Alex Thomas - Related publications

Affiliations: 
2011-2015 Bioinformatics and Systems Biology University of California, San Diego, La Jolla, CA 
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50 most relevant papers in past 60 days:
Year Citation  Score
2020 McCubbin T, Gonzalez-Garcia RA, Palfreyman RW, Stowers C, Nielsen LK, Marcellin E. A Pan-Genome Guided Metabolic Network Reconstruction of Five Species Reveals Extensive Metabolic Diversity. Genes. 11. PMID 32977700 DOI: 10.3390/genes11101115   
2020 Fang X, Lloyd CJ, Palsson BO. Reconstructing organisms in silico: genome-scale models and their emerging applications. Nature Reviews. Microbiology. PMID 32958892 DOI: 10.1038/s41579-020-00440-4   
2020 M A Basher AR, McLaughlin RJ, Hallam SJ. Metabolic pathway inference using multi-label classification with rich pathway features. Plos Computational Biology. 16: e1008174. PMID 33001968 DOI: 10.1371/journal.pcbi.1008174   
2020 Wang B, Yang J, Gao C, Hao T, Li J, Sun J. Reconstruction of Y-organ Genome-Scale Metabolic Network and Differential Analysis After Eyestalk Ablation. Frontiers in Genetics. 11: 532492. PMID 33101373 DOI: 10.3389/fgene.2020.532492   
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 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 Chen Y, Yu L, Qiao N, Xiao Y, Tian F, Zhao J, Zhang H, Chen W, Zhai Q. : A Candidate Probiotic with Excellent Fermentation Properties and Health Benefits. Foods (Basel, Switzerland). 9. PMID 32993033 DOI: 10.3390/foods9101366   
2020 Yang Z, Blenner M. Genome editing systems across yeast species. Current Opinion in Biotechnology. 66: 255-266. PMID 33011454 DOI: 10.1016/j.copbio.2020.08.011   
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 Hao W, Suo F, Lin Q, Chen Q, Zhou L, Liu Z, Cui W, Zhou Z. Design and Construction of Portable CRISPR-Cpf1-Mediated Genome Editing in 168 Oriented Toward Multiple Utilities. Frontiers in Bioengineering and Biotechnology. 8: 524676. PMID 32984297 DOI: 10.3389/fbioe.2020.524676   
2020 Garcia-Morales L, Ruiz E, Gourgues G, Rideau F, Piñero-Lambea C, Lluch-Senar M, Blanchard A, Lartigue C. A RAGE Based Strategy for the Genome Engineering of the Human Respiratory Pathogen . Acs Synthetic Biology. PMID 33017534 DOI: 10.1021/acssynbio.0c00263   
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 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 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 Aliaga Goltsman DS, Alexander LM, Devoto AE, Albers JB, Liu J, Butterfield CN, Brown CT, Thomas BC. Novel Type V-A CRISPR Effectors Are Active Nucleases with Expanded Targeting Capabilities. The Crispr Journal. PMID 33146573 DOI: 10.1089/crispr.2020.0043   
2020 Gong Y, Kang NK, Kim YU, Wang Z, Wei L, Xin Y, Shen C, Wang Q, You W, Lim JM, Jeong SW, Park YI, Oh HM, Pan K, Poliner E, et al. The NanDeSyn Database for Nannochloropsis systems and synthetic biology. The Plant Journal : For Cell and Molecular Biology. PMID 33103271 DOI: 10.1111/tpj.15025   
2020 Norsigian CJ, Danhof HA, Brand CK, Oezguen N, Midani FS, Palsson BO, Savidge TC, Britton RA, Spinler JK, Monk JM. Systems biology analysis of the Clostridioides difficile core-genome contextualizes microenvironmental evolutionary pressures leading to genotypic and phenotypic divergence. Npj Systems Biology and Applications. 6: 31. PMID 33082337 DOI: 10.1038/s41540-020-00151-9   
