOI: 10.3390/jof7100864   
2021 Shim S, Park CM, Seo PJ. iRegNet: an integrative Regulatory Network analysis tool for Arabidopsis thaliana. Plant Physiology. PMID 34618085 DOI: 10.1093/plphys/kiab389   
2021 Yu Z, Zhang W, Fu H, Zou X, Zhao M, Liang S, Gu C, Yang Q, He M, Xiao Q, Xiao W, He L, Lü M. Genomic analysis of Poxviridae and exploring qualified gene sequences for phylogenetics. Computational and Structural Biotechnology Journal. 19: 5479-5486. PMID 34712393 DOI: 10.1016/j.csbj.2021.09.031   
2021 Singh A, Schermann G, Reislöhner S, Kellner N, Hurt E, Brunner M. Global Transcriptome Characterization and Assembly of the Thermophilic Ascomycete . Genes. 12. PMID 34680944 DOI: 10.3390/genes12101549   
2021 Awan F, Ali MM, Hamid M, Awan MH, Mushtaq MH, Kalsoom S, Ijaz M, Mehmood K, Liu Y. Epi-Gene: An R-Package for Easy Pan-Genome Analysis. Biomed Research International. 2021: 5585586. PMID 34595238 DOI: 10.1155/2021/5585586   
2021 Cooley NP, Wright ES. Accurate annotation of protein coding sequences with IDTAXA. Nar Genomics and Bioinformatics. 3: lqab080. PMID 34541527 DOI: 10.1093/nargab/lqab080   
2021 Kim P, Tan H, Liu J, Yang M, Zhou X. FusionAI: Predicting fusion breakpoint from DNA sequence with deep learning. Iscience. 24: 103164. PMID 34646994 DOI: 10.1016/j.isci.2021.103164   
2021 Di Sera T, Velinder M, Ward A, Qiao Y, Georges S, Miller C, Pitman A, Richards W, Ekawade A, Viskochil D, Carey JC, Pace L, Bale J, Clardy SL, Andrews A, et al. Gene.iobio: an interactive web tool for versatile, clinically-driven variant interrogation and prioritization. Scientific Reports. 11: 20307. PMID 34645894 DOI: 10.1038/s41598-021-99752-5   
2021 Avsec Ž, Agarwal V, Visentin D, Ledsam JR, Grabska-Barwinska A, Taylor KR, Assael Y, Jumper J, Kohli P, Kelley DR. Effective gene expression prediction from sequence by integrating long-range interactions. Nature Methods. 18: 1196-1203. PMID 34608324 DOI: 10.1038/s41592-021-01252-x   
2021 Xu L, Yin L, Qi Y, Tan X, Gao M, Peng J. 3D disorganization and rearrangement of genome provide insights into pathogenesis of NAFLD by integrated Hi-C, Nanopore, and RNA sequencing. Acta Pharmaceutica Sinica. B. 11: 3150-3164. PMID 34729306 DOI: 10.1016/j.apsb.2021.03.022   
2021 Libbrecht MW, Chan RCW, Hoffman MM. Segmentation and genome annotation algorithms for identifying chromatin state and other genomic patterns. Plos Computational Biology. 17: e1009423. PMID 34648491 DOI: 10.1371/journal.pcbi.1009423   
2021 Zhou J, Wu P, Xiong Z, Liu N, Zhao N, Ji M, Qiu Y, Yang B. Chromosome-Level Genome Assembly Reveals Significant Gene Expansion in the Toll and IMD Signaling Pathways of . Frontiers in Genetics. 12: 728418. PMID 34777464 DOI: 10.3389/fgene.2021.728418   
2021 Huang D, Zhou Y, Yi X, Fan X, Wang J, Yao H, Sham PC, Hao J, Chen K, Li MJ. VannoPortal: multiscale functional annotation of human genetic variants for interrogating molecular mechanism of traits and diseases. Nucleic Acids Research. PMID 34570217 DOI: 10.1093/nar/gkab853   
2021 Decker KT, Gao Y, Rychel K, Al Bulushi T, Chauhan SM, Kim D, Cho BK, Palsson BO. proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms. Nucleic Acids Research. PMID 34791440 DOI: 10.1093/nar/gkab1043   
2021 Leong PPT, Mihajlović A, Bogdanović N, Breberina L, Xi L. Reconstructing and counting genomic fragments through tagmentation-based haploid phasing. Scientific Reports. 11: 18907. PMID 34556684 DOI: 10.1038/s41598-021-97852-w   
