Ruchi Chaudhary, Ph.D. - Publications

2013 Computer Science Iowa State University, Ames, IA, United States 
Computer Science

19 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
2020 Merino DM, McShane LM, Fabrizio D, Funari V, Chen SJ, White JR, Wenz P, Baden J, Barrett JC, Chaudhary R, Chen L, Chen WS, Cheng JH, Cyanam D, Dickey JS, et al. Establishing guidelines to harmonize tumor mutational burden (TMB): in silico assessment of variation in TMB quantification across diagnostic platforms: phase I of the Friends of Cancer Research TMB Harmonization Project. Journal For Immunotherapy of Cancer. 8. PMID 32217756 DOI: 10.1136/Jitc-2019-000147  0.366
2019 Chaudhary R, Scafe C, Cyanam D, Mittal V, Tom W, Au-Young J, Sadis S, Hyland F. Abstract 5132: Assessing tumor mutational burden and profiling variants from FFPE samples using a PCR-based next-generation sequencing assay Cancer Research. 79: 5132-5132. DOI: 10.1158/1538-7445.Am2019-5132  0.367
2019 Tom W, Chaudhary R, Mittal V, Cyanam D, Casuga I, Wong-Ho E, Bennett R, Hyland F, Sadis S, Au-Young J. Abstract 1701: Improvement of tumor mutation burden measurement by removal of deaminated bases in FFPE DNA Cancer Research. 79: 1701-1701. DOI: 10.1158/1538-7445.Am2019-1701  0.35
2018 Chaudhary R, Cyanam D, Mittal V, Tom W, Au-Young J, Allen C, Sadis S, Hyland F. Tumor mutation burden assessment on FFPE samples using a targeted next-generation sequencing assay. Annals of Oncology : Official Journal of the European Society For Medical Oncology. 29: viii54-viii55. PMID 32137403 DOI: 10.1093/Annonc/Mdy269.171  0.301
2018 Chaudhary R, Quagliata L, Martin JP, Alborelli I, Cyanam D, Mittal V, Tom W, Au-Young J, Sadis S, Hyland F. A scalable solution for tumor mutational burden from formalin-fixed, paraffin-embedded samples using the Oncomine Tumor Mutation Load Assay. Translational Lung Cancer Research. 7: 616-630. PMID 30505706 DOI: 10.21037/Tlcr.2018.08.01  0.314
2018 Chaudhary R, Cyanam D, Mittal VK, Tom W, Au-Young J, Sadis S, Hyland F. Estimating mutation load at 5% LOD from FFPE samples using a targeted next-generation sequencing assay. Journal of Clinical Oncology. 36: 28-28. DOI: 10.1200/Jco.2018.36.5_Suppl.28  0.329
2018 Chaudhary R, Cyanam D, Mittal V, Tom W, Au-Young J, Sadis S, Hyland F. Abstract 580: A method for estimating mutation load from tumor research samples using a targeted next-generation sequencing panel Cancer Research. 78: 580-580. DOI: 10.1158/1538-7445.Am2018-580  0.351
2018 Costa J, Reis J, Fernandes M, Silva R, Cirnes L, Chaudhary R, Carneiro F, Machado JC. Abstract 1712: Assessing tumor mutation load using an NGS-based, routine-friendly target gene panel Cancer Research. 78: 1712-1712. DOI: 10.1158/1538-7445.Am2018-1712  0.341
2017 Cyanam D, Broomer A, Mandelman D, Chaudhary R, Williams PD, Nistala G, Gottimukkala R, Rhodes K, Bishop J, Hyland F, Sadis S. Somatic mutation burden in cancer samples determined by targeted next generation sequencing. Journal of Clinical Oncology. 35: 15-15. DOI: 10.1200/Jco.2017.35.7_Suppl.15  0.372
2017 Chien R, Brinza D, Gu J, Dhingra D, Banjara K, Li Y, Bagai V, Schageman J, Ballesteros-Villagrana E, Chaudhary R, Hanif K, Au-Young J, Hyland F, Bramlett K. Comprehensive detection of ctDNA variants at 0.1% allelic frequency using a broad targeted NGS panel for liquid biopsy research. Journal of Clinical Oncology. 35: e23065-e23065. DOI: 10.1200/Jco.2017.35.15_Suppl.E23065  0.323
2017 Chaudhary R, Bishop J, Broomer A, Cyanam D, Mandelman D, Nistala G, Hyland F, Sadis S. Estimating tumor mutation burden using next-generation sequencing assay. Journal of Clinical Oncology. 35: e14529-e14529. DOI: 10.1200/Jco.2017.35.15_Suppl.E14529  0.356
2017 Dhingra D, Chien R, Gu J, Brinza D, Chaudhary R, Banjara K, Li Y, Ballesteros-Villagrana E, Bramlett K. Abstract 5396: An NGS workflow to detect down to 0.1% allelic frequency in cfDNA for breast and colon cancers Cancer Research. 77: 5396-5396. DOI: 10.1158/1538-7445.Am2017-5396  0.311
2015 Hinchliff CE, Smith SA, Allman JF, Burleigh JG, Chaudhary R, Coghill LM, Crandall KA, Deng J, Drew BT, Gazis R, Gude K, Hibbett DS, Katz LA, Laughinghouse HD, McTavish EJ, et al. Synthesis of phylogeny and taxonomy into a comprehensive tree of life. Proceedings of the National Academy of Sciences of the United States of America. PMID 26385966 DOI: 10.1073/Pnas.1423041112  0.416
2015 Chaudhary R, Boussau B, Burleigh JG, Fernández-Baca D. Assessing approaches for inferring species trees from multi-copy genes. Systematic Biology. 64: 325-39. PMID 25540456 DOI: 10.1093/Sysbio/Syu128  0.65
2015 Chaudhary R, Fernández-Baca D, Burleigh JG. MulRF: a software package for phylogenetic analysis using multi-copy gene trees. Bioinformatics (Oxford, England). 31: 432-3. PMID 25273112 DOI: 10.1093/Bioinformatics/Btu648  0.657
2013 Chaudhary R, Burleigh JG, Fernández-Baca D. Inferring species trees from incongruent multi-copy gene trees using the Robinson-Foulds distance. Algorithms For Molecular Biology : Amb. 8: 28. PMID 24180377 DOI: 10.1186/1748-7188-8-28  0.658
2012 Chaudhary R, Burleigh JG, Eulenstein O. Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence. Bmc Bioinformatics. 13: S11. PMID 22759416 DOI: 10.1186/1471-2105-13-S10-S11  0.545
2012 Chaudhary R, Burleigh JG, Fernández-Baca D. Fast local search for unrooted Robinson-Foulds supertrees. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 9: 1004-13. PMID 22431553 DOI: 10.1109/Tcbb.2012.47  0.597
2010 Chaudhary R, Bansal MS, Wehe A, Fernández-Baca D, Eulenstein O. iGTP: a software package for large-scale gene tree parsimony analysis. Bmc Bioinformatics. 11: 574. PMID 21092314 DOI: 10.1186/1471-2105-11-574  0.653
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