Ohad Shamir, Ph.D - Related publications

Microsoft Research, Redmond, WA, United States 
Machine Learning
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50 most relevant papers in past 60 days:
Year Citation  Score
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 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 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 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 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 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 Lagerborg KA, Normandin E, Bauer MR, Adams G, Figueroa K, Loreth C, Gladden-Young A, Shaw B, Pearlman L, Shenoy ES, Hooper D, Pierce VM, Zachary KC, Park DJ, MacInnis BL, et al. DNA spike-ins enable confident interpretation of SARS-CoV-2 genomic data from amplicon-based sequencing. Biorxiv : the Preprint Server For Biology. PMID 33758855 DOI: 10.1101/2021.03.16.435654   
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 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 Lee K, Kim DW, Cha CJ. Overview of bioinformatic methods for analysis of antibiotic resistome from genome and metagenome data. Journal of Microbiology (Seoul, Korea). 59: 270-280. PMID 33624264 DOI: 10.1007/s12275-021-0652-4   
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 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 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 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 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 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 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 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 Tourancheau A, Mead EA, Zhang XS, Fang G. Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing. Nature Methods. PMID 33820988 DOI: 10.1038/s41592-021-01109-3   
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 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 Markov SA, Church JC, Lee L, Bell CM, Binkley SD, Bouma KM, Hutson KM, Markov GS, Mason EC, Rueff GB, Sennuga TO, Simpson MH, Zimmer RJ, Villalpando DG. Complete Genome Sequences of Bacteriophages Danno, Otwor, and Scumberland, Isolated in Clarksville, Tennessee. Microbiology Resource Announcements. 10. PMID 33795346 DOI: 10.1128/MRA.00209-21   
2021 Papić B, Diricks M, Kušar D. Analysis of the Global Population Structure of and Outbreak Investigation of American Foulbrood Using a Stable wgMLST Scheme. Frontiers in Veterinary Science. 8: 582677. PMID 33718463 DOI: 10.3389/fvets.2021.582677   
2021 Kerkhof LJ. Is Oxford Nanopore sequencing ready for analyzing complex microbiomes? Fems Microbiology Ecology. 97. PMID 33444433 DOI: 10.1093/femsec/fiab001   
2021 Zhang G, Wang H, Yin X, Kong W, Wang Q, Chen Y, Wei J, Liu J, Guo X. Characterization of the complete chloroplast genome of N. P. Balakr. (Apiaceae) and its phylogenetic implications. Mitochondrial Dna. Part B, Resources. 6: 447-449. PMID 33628883 DOI: 10.1080/23802359.2020.1870902   
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 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 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 Ingle DJ, Howden BP, Duchene S. Development of Phylodynamic Methods for Bacterial Pathogens. Trends in Microbiology. PMID 33736902 DOI: 10.1016/j.tim.2021.02.008   
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 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   
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 Li T, Chung HK, Pireku PK, Beitzel BF, Sanborn MA, Tang CY, Hammer R, Ritter D, Wan X, Maljkovic Berry I, Hang J. Rapid High Throughput Whole Genome Sequencing of SARS-CoV-2 by using One-step RT-PCR Amplification with Integrated Microfluidic System and Next-Gen Sequencing. Journal of Clinical Microbiology. PMID 33653700 DOI: 10.1128/JCM.02784-20   
2021 Karki S, Moniruzzaman M, Aylward FO. Comparative Genomics and Environmental Distribution of Large dsDNA Viruses in the Family . Frontiers in Microbiology. 12: 657471. PMID 33790885 DOI: 10.3389/fmicb.2021.657471   
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 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 Ramazzotti D, Angaroni F, Maspero D, Gambacorti-Passerini C, Antoniotti M, Graudenzi A, Piazza R. VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples. Patterns (New York, N.Y.). 2: 100212. PMID 33728416 DOI: 10.1016/j.patter.2021.100212   
2021 Yi H, Lin Y, Lin C, Jin W. Kssd: sequence dimensionality reduction by k-mer substring space sampling enables real-time large-scale datasets analysis. Genome Biology. 22: 84. PMID 33726811 DOI: 10.1186/s13059-021-02303-4   
2021 Alzahrani FM, Al-Amri A, Shaikh SS, Muzaheed, Alomar AI, Acharya S, Aldossary MA, Hassan FM. Direct DNA Sequencing-Based Analysis of Microbiota Associated with Hematological Malignancies in the Eastern Province of Saudi Arabia. Biomed Research International. 2021: 4202019. PMID 33623780 DOI: 10.1155/2021/4202019   
2021 Li N, Bai JQ, Gao S, Yang L, Li J, Du SB, Wang XP. The complete molecular sequence of chloroplast genome of (L.) Sweet. Mitochondrial Dna. Part B, Resources. 6: 758-759. PMID 33763570 DOI: 10.1080/23802359.2021.1878958   
2021 Wu X, Li H, Chen S. Characterization of the chloroplast genome and its inference on the phylogenetic position of Lam. (Bignoniaceae). Mitochondrial Dna. Part B, Resources. 6: 263-264. PMID 33659649 DOI: 10.1080/23802359.2020.1860722   
2021 Fridman H, Bormans C, Einhorn M, Au D, Bormans A, Porat Y, Sanchez LF, Manning B, Levy-Lahad E, Behar DM. Performance comparison: exome sequencing as a single test replacing Sanger sequencing. Molecular Genetics and Genomics : Mgg. PMID 33694043 DOI: 10.1007/s00438-021-01772-3   
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 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 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 Lim SY, Jang JH, Lee HJ, Park SS, Kim SR, Lee KM, Kim JK, Park H, Jung HK. Characteristics and phylogenetic analysis of the complete chloroplast genome of (Paeoniaceae). Mitochondrial Dna. Part B, Resources. 6: 734-735. PMID 33763563 DOI: 10.1080/23802359.2020.1860718   
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 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/j.sbi.2021.01.008   
2021 Ling Q, Cheng L, Li Z, Zhao Y, Wang Y. Characterization of the complete chloroplast genome of a Chinese Endangered species . Mitochondrial Dna. Part B, Resources. 6: 708-709. PMID 33796643 DOI: 10.1080/23802359.2020.1851152