2021 Tang M, He S, Gong X, Lü P, Taha RH, Chen K. High-Quality Chromosome-Level Genome Assembly of a Single With Resistance by a Combination of PacBio Long-Read Sequencing, Illumina Short-Read Sequencing, and Hi-C Sequencing. Frontiers in Genetics. 12: 718266. PMID 34603381 DOI: 10.3389/fgene.2021.718266   
2021 Oh J, Lee SG, Park C. PIC-Me: paralogs and isoforms classifier based on machine-learning approaches. Bmc Bioinformatics. 22: 311. PMID 34674638 DOI: 10.1186/s12859-021-04229-x   
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 Sun J, Wang Y, Garran TA, Qiao P, Wang M, Yuan Q, Guo L, Huang L. Heterogeneous Genetic Diversity Estimation of a Promising Domestication Medicinal Motherwort Based on Chloroplast Genome Resources. Frontiers in Genetics. 12: 721022. PMID 34603384 DOI: 10.3389/fgene.2021.721022   
2021 Wen G, Chen S, Fan L, Zeng L, Xu B. The complete chloroplast genome of H.S.Lo (Menispermaceae), an important traditional medicine from South China. Mitochondrial Dna. Part B, Resources. 6: 3269-3270. PMID 34712807 DOI: 10.1080/23802359.2021.1993099   
2021 Thaxton C, Good ME, DiStefano MT, Luo X, Andersen EF, Thorland E, Berg J, Martin CL, Rehm HL, Riggs ER, . Utilizing ClinGen Gene-Disease Validity and Dosage Sensitivity Curations to Inform Variant Classification. Human Mutation. PMID 34694049 DOI: 10.1002/humu.24291   
2021 Peterson KA, Murray SA. Progress towards completing the mutant mouse null resource. Mammalian Genome : Official Journal of the International Mammalian Genome Society. PMID 34698892 DOI: 10.1007/s00335-021-09905-0   
2021 Hawley JR, Zhou S, Arlidge C, Grillo G, Kron KJ, Hugh-White R, van der Kwast TH, Fraser M, Boutros PC, Bristow RG, Lupien M. Reorganization of the 3D genome pinpoints non-coding drivers of primary prostate tumors. Cancer Research. PMID 34642184 DOI: 10.1158/0008-5472.CAN-21-2056   
2021 Fouladi F, Young JB, Fodor AA. HashSeq: a Simple, Scalable, and Conservative Variant Caller for 16S rRNA Gene Data Sets. Msystems. e0069721. PMID 34751586 DOI: 10.1128/mSystems.00697-21   
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 Jiang L, Guo F, Tang J, Yu H, Ness S, Duan M, Mao P, Zhao YY, Guo Y. SBSA: an online service for somatic binding sequence annotation. Nucleic Acids Research. PMID 34606615 DOI: 10.1093/nar/gkab877   
2021 Yamamoto T. Genomic Aberrations Associated with the Pathophysiological Mechanisms of Neurodevelopmental Disorders. Cells. 10. PMID 34571966 DOI: 10.3390/cells10092317   
2021 Liu Y, Xu Y, Jia X. The complete chloroplast genome of , an edible oil Camellia. Mitochondrial Dna. Part B, Resources. 6: 3169-3170. PMID 34660893 DOI: 10.1080/23802359.2021.1987169   
2021 Baptista RP, Li Y, Sateriale A, Brooks KL, Tracey A, Sanders MJ, Ansell BRE, Jex AR, Cooper GW, Smith ED, Xiao R, Dumaine JE, Georgeson P, Pope B, Berriman M, et al. Long-read assembly and comparative evidence-based reanalysis of genome sequences reveals expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions. Genome Research. PMID 34764149 DOI: 10.1101/gr.275325.121   
2021 Barber AE, Sae-Ong T, Kang K, Seelbinder B, Li J, Walther G, Panagiotou G, Kurzai O. Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection. Nature Microbiology. 6: 1526-1536. PMID 34819642 DOI: 10.1038/s41564-021-00993-x   
2021 Jiang T, Yin Z, Cai R, Yu H, Lu Q, Zhao S, Tian Y, Yan Y, Chen X, Guo J. Chromosomal-level Genome Assembly of a True Bug, Aspongopus chinensis Dallas, 1851 (Hemiptera: Dinidoridae). Genome Biology and Evolution. PMID 34623414 DOI: 10.1093/gbe/evab232   
