Ariel S. Schwartz, Ph.D. - Related publications

2007 University of California, Berkeley, Berkeley, CA 
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Zou Y, Zhu Y, Li Y, Wu FX, Wang J. Parallel computing for genome sequence processing. Briefings in Bioinformatics. PMID 33822883 DOI: 10.1093/bib/bbab070   
2021 Benjamino J, Leopold B, Phillips D, Adams MD. Genome-Based Targeted Sequencing as a Reproducible Microbial Community Profiling Assay. Msphere. 6. PMID 33827913 DOI: 10.1128/mSphere.01325-20   
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 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 De Maio N, Weilguny L, Walker CR, Turakhia Y, Corbett-Detig R, Goldman N. phastSim: efficient simulation of sequence evolution for pandemic-scale datasets. Biorxiv : the Preprint Server For Biology. PMID 33758852 DOI: 10.1101/2021.03.15.435416   
2021 Tian L, Mazloom R, Heath LS, Vinatzer BA. LINflow: a computational pipeline that combines an alignment-free with an alignment-based method to accelerate generation of similarity matrices for prokaryotic genomes. Peerj. 9: e10906. PMID 33828908 DOI: 10.7717/peerj.10906   
2021 Wittmann BJ, Johnston KE, Wu Z, Arnold FH. Advances in machine learning for directed evolution. Current Opinion in Structural Biology. 69: 11-18. PMID 33647531 DOI: 10.1016/   
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 Liu P, Ewald J, Galvez JH, Head J, Crump D, Bourque G, Basu N, Xia J. Ultrafast functional profiling of RNA-seq data for nonmodel organisms. Genome Research. PMID 33731361 DOI: 10.1101/gr.269894.120   
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 Kayani MUR, Huang W, Feng R, Chen L. Genome-resolved metagenomics using environmental and clinical samples. Briefings in Bioinformatics. PMID 33758906 DOI: 10.1093/bib/bbab030   
2021 Neal-McKinney JM, Liu KC, Lock CM, Wu WH, Hu J. Comparison of MiSeq, MinION, and hybrid genome sequencing for analysis of Campylobacter jejuni. Scientific Reports. 11: 5676. PMID 33707610 DOI: 10.1038/s41598-021-84956-6   
2021 Caurcel C, Laetsch DR, Challis R, Kumar S, Gharbi K, Blaxter M. MolluscDB: a genome and transcriptome database for molluscs. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 376: 20200157. PMID 33813885 DOI: 10.1098/rstb.2020.0157   
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 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 Huang S, He X, Wang G, Bao E. AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads. Briefings in Bioinformatics. PMID 33621981 DOI: 10.1093/bib/bbab022   
2021 Zhang Z, Liu G, Chen Y, Xue W, Ji Q, Xu Q, Zhang H, Fan G, Huang H, Jiang L, Chen J. Comparison of different sequencing strategies for assembling chromosome-level genomes of extremophiles with variable GC content. Iscience. 24: 102219. PMID 33748707 DOI: 10.1016/j.isci.2021.102219   
2021 Zhao X, Collins RL, Lee WP, Weber AM, Jun Y, Zhu Q, Weisburd B, Huang Y, Audano PA, Wang H, Walker M, Lowther C, Fu J, , Gerstein MB, et al. Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies. American Journal of Human Genetics. PMID 33789087 DOI: 10.1016/j.ajhg.2021.03.014   
2021 Arumugam K, Bessarab I, Haryono MAS, Liu X, Zuniga-Montanez RE, Roy S, Qiu G, Drautz-Moses DI, Law YY, Wuertz S, Lauro FM, Huson DH, Williams RBH. Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing. Npj Biofilms and Microbiomes. 7: 23. PMID 33727564 DOI: 10.1038/s41522-021-00196-6   
