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Sayaka Miura - Publications

Affiliations: 
2012 Pennsylvania State University, State College, PA, United States 
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29 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Craig JM, Gerhard GS, Sharma S, Yankovskiy A, Miura S, Kumar S. Methods for Estimating Personal Disease Risk and Phylogenetic Diversity of Hematopoietic Stem Cells. Molecular Biology and Evolution. PMID 38124397 DOI: 10.1093/molbev/msad279  0.357
2023 Miura S, Dolker T, Sanderford M, Kumar S. Improving cellular phylogenies through the integrated use of mutation order and optimality principles. Computational and Structural Biotechnology Journal. 21: 3894-3903. PMID 37602230 DOI: 10.1016/j.csbj.2023.07.018  0.507
2023 Huzar J, Shenoy M, Sanderford MD, Kumar S, Miura S. Bootstrap confidence for molecular evolutionary estimates from tumor bulk sequencing data. Frontiers in Bioinformatics. 3: 1090730. PMID 37261293 DOI: 10.3389/fbinf.2023.1090730  0.517
2022 Chroni A, Miura S, Hamilton L, Vu T, Gaffney SG, Aly V, Karim S, Sanderford M, Townsend JP, Kumar S. Clone Phylogenetics Reveals Metastatic Tumor Migrations, Maps, and Models. Cancers. 14. PMID 36077861 DOI: 10.3390/cancers14174326  0.445
2022 Amendola A, Canuti M, Bianchi S, Kumar S, Fappani C, Gori M, Colzani D, Kosakovsky Pond SL, Miura S, Baggieri M, Marchi A, Borghi E, Zuccotti G, Raviglione MC, Magurano F, et al. Molecular evidence for SARS-CoV-2 in samples collected from patients with morbilliform eruptions since late 2019 in Lombardy, northern Italy. Environmental Research. 113979. PMID 36029839 DOI: 10.1016/j.envres.2022.113979  0.394
2022 Miura S, Vu T, Choi J, Townsend JP, Karim S, Kumar S. A phylogenetic approach to study the evolution of somatic mutational processes in cancer. Communications Biology. 5: 617. PMID 35732905 DOI: 10.1038/s42003-022-03560-0  0.462
2022 Caraballo-Ortiz MA, Miura S, Sanderford M, Dolker T, Tao Q, Weaver S, Pond SLK, Kumar S. TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity. Bioinformatics (Oxford, England). 38: 2719-2726. PMID 35561179 DOI: 10.1093/bioinformatics/btac186  0.478
2022 Huzar J, Kim H, Kumar S, Miura S. MOCA for Integrated Analysis of Gene Expression and Genetic Variation in Single Cells. Frontiers in Genetics. 13: 831040. PMID 35432484 DOI: 10.3389/fgene.2022.831040  0.43
2022 Caraballo-Ortiz MA, Miura S, Sanderford M, Dolker T, Tao Q, Weaver S, Pond SLK, Kumar S. TopHap: Rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity. Bioinformatics (Oxford, England). PMID 35325058 DOI: 10.1093/bioinformatics/btac186  0.479
2021 Caraballo-Ortiz MA, Miura S, Sanderford M, Dolker T, Tao Q, Weaver S, Pond SLK, Kumar S. TopHap: Rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity. Biorxiv : the Preprint Server For Biology. PMID 34931186 DOI: 10.1101/2021.12.13.472454  0.479
2021 Townsend JP, Hassler HB, Wang Z, Miura S, Singh J, Kumar S, Ruddle NH, Galvani AP, Dornburg A. The durability of immunity against reinfection by SARS-CoV-2: a comparative evolutionary study. The Lancet. Microbe. PMID 34632431 DOI: 10.1016/S2666-5247(21)00219-6  0.336
2021 Chroni A, Miura S, Oladeinde O, Aly V, Kumar S. Migrations of cancer cells through the lens of phylogenetic biogeography. Scientific Reports. 11: 17184. PMID 34433859 DOI: 10.1038/s41598-021-96215-9  0.456
2021 Kumar S, Tao Q, Weaver S, Sanderford M, Caraballo-Ortiz MA, Sharma S, Pond SLK, Miura S. An evolutionary portrait of the progenitor SARS-CoV-2 and its dominant offshoots in COVID-19 pandemic. Molecular Biology and Evolution. PMID 33942847 DOI: 10.1093/molbev/msab118  0.478
