Olga G. Troyanskaya - Related publications

Affiliations: 
Computer Science Princeton University, Princeton, NJ 
 2003 Stanford University, Palo Alto, CA 
Area:
Bioinformatics; analysis of large-scale biological data sets (genomics, gene expression, proteomics, biological networks); algorithms for integration of data from multiple data sources; visualization of biological data; machine learning methods in bioinfo
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Zhang Y, Chen F, Creighton CJ. SVExpress: identifying gene features altered recurrently in expression with nearby structural variant breakpoints. Bmc Bioinformatics. 22: 135. PMID 33743584 DOI: 10.1186/s12859-021-04072-0   
2021 Pereira J. GCsnap: interactive snapshots for the comparison of protein-coding genomic contexts. Journal of Molecular Biology. 166943. PMID 33737026 DOI: 10.1016/j.jmb.2021.166943   
2021 Mao Y, Chen R, Xia M, Guo P, Zeng F, Huang J, He M. Identification of an immune-based mRNA-lncRNA signature for overall survival in cervical squamous cell carcinoma. Future Oncology (London, England). PMID 33724869 DOI: 10.2217/fon-2020-1153   
2021 Moro G, Masseroli M. Gene function finding through cross-organism ensemble learning. Biodata Mining. 14: 14. PMID 33579334 DOI: 10.1186/s13040-021-00239-w   
2021 Linard B, Ebersberger I, McGlynn SE, Glover N, Mochizuki T, Patricio M, Lecompte O, Nevers Y, , Thomas PD, Gabaldón T, Sonnhammer E, Dessimoz C, Uchiyama I. Ten years of collaborative progress in the Quest for Orthologs. Molecular Biology and Evolution. PMID 33822172 DOI: 10.1093/molbev/msab098   
2021 Sommer MJ, Salzberg SL. Balrog: A universal protein model for prokaryotic gene prediction. Plos Computational Biology. 17: e1008727. PMID 33635857 DOI: 10.1371/journal.pcbi.1008727   
2021 Lee BH, Rhie SK. Molecular and computational approaches to map regulatory elements in 3D chromatin structure. Epigenetics & Chromatin. 14: 14. PMID 33741028 DOI: 10.1186/s13072-021-00390-y   
2021 Qing J, Du Q, Meng Y, Liu P, Du H, Wang L. Genome-wide identification and expression pattern analysis of the ribonuclease T2 family in Eucommia ulmoides. Scientific Reports. 11: 6900. PMID 33767357 DOI: 10.1038/s41598-021-86337-5   
2021 He X, Lu T, Zhou X. Whole Genome Sequencing and Comparative GenomicsAnalysis of Pectobacterium carotovorum IdentifiesKey Pathogenic Genes. Molecular Phylogenetics and Evolution. 107114. PMID 33744402 DOI: 10.1016/j.ympev.2021.107114   
2021 Singh-Babak SD, Babak T, Fraser HB, Johnson AD. Lineage-specific selection and the evolution of virulence in the clade. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33723044 DOI: 10.1073/pnas.2016818118   
2021 Arora D, Srikanth K, Lee J, Lee D, Park N, Wy S, Kim H, Park JE, Chai HH, Lim D, Cho IC, Kim J, Park W. Integration of multi-omics approaches for functional characterization of muscle related selective sweep genes in Nanchukmacdon. Scientific Reports. 11: 7219. PMID 33785872 DOI: 10.1038/s41598-021-86683-4   
2021 Kundu S, Ray MD, Sharma A. Interplay between genome organization and epigenomic alterations of pericentromeric DNA in cancer. Journal of Genetics and Genomics = Yi Chuan Xue Bao. PMID 33840602 DOI: 10.1016/j.jgg.2021.02.004   