2020 Nagar S, Talwar C, Haider S, Puri A, Ponnusamy K, Gupta M, Sood U, Bajaj A, Lal R, Kumar R. Phylogenetic Relationships and Potential Functional Attributes of the Genus : A Member of Family . Frontiers in Microbiology. 11: 1725. PMID 33013721 DOI: 10.3389/fmicb.2020.01725   
2020 Felestrino ÉB, Sanchez AB, Caneschi WL, Lemes CGC, Assis RAB, Cordeiro IF, Fonseca NP, Villa MM, Vieira IT, Kamino LHY, do Carmo FF, da Silva AM, Thomas AM, Patané JSL, Ferreira FC, et al. Complete genome sequence and analysis of Alcaligenes faecalis strain Mc250, a new potential plant bioinoculant. Plos One. 15: e0241546. PMID 33151992 DOI: 10.1371/journal.pone.0241546   
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 Huang WC, Hu Y, Zhang G, Li M. Comparative genomic analysis reveals metabolic diversity of different Paenibacillus groups. Applied Microbiology and Biotechnology. PMID 33128615 DOI: 10.1007/s00253-020-10984-3   
2020 Timouma S, Schwartz JM, Delneri D. HybridMine: A Pipeline for Allele Inheritance and Gene Copy Number Prediction in Hybrid Genomes and Its Application to Industrial Yeasts. Microorganisms. 8. PMID 33050146 DOI: 10.3390/microorganisms8101554   
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 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 Ramsey J, Rasche H, Maughmer C, Criscione A, Mijalis E, Liu M, Hu JC, Young R, Gill JJ. Galaxy and Apollo as a biologist-friendly interface for high-quality cooperative phage genome annotation. Plos Computational Biology. 16: e1008214. PMID 33137082 DOI: 10.1371/journal.pcbi.1008214   
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 Li Q, Xu J, Yang L, Zhou X, Cai Y, Zhang Y. Transcriptome Analysis of Different Tissues Reveals Key Genes Associated With Galanthamine Biosynthesis in . Frontiers in Plant Science. 11: 519752. PMID 33042169 DOI: 10.3389/fpls.2020.519752   
2020 Feder A, Jensen S, Wang A, Courtney L, Middleton L, Van Eck J, Liu Y, Giovannoni JJ. Tomato fruit as a model for tissue-specific gene silencing in crop plants. Horticulture Research. 7: 142. PMID 32922814 DOI: 10.1038/s41438-020-00363-4   
2020 He S, Dong X, Zhang G, Fan W, Duan S, Shi H, Li D, Li R, Chen G, Long G, Zhao Y, Chen M, Yan M, Yang J, Lu Y, et al. High quality genome of Erigeron breviscapus provides a reference for herbal plants in Asteraceae. Molecular Ecology Resources. PMID 32985109 DOI: 10.1111/1755-0998.13257   
2020 van Opijnen T, Levin HL. Transposon Insertion Sequencing, a Global Measure of Gene Function. Annual Review of Genetics. PMID 32886545 DOI: 10.1146/annurev-genet-112618-043838   
2020 Georgiou MA, Dommaraju SR, Guo X, Mast DH, Mitchell DA. Bioinformatic and Reactivity-Based Discovery of Linaridins. Acs Chemical Biology. PMID 33170617 DOI: 10.1021/acschembio.0c00620   
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 Garczarek L, Guyet U, Doré H, Farrant GK, Hoebeke M, Brillet-Guéguen L, Bisch A, Ferrieux M, Siltanen J, Corre E, Le Corguillé G, Ratin M, Pitt FD, Ostrowski M, Conan M, et al. Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes. Nucleic Acids Research. PMID 33125079 DOI: 10.1093/nar/gkaa958   
