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Samuel Angiuoli - Publications

Affiliations: 
2011 Computer Sciene University of Maryland, College Park, College Park, MD 
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52 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
2022 Keefer LA, White JR, Wood DE, Gerding KMR, Valkenburg KC, Riley D, Gault C, Papp E, Vollmer CM, Greer A, Hernandez J, McGregor PM, Zingone A, Ryan BM, Deak K, ... ... Angiuoli SV, et al. Automated next-generation profiling of genomic alterations in human cancers. Nature Communications. 13: 2830. PMID 35595835 DOI: 10.1038/s41467-022-30380-x  0.751
2021 Lee Deak K, Jackson JB, Valkenburg KC, Keefer LA, Robinson Gerding KM, Angiuoli SV, Datto MB, McCall SJ. Next-Generation Sequencing Concordance Analysis of Comprehensive Solid Tumor Profiling between a Centralized Specialty Laboratory and the Decentralized PGDx Elio Tissue Complete Kitted solution. The Journal of Molecular Diagnostics : Jmd. PMID 34314880 DOI: 10.1016/j.jmoldx.2021.07.004  0.408
2019 Georgiadis A, Durham JN, Keefer LA, Bartlett BR, Zielonka M, Murphy D, White JR, Lu S, Verner EL, Ruan F, Riley D, Anders RA, Gedvilaite E, Angiuoli S, Jones S, et al. Noninvasive Detection of Microsatellite Instability and High Tumor Mutation Burden in Cancer Patients Treated with PD-1 Blockade. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 31506389 DOI: 10.1158/1078-0432.Ccr-19-1372  0.356
2019 Chowbina S, Cerqueira G, Sweeney D, Shewale S, Hernandez J, Papp E, Sausen M, Thompson J, Riley D, Angiuoli S. Abstract 1665: Development of standardized assay and software systems to deliver concordant results across sequencing platforms Cancer Research. 79: 1665-1665. DOI: 10.1158/1538-7445.Am2019-1665  0.443
2019 Gerding KMR, Valkenburg KC, Oliveras C, White JR, Ettehadieh L, Cerquiera G, Gault C, Hernandez J, Kong E, Angiuoli S, Simmons J, Loftin I, McElhinny A. Abstract B027: Analytical validation of a 500+ gene comprehensive NGS assay to detect genomic alterations across 35 tumor types Molecular Cancer Therapeutics. 18. DOI: 10.1158/1535-7163.Targ-19-B027  0.454
2018 Wood DE, White JR, Georgiadis A, Van Emburgh B, Parpart-Li S, Mitchell J, Anagnostou V, Niknafs N, Karchin R, Papp E, McCord C, LoVerso P, Riley D, Diaz LA, Jones S, ... ... Angiuoli SV, et al. A machine learning approach for somatic mutation discovery. Science Translational Medicine. 10. PMID 30185652 DOI: 10.1126/Scitranslmed.Aar7939  0.718
2018 Wood D, White J, Georgiadis A, Emburgh BV, Parpart-Li S, Mitchell J, Anagnostou V, Niknafs N, Karchin R, Papp E, McCord C, Loverso P, Riley D, Diaz LA, Jones S, ... ... Angiuoli S, et al. Abstract 3271: A machine learning approach for somatic mutation discovery Cancer Research. 78: 3271-3271. DOI: 10.1158/1538-7445.Am2018-3271  0.378
2018 Nesselbush M, Jones S, Keefer L, Sengamalay N, Velculescu V, Diaz L, Sausen M, Angiuoli S. Abstract A027: Analytic validation of a pan-cancer tumor mutational burden assay Molecular Cancer Therapeutics. 17. DOI: 10.1158/1535-7163.Targ-17-A027  0.373
2017 Phallen J, Sausen M, Adleff V, Leal A, Hruban C, White J, Anagnostou V, Fiksel J, Cristiano S, Papp E, Speir S, Reinert T, Orntoft MW, Woodward BD, Murphy D, ... ... Angiuoli S, et al. Direct detection of early-stage cancers using circulating tumor DNA. Science Translational Medicine. 9. PMID 28814544 DOI: 10.1126/Scitranslmed.Aan2415  0.411