2021 Kim J, Jiang S, Wang Y, Xiao G, Xie Y, Liu DJ, Li Q, Koh A, Zhan X. MetaPrism: A Versatile Toolkit for Joint Taxa/Gene Analysis of Metagenomic Sequencing Data. G3 (Bethesda, Md.). PMID 33713107 DOI: 10.1093/g3journal/jkab046   
2021 Zhang H, Xie J, Wang W, Wang J. Comparison of Brassica Genomes reveals asymmetrical gene retention between functional groups of genes in recurrent polyploidizations. Plant Molecular Biology. PMID 33742369 DOI: 10.1007/s11103-021-01137-9   
2021 Horesh G, Blackwell GA, Tonkin-Hill G, Corander J, Heinz E, Thomson NR. A comprehensive and high-quality collection of genomes and their genes. Microbial Genomics. 7. PMID 33417534 DOI: 10.1099/mgen.0.000499   
2021 Barshir R, Fishilevich S, Iny-Stein T, Zelig O, Mazor Y, Guan-Golan Y, Safran M, Lancet D. GeneCaRNA: a comprehensive gene-centric database of human non-coding RNAs in the GeneCards Suite. Journal of Molecular Biology. 166913. PMID 33676929 DOI: 10.1016/j.jmb.2021.166913   
2021 Agius JE, Phalen DN, Rose K, Eden JS. Genomic Insights Into the Pathogenicity of a Novel Biofilm-Forming sp. Bacteria () Identified in Reptiles. Frontiers in Microbiology. 12: 635208. PMID 33737921 DOI: 10.3389/fmicb.2021.635208   
2021 Zhao Z, Li S, Ji C, Zhou Y, Li C, Wang W. Genetic Variation of the Serine Acetyltransferase Gene Family for Sulfur Assimilation in Maize. Genes. 12. PMID 33808582 DOI: 10.3390/genes12030437   
2021 Fu S, Duan Y, Wang S, Ren Y, Bu W. Comparative Transcriptomic Analysis of (Hemiptera: Alydidae) to Characterize Wing Formation across All Developmental Stages. Insects. 12. PMID 33807991 DOI: 10.3390/insects12030226   
2021 Yuan X, Scott IC, Wilson MD. Heart Enhancers: Development and Disease Control at a Distance. Frontiers in Genetics. 12: 642975. PMID 33777110 DOI: 10.3389/fgene.2021.642975   
2021 He X, Zheng Z, Wang Q, Zhou M, Liao G, Ge Y, Cheng R. Complete chloroplast genome sequence of the medicinal plant ramie ( L. gaud) and its phylogenetic relationship to other Urticaceae species. Mitochondrial Dna. Part B, Resources. 6: 1136-1137. PMID 33796767 DOI: 10.1080/23802359.2021.1878959   
2021 Wang R, Han T, Sun J, Xu L, Fan J, Cao H, Liu C. Genome-wide identification and characterization of the gene family in Chinese cabbage ( L. ssp. ). Peerj. 9: e10934. PMID 33717690 DOI: 10.7717/peerj.10934   
2021 Liu Y, Wang W. Characterization of the GRAS gene family reveals their contribution to the high adaptability of wheat. Peerj. 9: e10811. PMID 33665016 DOI: 10.7717/peerj.10811   
2021 Panta M, Mishra A, Hoque MT, Atallah J. ClassifyTE: A stacking based prediction of hierarchical classification of transposable elements. Bioinformatics (Oxford, England). PMID 33682878 DOI: 10.1093/bioinformatics/btab146   
2021 Jefferson OA, Lang S, Williams K, Koellhofer D, Ballagh A, Warren B, Schellberg B, Sharma R, Jefferson R. Mapping CRISPR-Cas9 public and commercial innovation using The Lens institutional toolkit. Transgenic Research. PMID 33721140 DOI: 10.1007/s11248-021-00237-y   
