Search Results - "Zhang, Simo"

A machine learning algorithm with subclonal sensitivity reveals widespread pan-cancer human leukocyte antigen loss of heterozygosity by Pyke, Rachel Marty, Mellacheruvu, Dattatreya, Dea, Steven, Abbott, Charles W., McDaniel, Lee, Bhave, Devayani P., Zhang, Simo V., Levy, Eric, Bartha, Gabor, West, John, Snyder, Michael P., Chen, Richard O., Boyle, Sean Michael

“…Human leukocyte antigen loss of heterozygosity (HLA LOH) allows cancer cells to escape immune recognition by deleting HLA alleles, causing the suppressed…”
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Intraspecific Genetic Variation Underlying Postmating Reproductive Barriers between Species in the Wild Tomato Clade (Solanum sect. Lycopersicon) by Jewell, Cathleen P, Zhang, Simo V, Gibson, Matthew J S, Tovar-Méndez, Alejandro, McClure, Bruce, Moyle, Leonie C

“…A goal of speciation genetics is to understand how the genetic components underlying interspecific reproductive barriers originate within species. Unilateral…”
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Precision Neoantigen Discovery Using Large-scale Immunopeptidomes and Composite Modeling of MHC Peptide Presentation by Pyke, Rachel Marty, Mellacheruvu, Dattatreya, Dea, Steven, Abbott, Charles W., Zhang, Simo V., Phillips, Nick A., Harris, Jason, Bartha, Gabor, Desai, Sejal, McClory, Rena, West, John, Snyder, Michael P., Chen, Richard, Boyle, Sean Michael

“…This article has been withdrawn by the authors. A publication of the manuscript with the correct figures and tables has been approved and the authors state the…”
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Prediction of Immunotherapy Response in Melanoma through Combined Modeling of Neoantigen Burden and Immune-Related Resistance Mechanisms by Abbott, Charles W, Boyle, Sean M, Pyke, Rachel Marty, McDaniel, Lee D, Levy, Eric, Navarro, Fábio C P, Mellacheruvu, Dattatreya, Zhang, Simo V, Tan, Mengyao, Santiago, Rose, Rusan, Zeid M, Milani, Pamela, Bartha, Gabor, Harris, Jason, McClory, Rena, Snyder, Michael P, Jang, Sekwon, Chen, Richard

“…While immune checkpoint blockade (ICB) has become a pillar of cancer treatment, biomarkers that consistently predict patient response remain elusive due to the…”
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Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies by Waterhouse, Robert M, Aganezov, Sergey, Anselmetti, Yoann, Lee, Jiyoung, Ruzzante, Livio, Reijnders, Maarten J M F, Feron, Romain, Bérard, Sèverine, George, Phillip, Hahn, Matthew W, Howell, Paul I, Kamali, Maryam, Koren, Sergey, Lawson, Daniel, Maslen, Gareth, Peery, Ashley, Phillippy, Adam M, Sharakhova, Maria V, Tannier, Eric, Unger, Maria F, Zhang, Simo V, Alekseyev, Max A, Besansky, Nora J, Chauve, Cedric, Emrich, Scott J, Sharakhov, Igor V

“…New sequencing technologies have lowered financial barriers to whole genome sequencing, but resulting assemblies are often fragmented and far from 'finished'…”
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The sequencing and interpretation of the genome obtained from a Serbian individual by Mohammed Ismail, Wazim, Pagel, Kymberleigh A, Pejaver, Vikas, Zhang, Simo V, Casasa, Sofia, Mort, Matthew, Cooper, David N, Hahn, Matthew W, Radivojac, Predrag

“…Recent genetic studies and whole-genome sequencing projects have greatly improved our understanding of human variation and clinically actionable genetic…”
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Precision Neoantigen Discovery Using Large-Scale Immunopeptidomes and Composite Modeling of MHC Peptide Presentation by Pyke, Rachel Marty, Mellacheruvu, Datta, Dea, Steven, Abbott, Charles, Zhang, Simo V., Phillips, Nick A., Harris, Jason, Bartha, Gabor, Desai, Sejal, McClory, Rena, West, John, Snyder, Michael P., Chen, Richard, Boyle, Sean Michael

“…Major histocompatibility complex (MHC)–bound peptides that originate from tumor-specific genetic alterations, known as neoantigens, are an important class of…”
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Rearrangement of macronucleus chromosomes correspond to TAD-like structures of micronucleus chromosomes in Tetrahymena thermophila by Luo, Zhengyu, Hu, Tengfei, Jiang, Hong, Wang, Ruoyu, Xu, Qianlan, Zhang, Simo, Cao, Jun, Song, Xiaoyuan

“…The somatic macronucleus (MAC) and germline micronucleus (MIC) of differ in chromosome numbers, sizes, functions, transcriptional activities, and cohesin…”
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Withdrawal of ‘Precision Neoantigen Discovery Using Large-scale Immunopeptidomes and Composite Modeling of MHC Peptide Presentation’ by Pyke, Rachel Marty, Mellacheruvu, Dattatreya, Dea, Steven, Abbott, Charles W., Zhang, Simo V., Phillips, Nick A., Harris, Jason, Bartha, Gabor, Desai, Sejal, McClory, Rena, West, John, Snyder, Michael P., Chen, Richard, Boyle, Sean Michael