2020 Kumar S, Chroni A, Tamura K, Sanderford M, Oladeinde O, Aly V, Vu T, Miura S. PathFinder: Bayesian inference of clone migration histories in cancer. Bioinformatics (Oxford, England). 36: i675-i683. PMID 33381835 DOI: 10.1093/bioinformatics/btaa795  0.463
2020 Kumar S, Tao Q, Weaver S, Sanderford M, Caraballo-Ortiz MA, Sharma S, Pond SLK, Miura S. An evolutionary portrait of the progenitor SARS-CoV-2 and its dominant offshoots in COVID-19 pandemic. Biorxiv : the Preprint Server For Biology. PMID 32995781 DOI: 10.1101/2020.09.24.311845  0.471
2020 Miura S, Vu T, Deng J, Buturla T, Oladeinde O, Choi J, Kumar S. Power and pitfalls of computational methods for inferring clone phylogenies and mutation orders from bulk sequencing data. Scientific Reports. 10: 3498. PMID 32103044 DOI: 10.1038/S41598-020-59006-2  0.554
2020 Miura S, Tamura K, Tao Q, Huuki LA, Kosakovsky Pond SL, Priest J, Deng J, Kumar S. A new method for inferring timetrees from temporally sampled molecular sequences. Plos Computational Biology. 16: e1007046. PMID 31951607 DOI: 10.1371/Journal.Pcbi.1007046  0.495
2019 Chroni A, Vu T, Miura S, Kumar S. Delineation of Tumor Migration Paths by Using a Bayesian Biogeographic Approach. Cancers. 11. PMID 31783570 DOI: 10.3390/Cancers11121880  0.504
2018 Miura S, Huuki LA, Buturla T, Vu T, Gomez K, Kumar S. Computational enhancement of single-cell sequences for inferring tumor evolution. Bioinformatics (Oxford, England). 34: i917-i926. PMID 30423071 DOI: 10.1093/Bioinformatics/Bty571  0.538
2018 Miura S, Gomez K, Murillo O, Huuki LA, Vu T, Buturla T, Kumar S. Predicting clone genotypes from tumor bulk sequencing of multiple samples. Bioinformatics (Oxford, England). PMID 29931046 DOI: 10.1093/Bioinformatics/Bty469  0.546
2018 Gomez K, Miura S, Huuki LA, Spell BS, Townsend JP, Kumar S. Somatic evolutionary timings of driver mutations. Bmc Cancer. 18: 85. PMID 29347918 DOI: 10.1186/S12885-017-3977-Y  0.531
2017 Miura S, Gomez K, Murillo O, Kumar S. Abstract 3591: A new method to infer clonal sequences and phylogenies from personal tumor genome profiles Cancer Research. 77: 3591-3591. DOI: 10.1158/1538-7445.Am2017-3591  0.399
2017 Gomez K, Miura S, Kumar S. Abstract 1573: Detection of late-arising driver mutations using multi-sample tumor sequencing data Cancer Research. 77: 1573-1573. DOI: 10.1158/1538-7445.Am2017-1573  0.403
2016 Shay JW, Homma N, Zhou R, Naseer MI, Chaudhary AG, Al-Qahtani M, Hirokawa N, Goudarzi M, Fornace AJ, Baeesa S, Hussain D, Bangash M, Alghamdi F, Schulten H, Carracedo A, ... ... Miura S, et al. Abstracts from the 3rd International Genomic Medicine Conference (3rd IGMC 2015) Bmc Genomics. 17: 487-487. PMID 27454254 DOI: 10.1186/S12864-016-2858-0  0.378
2015 Miura S, Tate S, Kumar S. Using Disease-Associated Coding Sequence Variation to Investigate Functional Compensation by Human Paralogous Proteins. Evolutionary Bioinformatics Online. 11: 245-251. PMID 26604664 DOI: 10.4137/Ebo.S30594  0.474
2013 Miura S, Zhang Z, Nei M. Random fluctuation of selection coefficients and the extent of nucleotide variation in human populations. Proceedings of the National Academy of Sciences of the United States of America. 110: 10676-81. PMID 23754436 DOI: 10.1073/Pnas.1308462110  0.523
2012 Nozawa M, Miura S, Nei M. Origins and evolution of microRNA genes in plant species. Genome Biology and Evolution. 4: 230-9. PMID 22223755 DOI: 10.1093/Gbe/Evs002  0.471
2011 Miura S, Nozawa M, Nei M. Evolutionary changes of the target sites of two microRNAs encoded in the Hox gene cluster of Drosophila and other insect species. Genome Biology and Evolution. 3: 129-39. PMID 21187351 DOI: 10.1093/Gbe/Evq088  0.493
2010 Nozawa M, Miura S, Nei M. Origins and evolution of microRNA genes in Drosophila species. Genome Biology and Evolution. 2: 180-9. PMID 20624724 DOI: 10.1093/Gbe/Evq009  0.484
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