2021 Natsidis P, Kapli P, Schiffer PH, Telford MJ. Systematic errors in orthology inference and their effects on evolutionary analyses. Iscience. 24: 102110. PMID 33659875 DOI: 10.1016/j.isci.2021.102110   
2021 Mitchell LA, McCulloch LH, Pinglay S, Berger H, Bosco N, Brosh R, Bulajić M, Huang E, Hogan MS, Martin JA, Mazzoni EO, Davoli T, Maurano MT, Boeke JD. De novo assembly and delivery to mouse cells of a 101 kb functional human gene. Genetics. PMID 33742653 DOI: 10.1093/genetics/iyab038   
2021 Liu JJ, Sniezko RA, Zamany A, Williams H, Omendja K, Kegley A, Savin DP. Comparative Transcriptomics and RNA-Seq-Based Bulked Segregant Analysis Reveals Genomic Basis Underlying Virulence. Frontiers in Microbiology. 12: 602812. PMID 33776951 DOI: 10.3389/fmicb.2021.602812   
2021 Ecale Zhou CL, Kimbrel J, Edwards R, McNair K, Souza BA, Malfatti S. MultiPhATE2: Code for functional annotation and comparison of phage genomes. G3 (Bethesda, Md.). PMID 33734357 DOI: 10.1093/g3journal/jkab074   
2021 Lin J, Jiang W, Chen L, Zhang H, Shi Y, Liu X, Cai W. Metagenomic sequencing revealed the potential of banknotes as a repository of microbial genes. Bmc Genomics. 22: 173. PMID 33706718 DOI: 10.1186/s12864-021-07424-5   
2021 Islamaj R, Wei CH, Cissel D, Miliaras N, Printseva O, Rodionov O, Sekiya K, Ward J, Lu Z. NLM-Gene, a richly annotated gold standard dataset for gene entities that addresses ambiguity and multi-species gene recognition. Journal of Biomedical Informatics. 103779. PMID 33839304 DOI: 10.1016/j.jbi.2021.103779   
2021 Zhou F, Lan K, Li X, Mei Y, Cai S, Wang J. The complete chloroplast genome sequence of Delile. Mitochondrial Dna. Part B, Resources. 6: 1134-1135. PMID 33796766 DOI: 10.1080/23802359.2021.1902411   
2021 Zhou F, Lan K, Li X, Mei Y, Cai S, Wang J. The complete chloroplast genome sequence of Delile. Mitochondrial Dna. Part B, Resources. 6: 1134-1135. PMID 33796766 DOI: 10.1080/23802359.2021.1902411   
2021 Choi BS, Kim DH, Kim MS, Park JC, Lee YH, Kim HJ, Jeong CB, Hagiwara A, Souissi S, Lee JS. The genome of the European estuarine calanoid copepod Eurytemora affinis: Potential use in molecular ecotoxicology. Marine Pollution Bulletin. 166: 112190. PMID 33711609 DOI: 10.1016/j.marpolbul.2021.112190   
2021 Dasgupta I, Flotte TR, Keeler AM. CRISPR/Cas-Dependent and Nuclease-Free Therapeutic Gene Editing. Human Gene Therapy. 32: 275-293. PMID 33750221 DOI: 10.1089/hum.2021.013   
2021 Li M, Zhao Q, Belloli R, Duffy CR, Cai HN. Insulator foci distance correlates with cellular and nuclear morphology in early Drosophila embryos. Developmental Biology. PMID 33844976 DOI: 10.1016/j.ydbio.2021.03.022   
2021 Wang Z, Zhang Y, Zang C. BART3D: Inferring transcriptional regulators associated with differential chromatin interactions from Hi-C data. Bioinformatics (Oxford, England). PMID 33720325 DOI: 10.1093/bioinformatics/btab173   
2021 Rai R, Pasion J, Majumdar T, Green CE, Hind SR. Genome sequencing and functional characterization of , the causal agent of bacterial spot disease of cucurbits. Phytopathology. PMID 33734871 DOI: 10.1094/PHYTO-06-20-0228-R   