2017 Agrawal S, Arze C, Adkins RS, Crabtree J, Riley D, Vangala M, Galens K, Fraser CM, Tettelin H, White O, Angiuoli SV, Mahurkar A, Fricke WF. CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline. Bmc Genomics. 18: 332. PMID 28449639 DOI: 10.1186/S12864-017-3717-3  0.436
2017 Novak M, Angiuoli S, Diaz LA, Georgiadis A, Jones S, Loverso PR, Parpart-Li S, Sevdali M, Velculescu VE, Verner EL, White J, Zhang T, Sausen M. Abstract 604: Accurate identification and prioritization of candidate neoantigens from integrated cancer exome and transcriptome sequencing of FFPE samples Cancer Research. 77: 604-604. DOI: 10.1158/1538-7445.Am2017-604  0.473
2016 White J, Simmons J, Angiuoli S, Sausen M, Jones S, Kann L, Shukla M, Sevdali M, Velculescu V, Diaz L, Zhang T. Abstract A039: Accurate identification and prioritization of candidate neoantigens from cancer exome sequencing Cancer Immunology Research. 4. DOI: 10.1158/2326-6066.Imm2016-A039  0.434
2016 White J, Angiuoli S, Sausen M, Jones S, Kann L, Shukla M, Sevdali M, Velculescu V, Diaz L, Zhang T. Abstract 528: Identify and prioritize candidate neoantigens from cancer exome sequencing with unmatched accuracy Cancer Research. 76: 528-528. DOI: 10.1158/1538-7445.Am2016-528  0.444
2016 Daigle SR, Angiuoli S, Jones S, Ribich S, Keilhack H, Sausen M, Ho PT, Blakemore SJ. Abstract 137: Development and application of a 62-gene panel for assessment of somatic sequence and structural variants in tumor DNA derived from non-Hodgkin lymphoma patients treated in a phase 1 clinical trial with the EZH2 inhibitor tazemetostat Cancer Research. 76: 137-137. DOI: 10.1158/1538-7445.Am2016-137  0.493
2015 Jones S, Anagnostou V, Lytle K, Parpart-Li S, Nesselbush M, Riley DR, Shukla M, Chesnick B, Kadan M, Papp E, Galens KG, Murphy D, Zhang T, Kann L, Sausen M, ... Angiuoli SV, et al. Personalized genomic analyses for cancer mutation discovery and interpretation. Science Translational Medicine. 7: 283ra53. PMID 25877891 DOI: 10.1200/Jco.2015.33.15_Suppl.1529  0.409
2015 Parpart-Li S, Angiuoli SV, Chesnick B, Galens K, Jones S, Kadan M, Kann L, Lytle K, Murphy DM, Nesselbush M, Phallen J, Riley D, Shukla M, Zhang T, Husain H, et al. A method for comprehensive genomic analysis of cell-free DNA. Journal of Clinical Oncology. 33: e22070-e22070. DOI: 10.1200/JCO.2015.33.15_SUPPL.E22070  0.303
2013 White JR, Maddox C, White O, Angiuoli SV, Fricke WF. CloVR-ITS: Automated internal transcribed spacer amplicon sequence analysis pipeline for the characterization of fungal microbiota. Microbiome. 1: 6. PMID 24451270 DOI: 10.1186/2049-2618-1-6  0.315
2013 Garralda E, Paz K, López-Casas PP, Jones S, Katz A, Kann LM, López-Ríos F, Sarno F, Al-Shahrour F, Vasquez D, Bruckheimer E, Angiuoli SV, Diaz LA, Valencia A, Velculescu VE, et al. Integrated genomics and avatar mouse models for personalized cancer treatment. Journal of Clinical Oncology. 31: 2511-2511. DOI: 10.1200/Jco.2013.31.15_Suppl.2511  0.356
2012 Riley DR, Angiuoli SV, Crabtree J, Dunning Hotopp JC, Tettelin H. Using Sybil for interactive comparative genomics of microbes on the web. Bioinformatics (Oxford, England). 28: 160-6. PMID 22121156 DOI: 10.1093/bioinformatics/btr652  0.342
