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Thomas E. Royce, Ph.D. - Publications

Affiliations: 
Yale University, New Haven, CT 
Area:
Computational Biology and Bioinformatics
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33 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 Basu GD, Drenner K, Ozols A, Bair CM, White T, LoBello JR, Royce T, Sharma S. Whole exome and transcriptome sequencing of colorectal and pancreatic cancer. Journal of Clinical Oncology. 38: e15666-e15666. DOI: 10.1200/Jco.2020.38.15_Suppl.E15666  0.355
2017 Norman PJ, Norberg SJ, Guethlein LA, Nemat-Gorgani N, Royce TE, Wroblewski EE, Mann T, Dunn T, Alicata C, Hollenbach JA, Chang W, Shults-Won M, Gunderson KL, Abi-Rached L, Ronaghi M, et al. Sequences of 95 human MHC haplotypes reveal extreme coding variation in genes other than highly polymorphic HLA class I and II. Genome Research. PMID 28360230 DOI: 10.1101/Gr.213538.116  0.406
2017 Basu GD, White T, LoBello J, Kurdoglu A, Trent J, Peng S, Halbert M, Royce T. Abstract 2779: Assessing germline and somatic alterations in DNA repair pathway in cancer Cancer Research. 77: 2779-2779. DOI: 10.1158/1538-7445.Am2017-2779  0.358
2016 Roller E, Ivakhno S, Lee S, Royce T, Tanner S. Canvas: versatile and scalable detection of copy number variants. Bioinformatics (Oxford, England). PMID 27153601 DOI: 10.1093/Bioinformatics/Btw163  0.385
2016 Basu GD, White T, LoBello JR, Lau KR, Syring M, Krishnan S, Gonzalez L, Royce T, Kurdoglu A, Halbert MJ, Kiefer J, Cherni I, Aldrich J, Izatt T, Russell M, et al. ARID1A alterations in gastrointestinal cancers as therapeutic opportunities. Journal of Clinical Oncology. 34: 671-671. DOI: 10.1200/Jco.2016.34.4_Suppl.671  0.347
2015 Norman PJ, Norberg SJ, Nemat-Gorgani N, Royce T, Hollenbach JA, Shults Won M, Guethlein LA, Gunderson KL, Ronaghi M, Parham P. Very long haplotype tracts characterized at high resolution from HLA homozygous cell lines. Immunogenetics. 67: 479-85. PMID 26198775 DOI: 10.1007/S00251-015-0857-Y  0.348
2014 Amini S, Pushkarev D, Christiansen L, Kostem E, Royce T, Turk C, Pignatelli N, Adey A, Kitzman JO, Vijayan K, Ronaghi M, Shendure J, Gunderson KL, Steemers FJ. Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing. Nature Genetics. 46: 1343-9. PMID 25326703 DOI: 10.1038/Ng.3119  0.445
2013 Norman PJ, Norberg S, Royce T, Won M, Mann T, Nemat-Gorgani N, Guethlein LA, Abi-Rached L, Gunderson KL, Ronaghi M, Parham P. 148-P Human Immunology. 74: 151. DOI: 10.1016/J.Humimm.2013.08.223  0.383
2013 Norman PJ, Norberg S, Nemat-Gorgani N, Won M, Moudgil A, Royce T, Guethlein LA, Abi-Rached L, Gunderson KL, Ronaghi M, Parham P. 34-OR Human Immunology. 74: 26. DOI: 10.1016/J.Humimm.2013.08.045  0.398
2010 Ivakhno S, Royce T, Cox AJ, Evers DJ, Cheetham RK, Tavaré S. CNAseg--a novel framework for identification of copy number changes in cancer from second-generation sequencing data. Bioinformatics (Oxford, England). 26: 3051-8. PMID 20966003 DOI: 10.1093/Bioinformatics/Btq587  0.368
2010 Pleasance ED, Cheetham RK, Stephens PJ, McBride DJ, Humphray SJ, Greenman CD, Varela I, Lin ML, Ordóñez GR, Bignell GR, Ye K, Alipaz J, Bauer MJ, Beare D, Butler A, ... ... Royce T, et al. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature. 463: 191-6. PMID 20016485 DOI: 10.1038/Nature08658  0.353
2010 Fan J, Chen J, April C, Klotzle B, Royce T, Cann G, Talasaz AH, Islam S, Kjallquist U, Linnarsson S. Abstract 1149: Genetic analysis of single cells Cancer Research. 70: 1149-1149. DOI: 10.1158/1538-7445.Am10-1149  0.328
2009 April C, Klotzle B, Royce T, Wickham-Garcia E, Boyaniwsky T, Izzo J, Cox D, Jones W, Rubio R, Holton K, Matulonis U, Quackenbush J, Fan JB. Whole-genome gene expression profiling of formalin-fixed, paraffin-embedded tissue samples. Plos One. 4: e8162. PMID 19997620 DOI: 10.1371/Journal.Pone.0008162  0.441
2008 Seringhaus M, Rozowsky J, Royce T, Nagalakshmi U, Jee J, Snyder M, Gerstein M. Mismatch oligonucleotides in human and yeast: Guidelines for probe design on tiling microarrays Bmc Genomics. 9. PMID 19117516 DOI: 10.1186/1471-2164-9-635  0.739
2007 Setlur SR, Royce TE, Sboner A, Mosquera JM, Demichelis F, Hofer MD, Mertz KD, Gerstein M, Rubin MA. Integrative microarray analysis of pathways dysregulated in metastatic prostate cancer. Cancer Research. 67: 10296-303. PMID 17974971 DOI: 10.1158/0008-5472.Can-07-2173  0.482
2007 Royce TE, Rozowsky JS, Gerstein MB. Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification. Nucleic Acids Research. 35: e99. PMID 17686789 DOI: 10.1093/Nar/Gkm549  0.597