2021 Nadin-Davis SA, Chmara J, Carrillo CD, Amoako K, Goji N, Duceppe MO, Devenish J. A comparison of fourteen fully characterized mammalian-associated isolates suggests that loss of defense mechanisms contribute to high genomic plasticity and subspecies evolution. Peerj. 9: e10586. PMID 33628630 DOI: 10.7717/peerj.10586   
2021 Li H, Liang X, Zhou J. [Progress in gene editing technologies for Saccharomyces cerevisiae]. Sheng Wu Gong Cheng Xue Bao = Chinese Journal of Biotechnology. 37: 950-965. PMID 33783160 DOI: 10.13345/j.cjb.200542   
2021 Castillo AI, Almeida RPP. Evidence of gene nucleotide composition favoring replication and growth in a fastidious plant pathogen. G3 (Bethesda, Md.). PMID 33715000 DOI: 10.1093/g3journal/jkab076   
2021 Wilks C, Ahmed O, Baker DN, Zhang D, Collado-Torres L, Langmead B. Megadepth: efficient coverage quantification for BigWigs and BAMs. Bioinformatics (Oxford, England). PMID 33693500 DOI: 10.1093/bioinformatics/btab152   
2021 Kern C, Wang Y, Xu X, Pan Z, Halstead M, Chanthavixay G, Saelao P, Waters S, Xiang R, Chamberlain A, Korf I, Delany ME, Cheng HH, Medrano JF, Van Eenennaam AL, et al. Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research. Nature Communications. 12: 1821. PMID 33758196 DOI: 10.1038/s41467-021-22100-8   
2021 Bao Y, Pan K, Muhammad Tahir K, Chen B, Zhang M. High-Quality Genome Sequence Resource for Fusarium andiyazi Causing Pokkah Boeng Disease of Sugarcane in China. Molecular Plant-Microbe Interactions : Mpmi. PMID 33797948 DOI: 10.1094/MPMI-11-20-0331-A   
2021 Bao Y, Pan K, Muhammad Tahir K, Chen B, Zhang M. High-Quality Genome Sequence Resource for Fusarium andiyazi Causing Pokkah Boeng Disease of Sugarcane in China. Molecular Plant-Microbe Interactions : Mpmi. PMID 33797948 DOI: 10.1094/MPMI-11-20-0331-A   
2021 Mishra A, Singh A, Mantri S, Pandey AK, Garg M, Deshmukh R, Sonah H, Kandoth PK, Sharma TR, Roy J. Decoding the genome of supreme chapatti quality Indian wheat variety 'C 306' unravelled novel genomic variants for chapatti and nutrition quality related genes. Genomics. PMID 33823224 DOI: 10.1016/j.ygeno.2021.03.031   
2021 Power JJ, Pinheiro F, Pompei S, Kovacova V, Yüksel M, Rathmann I, Förster M, Lässig M, Maier B. Adaptive evolution of hybrid bacteria by horizontal gene transfer. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33649202 DOI: 10.1073/pnas.2007873118   
2021 Zhang Q, Wang Y, Zhou J. Complete genome sequence of Stenotrophomonas rhizophila KC1, a quorum sensing-producing algicidal bacterium, isolated from mangrove Kandelia candel. Molecular Plant-Microbe Interactions : Mpmi. PMID 33673750 DOI: 10.1094/MPMI-12-20-0346-A   
2021 van Kruistum H, Nijland R, Reznick DN, Groenen MAM, Megens HJ, Pollux BJA. Parallel genomic changes drive repeated evolution of placentas in live-bearing fish. Molecular Biology and Evolution. PMID 33620468 DOI: 10.1093/molbev/msab057   
2021 Wang H, Wang Y, Cheng H, Xue M, Wang J, Yue Z. The complete chloroplast genome of (Benth.) Briq., a traditional Chinese herb. Mitochondrial Dna. Part B, Resources. 6: 907-908. PMID 33796676 DOI: 10.1080/23802359.2021.1886884