2012 Garralda E, Calles A, López-Ríos F, Jones S, Kann LM, Angiuoli SV, Diaz LA, Velculescu VE, López-Casas PP, Sarno F, Martinez R, Gomez-Martin C, Conde E, Belda-Iniesta C, Valencia A, et al. Integrated next-generation sequencing and patient-derived xenografts to personalized cancer treatment. Journal of Clinical Oncology. 30: 3068-3068. DOI: 10.1200/Jco.2012.30.15_Suppl.3068  0.335
2011 Bogdanove AJ, Koebnik R, Lu H, Furutani A, Angiuoli SV, Patil PB, Van Sluys MA, Ryan RP, Meyer DF, Han SW, Aparna G, Rajaram M, Delcher AL, Phillippy AM, Puiu D, et al. Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp. Journal of Bacteriology. 193: 5450-64. PMID 21784931 DOI: 10.1128/Jb.05262-11  0.762
2011 Angiuoli SV, Dunning Hotopp JC, Salzberg SL, Tettelin H. Improving pan-genome annotation using whole genome multiple alignment. Bmc Bioinformatics. 12: 272. PMID 21718539 DOI: 10.1186/1471-2105-12-272  0.632
2011 Galens K, Orvis J, Daugherty S, Creasy HH, Angiuoli S, White O, Wortman J, Mahurkar A, Giglio MG. The IGS Standard Operating Procedure for Automated Prokaryotic Annotation. Standards in Genomic Sciences. 4: 244-51. PMID 21677861 DOI: 10.4056/Sigs.1223234  0.469
2011 Angiuoli SV, Salzberg SL. Mugsy: Fast multiple alignment of closely related whole genomes Bioinformatics. 27: 334-342. PMID 21148543 DOI: 10.1093/bioinformatics/btq665  0.655
2011 Sahl JW, Steinsland H, Redman JC, Angiuoli SV, Nataro JP, Sommerfelt H, Rasko DA. A comparative genomic analysis of diverse clonal types of enterotoxigenic Escherichia coli reveals pathovar-specific conservation. Infection and Immunity. 79: 950-60. PMID 21078854 DOI: 10.1128/Iai.00932-10  0.49
2011 Donati C, Hiller NL, Tettelin H, Muzzi A, Croucher NJ, Angiuoli SV, Oggioni M, Hotopp J, Hu FZ, Riley DR, Covacci A, Mitchell TJ, Bentley SD, Kilian M, Ehrlich GD, et al. Correction: Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species Genome Biology. 12: 140. DOI: 10.1186/Gb-2011-12-10-140  0.359
2010 Donati C, Hiller NL, Tettelin H, Muzzi A, Croucher NJ, Angiuoli SV, Oggioni M, Dunning Hotopp JC, Hu FZ, Riley DR, Covacci A, Mitchell TJ, Bentley SD, Kilian M, Ehrlich GD, et al. Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species. Genome Biology. 11: R107. PMID 21034474 DOI: 10.1186/Gb-2010-11-10-R107  0.323
2010 Schriml LM, Arze C, Nadendla S, Ganapathy A, Felix V, Mahurkar A, Phillippy K, Gussman A, Angiuoli S, Ghedin E, White O, Hall N. GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database. Nucleic Acids Research. 38: D754-64. PMID 19850722 DOI: 10.1093/nar/gkp832  0.37
2009 Tsolis RM, Seshadri R, Santos RL, Sangari FJ, Lobo JM, de Jong MF, Ren Q, Myers G, Brinkac LM, Nelson WC, Deboy RT, Angiuoli S, Khouri H, Dimitrov G, Robinson JR, et al. Genome degradation in Brucella ovis corresponds with narrowing of its host range and tissue tropism. Plos One. 4: e5519. PMID 19436743 DOI: 10.1371/Journal.Pone.0005519  0.493
2008 Carlton JM, Adams JH, Silva JC, Bidwell SL, Lorenzi H, Caler E, Crabtree J, Angiuoli SV, Merino EF, Amedeo P, Cheng Q, Coulson RM, Crabb BS, Del Portillo HA, Essien K, et al. Comparative genomics of the neglected human malaria parasite Plasmodium vivax. Nature. 455: 757-63. PMID 18843361 DOI: 10.1038/Nature07327  0.64