2020 Lee KY, Lee HJ, Choi HJ, Han ST, Lee KH, Park KJ, Park JS, Jung KM, Kim YM, Han HJ, Han JY. Highly elevated base excision repair pathway in primordial germ cells causes low base editing activity in chickens. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. PMID 33031594 DOI: 10.1096/fj.202001065RRR   
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 Fazle Rabbee M, Baek KH. Antimicrobial Activities of Lipopeptides and Polyketides of for Agricultural Applications. Molecules (Basel, Switzerland). 25. PMID 33121115 DOI: 10.3390/molecules25214973   
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 Lao J, Guédon G, Lacroix T, Charron-Bourgoin F, Libante V, Loux V, Chiapello H, Payot S, Leblond-Bourget N. Abundance, Diversity and Role of ICEs and IMEs in the Adaptation of to the Environment. Genes. 11. PMID 32858915 DOI: 10.3390/genes11090999   
2020 Jin L, Chen Y, Yang W, Qiao Z, Zhang X. Complete genome sequence of fish-pathogenic Aeromonas hydrophila HX-3 and a comparative analysis: insights into virulence factors and quorum sensing. Scientific Reports. 10: 15479. PMID 32968153 DOI: 10.1038/s41598-020-72484-8   
2020 Tello-Ruiz MK, Naithani S, Gupta P, Olson A, Wei S, Preece J, Jiao Y, Wang B, Chougule K, Garg P, Elser J, Kumari S, Kumar V, Contreras-Moreira B, Naamati G, et al. Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. Nucleic Acids Research. PMID 33170273 DOI: 10.1093/nar/gkaa979   
2020 Beam JP, Becraft ED, Brown JM, Schulz F, Jarett JK, Bezuidt O, Poulton NJ, Clark K, Dunfield PF, Ravin NV, Spear JR, Hedlund BP, Kormas KA, Sievert SM, Elshahed MS, et al. Ancestral Absence of Electron Transport Chains in Patescibacteria and DPANN. Frontiers in Microbiology. 11: 1848. PMID 33013724 DOI: 10.3389/fmicb.2020.01848   
2020 Li J, Fan Z, Shen F, Pendleton AL, Song Y, Xing J, Yue B, Kidd JM, Li J. Genomic copy number variation study of nine Macaca species provides new insights into their genetic divergence, adaptation and biomedical application. Genome Biology and Evolution. PMID 32970804 DOI: 10.1093/gbe/evaa200   
2020 Yang X, Zhu ZH, Ji X, Liu ZM, Zhang H, Wei B. Complete genome sequence of Micromonospora craniellae LHW63014, a potential metal ion-chelating agent producer. Marine Genomics. 100830. PMID 33160875 DOI: 10.1016/j.margen.2020.100830   
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 van Rhijn N, Furukawa T, Zhao C, McCann BL, Bignell E, Bromley MJ. Development of a marker-free mutagenesis system using CRISPR-Cas9 in the pathogenic mould Aspergillus fumigatus. Fungal Genetics and Biology : Fg & B. 103479. PMID 33122116 DOI: 10.1016/j.fgb.2020.103479   
2020 Nakai R, Naganuma T, Tazato N, Morohoshi S, Koide T. Cell Plasticity and Genomic Structure of a Novel Filterable Bacterium that Belongs to a Widely Distributed Lineage. Microorganisms. 8. PMID 32906802 DOI: 10.3390/microorganisms8091373   
2020 Ireland WT, Beeler SM, Flores-Bautista E, McCarty NS, Röschinger T, Belliveau NM, Sweredoski MJ, Moradian A, Kinney JB, Phillips R. Deciphering the regulatory genome of , one hundred promoters at a time. Elife. 9. PMID 32955440 DOI: 10.7554/eLife.55308   
2020 Lesk AM, Konagurthu AS. Neighbourhoods in the Yeast Regulatory Network in Different Physiological States. Bioinformatics (Oxford, England). PMID 32976569 DOI: 10.1093/bioinformatics/btaa831   
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