2021 Jin YT, Ma C, Wang X, Wang SX, Zhang KY, Zheng WX, Deng Z, Wang J, Guo FB. Consistent Clustering Pattern of Prokaryotic Genes Based on Base Frequency at the Second Codon Position and its Association with Functional Category Preference. Interdisciplinary Sciences, Computational Life Sciences. PMID 34817803 DOI: 10.1007/s12539-021-00493-w   
2021 Fang H, Knight JC. Priority index: database of genetic targets in immune-mediated disease. Nucleic Acids Research. PMID 34751399 DOI: 10.1093/nar/gkab994   
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 Kiran K, Rawal HC, Dubey H, Jaswal R, Bhardwaj SC, Deshmukh R, Sharma TR. Genome-Wide Analysis of Four Pathotypes of Wheat Rust Pathogen () Reveals Structural Variations and Diversifying Selection. Journal of Fungi (Basel, Switzerland). 7. PMID 34575739 DOI: 10.3390/jof7090701   
2021 Kim P, Tan H, Liu J, Lee H, Jung H, Kumar H, Zhou X. FusionGDB 2.0: fusion gene annotation updates aided by deep learning. Nucleic Acids Research. PMID 34755868 DOI: 10.1093/nar/gkab1056   
2021 Martin R, Dreßler H, Hattab G, Hackl T, Fischer MG, Heider D. MOSGA 2: Comparative genomics and validation tools. Computational and Structural Biotechnology Journal. 19: 5504-5509. PMID 34712396 DOI: 10.1016/j.csbj.2021.09.024   
2021 Bao J, Wang R, Gao S, Wang Z, Fang Y, Wu L, Wang M. High-Quality Genome Sequence Resource of a Rice False Smut Fungus Isolate, UV-FJ-1. Phytopathology. PHYTO01210007A. PMID 34732059 DOI: 10.1094/PHYTO-01-21-0007-A   
2021 Zhou Q, Jiao L, Li W, Hu Z, Li Y, Zhang H, Yang M, Xu L, Yan Y. A Novel Cre/-Based Genetic Tool for Repeated, Targeted and Markerless Gene Integration in . International Journal of Molecular Sciences. 22. PMID 34639080 DOI: 10.3390/ijms221910739   
2021 Jain S, Xiao X, Bogdan P, Bruck J. Generator based approach to analyze mutations in genomic datasets. Scientific Reports. 11: 21084. PMID 34702945 DOI: 10.1038/s41598-021-00609-8   
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 Guo W, Liang X, Wu Y, Yu W. The complete mitochondrial genome of (Chiroptera: Vespertilionidae) in South China. Mitochondrial Dna. Part B, Resources. 6: 3274-3275. PMID 34712809 DOI: 10.1080/23802359.2021.1993103   
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 Dou M, Hao Y, Yang J, Yuan X, Yin X, Jiao Y, Zhao J, Chen T, Wang Y, Xu Y. Genome Sequence Resource for Colletotrichum viniferum, the cause of grapevine ripe rot in China. Molecular Plant-Microbe Interactions : Mpmi. PMID 34569260 DOI: 10.1094/MPMI-04-21-0077-A   
2021 Iqbal Qureshi AM, Sofi MU, Dar NA, Khan MH, Mahdi SS, Dar ZA, Bangroo S, El-Serehy HA, Hefft DI, Popescu SM. Insilco identification and characterization of superoxide dismutase gene family in . Saudi Journal of Biological Sciences. 28: 5526-5537. PMID 34588862 DOI: 10.1016/j.sjbs.2021.08.009   
2021 Ren Z, Wang Z, Gu D, Ma H, Zhu Y, Cai M, Zhang J. Genome Instability and Long Noncoding RNA Reveal Biomarkers for Immunotherapy and Prognosis and Novel Competing Endogenous RNA Mechanism in Colon Adenocarcinoma. Frontiers in Cell and Developmental Biology. 9: 740455. PMID 34746134 DOI: 10.3389/fcell.2021.740455   
2021 Pema Y, Ma C, Bautista MAC, Chen T. The complete chloroplast genome sequence of the Tibetan herb (Benth. ex Hook.f.) Mathiesen (Lamiaceae). Mitochondrial Dna. Part B, Resources. 6: 3261-3262. PMID 34693018 DOI: 10.1080/23802359.2021.1993459