2008 Garrity GM, Field D, Kyrpides N, Hirschman L, Sansone SA, Angiuoli S, Cole JR, Glöckner FO, Kolker E, Kowalchuk G, Moran MA, Ussery D, White O. Toward a standards-compliant genomic and metagenomic publication record. Omics : a Journal of Integrative Biology. 12: 157-60. PMID 18564916 DOI: 10.1089/Omi.2008.A2B2  0.444
2008 Field D, Garrity GM, Sansone SA, Sterk P, Gray T, Kyrpides N, Hirschman L, Glöckner FO, Kottmann R, Angiuoli S, White O, Dawyndt P, Thomson N, Gil IS, Morrison N, et al. Meeting report: the fifth Genomic Standards Consortium (GSC) workshop. Omics : a Journal of Integrative Biology. 12: 109-13. PMID 18564915 DOI: 10.1089/omi.2008.A3B3  0.312
2008 Field D, Glöckner FO, Garrity GM, Gray T, Sterk P, Cochrane G, Vaughan R, Kolker E, Kottmann R, Kyrpides N, Angiuoli S, Dawyndt P, Guralnick R, Goldstein P, Hall N, et al. Meeting report: the fourth Genomic Standards Consortium (GSC) workshop. Omics : a Journal of Integrative Biology. 12: 101-8. PMID 18564914 DOI: 10.1089/Omi.2008.0014  0.476
2008 Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, et al. The minimum information about a genome sequence (MIGS) specification. Nature Biotechnology. 26: 541-7. PMID 18464787 DOI: 10.1038/Nbt1360  0.427
2008 Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D, Garrity G, Kodira CD, Kyrpides N, Madupu R, Markowitz V, Tatusova T, Thomson N, White O. Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation. Omics : a Journal of Integrative Biology. 12: 137-41. PMID 18416670 DOI: 10.1089/Omi.2008.0017  0.373
2008 Fedorova ND, Khaldi N, Joardar VS, Maiti R, Amedeo P, Anderson MJ, Crabtree J, Silva JC, Badger JH, Albarraq A, Angiuoli S, Bussey H, Bowyer P, Cotty PJ, Dyer PS, et al. Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. Plos Genetics. 4: e1000046. PMID 18404212 DOI: 10.1371/Journal.Pgen.1000046  0.51
2007 Crabtree J, Angiuoli SV, Wortman JR, White OR. Sybil: methods and software for multiple genome comparison and visualization. Methods in Molecular Biology (Clifton, N.J.). 408: 93-108. PMID 18314579 DOI: 10.1007/978-1-59745-547-3_6  0.397
2007 Ghedin E, Wang S, Spiro D, Caler E, Zhao Q, Crabtree J, Allen JE, Delcher AL, Guiliano DB, Miranda-Saavedra D, Angiuoli SV, Creasy T, Amedeo P, Haas B, El-Sayed NM, et al. Draft genome of the filarial nematode parasite Brugia malayi. Science (New York, N.Y.). 317: 1756-60. PMID 17885136 DOI: 10.1126/Science.1145406  0.785
2007 Heinicke S, Livstone MS, Lu C, Oughtred R, Kang F, Angiuoli SV, White O, Botstein D, Dolinski K. The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists. Plos One. 2: e766. PMID 17712414 DOI: 10.1371/Journal.Pone.0000766  0.344
2006 Dunning Hotopp JC, Lin M, Madupu R, Crabtree J, Angiuoli SV, Eisen JA, Eisen J, Seshadri R, Ren Q, Wu M, Utterback TR, Smith S, Lewis M, Khouri H, Zhang C, et al. Comparative genomics of emerging human ehrlichiosis agents. Plos Genetics. 2: e21. PMID 16482227 DOI: 10.1371/Journal.Pgen.0020021  0.395
2006 Wortman JR, Fedorova N, Crabtree J, Joardar V, Maiti R, Haas BJ, Amedeo P, Lee E, Angiuoli SV, Jiang B, Anderson MJ, Denning DW, White OR, Nierman WC. Whole genome comparison of the A. fumigatus family Medical Mycology. 44: 3-7. DOI: 10.1080/13693780600835799  0.497
2005 Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, Deboy RT, Davidsen TM, Mora M, Scarselli M, Margarit y Ros I, et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proceedings of the National Academy of Sciences of the United States of America. 102: 13950-5. PMID 16172379 DOI: 10.1073/Pnas.0506758102  0.501