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 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 Yu Y, Wang K, Fahira A, Yang Q, Sun R, Li Z, Wang Z, Shi Y. Systematic comparative study of computational methods for HLA typing from next-generation sequencing. Hla. PMID 33655664 DOI: 10.1111/tan.14244   
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 Sahlin K, Lim MCW, Prost S. NGSpeciesID: DNA barcode and amplicon consensus generation from long-read sequencing data. Ecology and Evolution. 11: 1392-1398. PMID 33598139 DOI: 10.1002/ece3.7146   
2021 Jinyu L, Shan Y, Yujun C, Tao W, Yue T. Research progress of bacterial minimal genome. Yi Chuan = Hereditas. 43: 142-159. PMID 33724217 DOI: 10.16288/j.yczz.20-301   
2021 Therrien DA, Konganti K, Gill JJ, Davis BW, Hillhouse AE, Michalik J, Cross HR, Smith GC, Taylor TM, Riggs PK. Complete Whole Genome Sequences of Surrogate Strains and Comparison of Sequence Methods with Application to the Food Industry. Microorganisms. 9. PMID 33809423 DOI: 10.3390/microorganisms9030608   
2021 Ciuffreda L, Rodríguez-Pérez H, Flores C. Nanopore sequencing and its application to the study of microbial communities. Computational and Structural Biotechnology Journal. 19: 1497-1511. PMID 33815688 DOI: 10.1016/j.csbj.2021.02.020   
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 Mascher M, Wicker T, Jenkins J, Plott C, Lux T, Koh CS, Ens J, Gundlach H, Boston LB, Tulpová Z, Holden S, Hernández-Pinzón I, Scholz U, Mayer KFX, Spannagl M, et al. Long-read sequence assembly: a technical evaluation in barley. The Plant Cell. PMID 33710295 DOI: 10.1093/plcell/koab077   
2021 Duarte GT, Volkova PY, Geras'kin SA. A Pipeline for Non-model Organisms for Transcriptome Assembly, Annotation, and Gene Ontology Analysis Using Open Tools: Case Study with Scots Pine. Bio-Protocol. 11: e3912. PMID 33732799 DOI: 10.21769/BioProtoc.3912   
2021 Mishra A, Siwach P, Misra P, Dhiman S, Pandey AK, Srivastava P, Jayaram B. Intron exon boundary junctions in human genome have in-built unique structural and energetic signals. Nucleic Acids Research. PMID 33621338 DOI: 10.1093/nar/gkab098   
2021 Kinkar L, Gasser RB, Webster BL, Rollinson D, Littlewood DTJ, Chang BCH, Stroehlein AJ, Korhonen PK, Young ND. Nanopore Sequencing Resolves Elusive Long Tandem-Repeat Regions in Mitochondrial Genomes. International Journal of Molecular Sciences. 22. PMID 33670420 DOI: 10.3390/ijms22041811   
2021 Chakraborty A, Morgenstern B, Bandyopadhyay S. S-conLSH: alignment-free gapped mapping of noisy long reads. Bmc Bioinformatics. 22: 64. PMID 33573603 DOI: 10.1186/s12859-020-03918-3   
2021 Qi H, Li L, Zhang G. Construction of a chromosome-level genome and variation map for the Pacific oyster Crassostrea gigas. Molecular Ecology Resources. PMID 33655634 DOI: 10.1111/1755-0998.13368   
2021 Liu L, Chen R, Fugina CJ, Siegel B, Jackson D. High-Throughput and Low-Cost Genotyping Method for Plant Genome Editing. Current Protocols. 1: e100. PMID 33826801 DOI: 10.1002/cpz1.100   
2021 Nunn A, Otto C, Stadler PF, Langenberger D. Comprehensive benchmarking of software for mapping whole genome bisulfite data: from read alignment to DNA methylation analysis. Briefings in Bioinformatics. PMID 33624017 DOI: 10.1093/bib/bbab021   