2007 Royce TE, Carriero NJ, Gerstein MB. An efficient pseudomedian filter for tiling microrrays. Bmc Bioinformatics. 8: 186. PMID 17555595 DOI: 10.1186/1471-2105-8-186  0.533
2007 Korbel JO, Urban AE, Grubert F, Du J, Royce TE, Starr P, Zhong G, Emanuel BS, Weissman SM, Snyder M, Gerstein MB. Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome. Proceedings of the National Academy of Sciences of the United States of America. 104: 10110-5. PMID 17551006 DOI: 10.1073/Pnas.0703834104  0.693
2007 Royce TE, Rozowsky JS, Gerstein MB. Assessing the need for sequence-based normalization in tiling microarray experiments. Bioinformatics (Oxford, England). 23: 988-97. PMID 17387113 DOI: 10.1093/Bioinformatics/Btm052  0.596
2007 Yu H, Nguyen K, Royce T, Qian J, Nelson K, Snyder M, Gerstein M. Positional artifacts in microarrays: experimental verification and construction of COP, an automated detection tool. Nucleic Acids Research. 35: e8. PMID 17158151 DOI: 10.1093/Nar/Gkl871  0.671
2006 Du J, Rozowsky JS, Korbel JO, Zhang ZD, Royce TE, Schultz MH, Snyder M, Gerstein M. A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge. Bioinformatics (Oxford, England). 22: 3016-24. PMID 17038339 DOI: 10.1093/Bioinformatics/Btl515  0.694
2006 Royce TE, Rozowsky JS, Luscombe NM, Emanuelsson O, Yu H, Zhu X, Snyder M, Gerstein MB. Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies. Methods in Enzymology. 411: 282-311. PMID 16939796 DOI: 10.1016/S0076-6879(06)11015-0  0.661
2005 Hartman SE, Bertone P, Nath AK, Royce TE, Gerstein M, Weissman S, Snyder M. Global changes in STAT target selection and transcription regulation upon interferon treatments. Genes & Development. 19: 2953-68. PMID 16319195 DOI: 10.1101/Gad.1371305  0.688
2005 Royce TE, Rozowsky JS, Bertone P, Samanta M, Stolc V, Weissman S, Snyder M, Gerstein M. Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. Trends in Genetics : Tig. 21: 466-75. PMID 15979196 DOI: 10.1016/J.Tig.2005.06.007  0.728
2005 Rozowsky J, Bertone P, Royce T, Weissman S, Snyder M, Gerstein M. Analysis of genomic tiling microarrays for transcript mapping and the identification of transcription factor binding sites Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science). 3594: 28-29.  0.682
2004 Lehnert U, Xia Y, Royce TE, Goh CS, Liu Y, Senes A, Yu H, Zhang ZL, Engelman DM, Gerstein M. Computational analysis of membrane proteins: genomic occurrence, structure prediction and helix interactions. Quarterly Reviews of Biophysics. 37: 121-46. PMID 15999419 DOI: 10.1017/S003358350400397X  0.64
2004 White EJ, Emanuelsson O, Scalzo D, Royce T, Kosak S, Oakeley EJ, Weissman S, Gerstein M, Groudine M, Snyder M, Schübeler D. DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states. Proceedings of the National Academy of Sciences of the United States of America. 101: 17771-6. PMID 15591350 DOI: 10.1073/Pnas.0408170101  0.571
2004 Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, Zhu X, Rinn JL, Tongprasit W, Samanta M, Weissman S, Gerstein M, Snyder M. Global identification of human transcribed sequences with genome tiling arrays. Science (New York, N.Y.). 306: 2242-6. PMID 15539566 DOI: 10.1126/Science.1103388  0.722
2004 Hall DA, Zhu H, Zhu X, Royce T, Gerstein M, Snyder M. Regulation of gene expression by a metabolic enzyme. Science (New York, N.Y.). 306: 482-4. PMID 15486299 DOI: 10.1126/Science.1096773  0.525
2004 Euskirchen G, Royce TE, Bertone P, Martone R, Rinn JL, Nelson FK, Sayward F, Luscombe NM, Miller P, Gerstein M, Weissman S, Snyder M. CREB binds to multiple loci on human chromosome 22. Molecular and Cellular Biology. 24: 3804-14. PMID 15082775 DOI: 10.1128/Mcb.24.9.3804-3814.2004  0.718
2003 Lian Z, Euskirchen G, Rinn J, Martone R, Bertone P, Hartman S, Royce T, Nelson K, Sayward F, Luscombe N, Yang J, Li JL, Miller P, Urban AE, Gerstein M, et al. Identification of novel functional elements in the human genome. Cold Spring Harbor Symposia On Quantitative Biology. 68: 317-22. PMID 15338632 DOI: 10.1101/Sqb.2003.68.317  0.678
2003 Martone R, Euskirchen G, Bertone P, Hartman S, Royce TE, Luscombe NM, Rinn JL, Nelson FK, Miller P, Gerstein M, Weissman S, Snyder M. Distribution of NF-kappaB-binding sites across human chromosome 22. Proceedings of the National Academy of Sciences of the United States of America. 100: 12247-52. PMID 14527995 DOI: 10.1073/Pnas.2135255100  0.692
2003 Luscombe NM, Royce TE, Bertone P, Echols N, Horak CE, Chang JT, Snyder M, Gerstein M. ExpressYourself: A modular platform for processing and visualizing microarray data. Nucleic Acids Research. 31: 3477-82. PMID 12824348 DOI: 10.1093/Nar/Gkg628  0.71
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