2005 El-Sayed NM, Myler PJ, Blandin G, Berriman M, Crabtree J, Aggarwal G, Caler E, Renauld H, Worthey EA, Hertz-Fowler C, Ghedin E, Peacock C, Bartholomeu DC, Haas BJ, Tran AN, ... ... Angiuoli S, et al. Comparative genomics of trypanosomatid parasitic protozoa. Science (New York, N.Y.). 309: 404-9. PMID 16020724 DOI: 10.1126/Science.1112181  0.656
2005 Gardner MJ, Bishop R, Shah T, de Villiers EP, Carlton JM, Hall N, Ren Q, Paulsen IT, Pain A, Berriman M, Wilson RJ, Sato S, Ralph SA, Mann DJ, Xiong Z, ... ... Angiuoli SV, et al. Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes. Science (New York, N.Y.). 309: 134-7. PMID 15994558 DOI: 10.1126/Science.1110439  0.779
2005 Gill SR, Fouts DE, Archer GL, Mongodin EF, Deboy RT, Ravel J, Paulsen IT, Kolonay JF, Brinkac L, Beanan M, Dodson RJ, Daugherty SC, Madupu R, Angiuoli SV, Durkin AS, et al. Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain. Journal of Bacteriology. 187: 2426-38. PMID 15774886 DOI: 10.1128/Jb.187.7.2426-2438.2005  0.326
2004 Nelson KE, Fouts DE, Mongodin EF, Ravel J, DeBoy RT, Kolonay JF, Rasko DA, Angiuoli SV, Gill SR, Paulsen IT, Peterson J, White O, Nelson WC, Nierman W, Beanan MJ, et al. Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species. Nucleic Acids Research. 32: 2386-95. PMID 15115801 DOI: 10.1093/Nar/Gkh562  0.31
2004 Ghedin E, Bringaud F, Peterson J, Myler P, Berriman M, Ivens A, Andersson B, Bontempi E, Eisen J, Angiuoli S, Wanless D, Von Arx A, Murphy L, Lennard N, Salzberg S, et al. Gene synteny and evolution of genome architecture in trypanosomatids. Molecular and Biochemical Parasitology. 134: 183-91. PMID 15003838 DOI: 10.1016/J.Molbiopara.2003.11.012  0.684
2004 Rasko DA, Ravel J, Økstad OA, Helgason E, Cer RZ, Jiang L, Shores KA, Fouts DE, Tourasse NJ, Angiuoli SV, Kolonay J, Nelson WC, Kolstø AB, Fraser CM, Read TD. The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1. Nucleic Acids Research. 32: 977-88. PMID 14960714 DOI: 10.1093/Nar/Gkh258  0.34
2002 Gardner MJ, Shallom SJ, Carlton JM, Salzberg SL, Nene V, Shoaibi A, Ciecko A, Lynn J, Rizzo M, Weaver B, Jarrahi B, Brenner M, Parvizi B, Tallon L, Moazzez A, ... ... Angiuoli S, et al. Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14. Nature. 419: 531-4. PMID 12368868 DOI: 10.1038/nature01094  0.756
2002 Carlton JM, Angiuoli SV, Suh BB, Kooij TW, Pertea M, Silva JC, Ermolaeva MD, Allen JE, Selengut JD, Koo HL, Peterson JD, Pop M, Kosack DS, Shumway MF, Bidwell SL, et al. Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature. 419: 512-9. PMID 12368865 DOI: 10.1038/Nature01099  0.784
2002 Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, Paulsen IT, James K, Eisen JA, Rutherford K, Salzberg SL, ... ... Angiuoli S, et al. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature. 419: 498-511. PMID 12368864 DOI: 10.1038/Nature01097  0.796
2001 Tettelin H, Nelson KE, Paulsen IT, Eisen JA, Read TD, Peterson S, Heidelberg J, DeBoy RT, Haft DH, Dodson RJ, Durkin AS, Gwinn M, Kolonay JF, Nelson WC, Peterson JD, ... ... Angiuoli S, et al. Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science (New York, N.Y.). 293: 498-506. PMID 11463916 DOI: 10.1126/Science.1061217  0.545
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