2021 Veluchamy A, Mehta P, Srividhya KV, Vikram H, Govind MK, Gupta R, Aziz Bin Dukhyil A, Abdullah Alharbi R, Abdullah Aloyuni S, Hassan MM, Krishnaswamy S. Information theoretic perspective on genome clustering. Saudi Journal of Biological Sciences. 28: 1867-1889. PMID 33732074 DOI: 10.1016/j.sjbs.2020.12.039   
2021 Wallace AD, Sasani TA, Swanier J, Gates BL, Greenland J, Pedersen BS, Varley KE, Quinlan AR. CaBagE: A Cas9-based Background Elimination strategy for targeted, long-read DNA sequencing. Plos One. 16: e0241253. PMID 33830997 DOI: 10.1371/journal.pone.0241253   
2021 Riaz N, Leung P, Barton K, Smith MA, Carswell S, Bull R, Lloyd AR, Rodrigo C. Adaptation of Oxford Nanopore technology for hepatitis C whole genome sequencing and identification of within-host viral variants. Bmc Genomics. 22: 148. PMID 33653280 DOI: 10.1186/s12864-021-07460-1   
2021 Parker MT, Knop K, Barton GJ, Simpson GG. 2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing. Genome Biology. 22: 72. PMID 33648554 DOI: 10.1186/s13059-021-02296-0   
2021 Vasiljevic N, Lim M, Humble E, Seah A, Kratzer A, Morf NV, Prost S, Ogden R. Developmental validation of Oxford Nanopore Technology MinION sequence data and the NGSpeciesID bioinformatic pipeline for forensic genetic species identification. Forensic Science International. Genetics. 53: 102493. PMID 33770699 DOI: 10.1016/j.fsigen.2021.102493   
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 Zhang Y, Zhang R, Deng C, Yang J, Deng G. The complete chloroplast genome sequence of (Moraceae). Mitochondrial Dna. Part B, Resources. 6: 299-301. PMID 33659654 DOI: 10.1080/23802359.2020.1863874   
2021 O'Loughlin SM, Forster AJ, Fuchs S, Dottorini T, Nolan T, Crisanti A, Burt A. Ultra-conserved sequences in the genomes of highly diverse Anopheles mosquitoes, with implications for malaria vector control. G3 (Bethesda, Md.). PMID 33730159 DOI: 10.1093/g3journal/jkab086   
2021 Farrow JM, Pesci EC, Slade DJ. Genome Sequences for Two Acinetobacter baumannii Strains Obtained Using the Unicycler Hybrid Assembly Pipeline. Microbiology Resource Announcements. 10. PMID 33707317 DOI: 10.1128/MRA.00017-21   
2021 Gangiredla J, Rand H, Benisatto D, Payne J, Strittmatter C, Sanders J, Wolfgang WJ, Libuit K, Herrick JB, Prarat M, Toro M, Farrell T, Strain E. GalaxyTrakr: a distributed analysis tool for public health whole genome sequence data accessible to non-bioinformaticians. Bmc Genomics. 22: 114. PMID 33568057 DOI: 10.1186/s12864-021-07405-8   
2021 Oh E. Monitoring Bacterial Translation Rates Genome-Wide. Methods in Molecular Biology (Clifton, N.J.). 2252: 3-26. PMID 33765269 DOI: 10.1007/978-1-0716-1150-0_1   
2021 Soyturk A, Sen F, Uncu AT, Celik I, Uncu AO. De novo assembly and characterization of the first draft genome of quince (Cydonia oblonga Mill.). Scientific Reports. 11: 3818. PMID 33589687 DOI: 10.1038/s41598-021-83113-3   
2021 Mun S, Kim S, Lee W, Kang K, Meyer TJ, Han BG, Han K, Kim HS. A study of transposable element-associated structural variations (TASVs) using a de novo-assembled Korean genome. Experimental & Molecular Medicine. PMID 33833373 DOI: 10.1038/s12276-021-00586-y