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Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes by Hall, Andrew Brantley, Papathanos, Philippos-Aris, Sharma, Atashi, Cheng, Changde, Akbari, Omar S., Assour, Lauren, Bergman, Nicholas H., Cagnetti, Alessia, Crisanti, Andrea, Dottorini, Tania, Fiorentini, Elisa, Galizi, Roberto, Hnath, Jonathan, Jiang, Xiaofang, Koren, Sergey, Nolan, Tony, Radune, Diane, Sharakhova, Maria V., Steele, Aaron, Timoshevskiy, Vladimir A., Windbichler, Nikolai, Zhang, Simo, Hahn, Matthew W., Phillippy, Adam M., Emrich, Scott J., Sharakhov, Igor V., Tu, Zhijian Jake, Besansky, Nora J.

“…Y chromosomes control essential male functions in many species, including sex determination and fertility. However, because of obstacles posed by repeat-rich…”
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AGOUTI: improving genome assembly and annotation using transcriptome data by Zhang, Simo V, Zhuo, Luting, Hahn, Matthew W

“…Genomes sequenced using short-read, next-generation sequencing technologies can have many errors and may be fragmented into thousands of small contigs. These…”
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A map of human cancer signaling by Wang, Edwin, Cui, Qinghua, Ma, Yun, Jaramillo, Maria, Bari, Hamza, Awan, Arif, Yang, Song, Zhang, Simo, Liu, Lixue, Lu, Meng, O'Connor-McCourt, Maureen, Purisima, Enrico O

“…We conducted a comprehensive analysis of a manually curated human signaling network containing 1634 nodes and 5089 signaling regulatory relations by…”
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Sequencing, assembling, and correcting draft genomes using recombinant populations by Hahn, Matthew W, Zhang, Simo V, Moyle, Leonie C

“…Current de novo whole-genome sequencing approaches often are inadequate for organisms lacking substantial preexisting genetic data. Problems with these methods…”
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79 Extensively validated HLA LOH algorithm demonstrates an association between HLA LOH and genomic instability by Pyke, Rachel, Dea, Steven, Mellacheruvu, Dattatreya, Abbott, Charles, Zhang, Simo, McDaniel, Lee, Levy, Eric, Bartha, Gabor, West, John, Snyder, Michael, Chen, Richard, Boyle, Sean

“…BackgroundHuman Leukocyte Antigen (HLA) genes are critical for the presentation of neoantigens to the immune system by cancer cells. Deletion of HLA alleles,…”
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73 Orthogonally and functionally validated algorithm for detecting HLA loss of heterozygosity by Pyke, Rachel, Mellacheruvu, Dattatreya, Abbott, Charles, Levy, Eric, Zhang, Simo, Bhave, Devayani, Chinnappa, Manjula, Bartha, Gabor, Lyle, John, West, John, Chen, Richard, Boyle, Sean

“…BackgroundHuman leukocyte antigen (HLA) genes facilitate communication between tumor cells and the immune system through the cell surface presentation of a…”
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29 Profiling tumor circulating cell-free DNA with an enhanced whole-exome to enable sensitive assessment of somatic mutations by Zhang, Simo, Tan, Mengyao, Navarro, Fabio CP, Northcott, Josette, Ma, Shuyuan, Nelson, Christopher, Bhave, Devayani, Gordon Bentley, L, Chinnappa, Manju, Norton, Dan, Bartha, Gabor, Harris, Jason, Lyle, John, Boyle, Sean, West, John, Chen, Richard

“…BackgroundAn increasing number of studies have demonstrated the potential use of circulating cell-free DNA (cfDNA) for diagnosis, prognosis, disease…”
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A novel cross‐coupled filter with triangular resonators by Zhang, Simo, Huang, Zhengwei, Cheng, Yong

“…In this article, a novel isosceles right triangle resonators filter is presented based on cross‐coupling technology. The whole filter is a square structure and…”
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1×3 optical switch with a V-shaped microchannel by Wan, Jing, Miao, Jiangyun, Xu, Peng, Zhang, Simo, Duan, Yixin

“…A 1×3 optical switch with a V-shaped microchannel is proposed. It can selectively switch optical signals from one channel to another by controlling liquid and…”
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Effect of Heterogeneous Deformation on Microstructure and Microtexture Evolution of Ti‐6Al‐4V Alloy during Multidirectional Isothermal Forging by Zhang, Simo, Huang, Wenhao, Yu, Jiajun, Zhang, Zhixiong, Zhang, Juntao, Yuan, Ruilin, Zhang, Changjiang, Han, Jianchao, Meng, Jianan, Wang, Tao

“…The heterogeneous deformation of Ti‐6Al‐4V alloy during multidirectional isothermal forging and its effect on microstructure, microtexture, and related…”
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Association mapping desiccation resistance within chromosomal inversions in the African malaria vector Anopheles gambiae by Ayala, Diego, Zhang, Simo, Chateau, Mathieu, Fouet, Caroline, Morlais, Isabelle, Costantini, Carlo, Hahn, Matthew W., Besansky, Nora J.

“…Inversion polymorphisms are responsible for many ecologically important phenotypes and are often found under balancing selection. However, the same features…”
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