Sequence Analysis

• 1494 · PDF Study on acquisition timing of KRAS mutations in the pancreatic ductal epithelium Tomonori Hirano, Yasuhide Takeuch, Kazuyuki Nagai, Takayuki Anazawa, Sachiko Minamiguchi, Hiroshi Seno, Seishi Ogawa, Nobuyuki Kakiuchi
• 1495 · PDF A novel, deep learning -based filtering tool for enhanced detection of technical artifacts in whole-genome sequencing data Julian Gascoyne, David Benjamin, Juan Gallegos, Lee T. Lichtenstein, Sachet Shukla
• 1496 · PDF Long-read sequencing of 15 Ewing sarcoma cell lines uncovers extensive GGAA microsatellite variation shaping the landscape of EWSR1::FLI1 binding Andrew Song, Xin Li, Egor Dolzhenko, Hélène Neyret Kahn, Kristine Jones, Difei Wang, Komal Jain, Aubrey Hubbard, Olivia Lee, Stephen Chanock, Diptavo Dutta, Olivier Delattre, Mitchell J. Machiela
• 1497 · PDF Long-read RNA-Seq reveals a novel isoform landscape of SRSF2 -mutant chronic myelomonocytic leukemia Nickolas Steinauer, Terra Lasho, Christy Finke, Pankaj Pradeep, Jenna Fernandez, Alejandro Ferrer, Moritz Binder, Abhishek Mangaonkar, Mrinal M. Patnaik
• 1498 · PDF A generalizable software framework for ultra-rapid sequence analysis and its application in enabling 1 day deep multi-omic data analysis turnaround for brain cancer precision oncology Anders Pitman, David Bean, Yi Qiao
• 1499 · PDF Pangenome-based somatic mutation landscape of early- and late-onset colorectal cancer in 99 Korean patients Jae-Yoon Kim, Soobok Joe, Sunwoo Lee, Yeo-Gyeong Yoon, Jongbum Jeon, Jong Hwan Kim, Jin Ok Yang, Seung-Woo Baek, Jong-Lyul Park, Seon-Kyu Kim, Seon-Young Kim
• 1500 · PDF Modeling base-pair level mutation rate in metastatic breast cancer using a sequence-based deep learning model Ariaki Dandawate, Christina Leslie, Ekta Khurana
• 1501 Cancer gene variant identification and functional interpretation using long-read RNA sequencing with FLAIR3 Colette Felton, Andrea Galvez, Tanvi Damle, Kevin Levine, Mark Diekhans, Eunice Lopez Fuentes, Taylor Won, Christopher Vollmers, Alejandro Sweet-Cordero, Alice Berger, Angela N. Brooks
• 1503 · PDF Single-cell multiomics analysis reveals cell type-specific genetic regulatory programs underlying immunotherapy resistance in hepatocellular carcinoma Siyuan Huang, Xiaohang Long, Stephen Lam Chan, Alfred Sze-Lok Cheng
• 1504 · PDF Fusobacterium-driven epithelial-stromal remodeling in CRC Sabin Park, Taeyul Kim, Kyung-A Kim, Minsun Jung, Sang Cheol Kim, Han Sang Kim, Semin Lee
• 1505 · PDF Long-read sequencing of pancreatic adenocarcinoma transcriptome uncovered aberrant isoforms and tumor progression Charny Park, Hyeyeong Hwang, Daejin Hyung, Namhee Yu, Sehwa Hong, Soo Young Cho, Sang Myung Woo
• 1506 · PDF Assessing allelic expression variation using somatic mutations vs. polymorphic germline variants Kohei Hagiwara, Bensheng Ju, Nadezhda V. Terekhanova, John Easton, Jinghui Zhang
• 1507 Health behavior associated CCL20 ligand variation contributes to the disparity in non-small cell lung cancer Murugesh Eswaran, Briana Alicia Brock, Hina Mir, Sejong Bae, Gabriella M. Oprea-Ilies, Eric L. Flenaugh, Sanjay R. Jain, Brian M. Rivers, Rick A. Kittles, James W. Lillard, Rajesh Singh, Shailesh Singh
• 1508 · PDF A large-scale resource of standardized pediatric somatic cancer variant classifications Alex H. Wagner, Kori Kuzma, Kathleen M. Schieffer, Wesley Goar, Don Corsmeier, Michael McCarrick, Kathryn Perry, Jennifer Bowser, James Stevenson, Mohammad Marhabaie, Matthew Cannon, Liana Hernandez, Doug Depoorter, Hongtao Jia, Amy Everest, Jessica Howard, Swetha Ramadesikan, Vijayakumar Jayaraman, Ying-Chen C. Hou, Mariam T. Mathew, Marco L. Leung, Yassmine M. N. Akkari, Daniel Puthawala, Anastasia Bratulin, Ben Kelly, Elaine R. Mardis, Catherine E. Cottrell
• 1509 · PDF Cost-effective, full-length transcriptome of chronic lymphocytic leukemia patient cd8 t cells reveals the impact of BTKi treatment on mRNA processing and gene expression Shanmugapriya Thangavadivel, Altan Turkoglu, Lianbo Yu, Rosario Distefano, Alexander Pan, Logan Walker, Tina Wang, Shrilekha Misra, Tzung-Huei Lai, Britten Gordon, Samon Benrashid, Alexander He, Meixiao Long, rosa Lapalombella, John C. Byrd, Kerry A. Rogers, Bradley Blaser, Ralf Bundschuh, Jennifer A. Woyach, Pearlly S. Yan
• 1510 · PDF CASTLE: long-read sequencing panel of cancer cell lines to improve standards of somatic variant calling and benchmarking Mikhail Kolmogorov, Ayse Gokce Kesus, Asher Bryant, Tanveer Ahmad, Byunggil Yoo, Sergey Aganezov, Anton Goretsky, Ataberk Donmez, Lisa Lansdon, Joshua Gardner, Brandy McNulty, Samuel Sacco, Jyoti Shetty, Yongmei Zhao, Bao Tran, Giuseppe Narzisi, Adrienne Hellend, Chengpeng Bi, Adam Walter, Margaret Gibson, Irina Pushel, Erin Guest, Tomi Pastinen, Nicolas Robine, Karen H. Miga, Midhat S. Farooqi, Benedict Paten
• 1511 · PDF Longitudinal whole genome sequencing to investigate clonal hematopoiesis dynamics Rohini Chebbi, Steven Estus, Elif P. Coskun, David W. Fardo, Gregory A. Jicha, Peter T. Nelson, Erin L. Abner, Yasminka A. Jakubek
• 1512 · PDF Enhanced detection of immune and oncogenic signals in HER2-positive breast cancer by a novel data-scaling method Chole Gunadi, Emily Xue, Amy Lei, Cindy Hu, Qian Wang
• 1513 · PDF Gene signatures and infiltration patterns of mast cells in breast cancer revealed by integrated bulk and single-cell RNA sequencing Analyses Eva Liu, Benjamin Jin, Cindy Hu, Qian Wang
• 1514 · PDF Mapping classifiability in the cancer DNA methylome: A data-learned disease hierarchy Hao Xu, Jenny Z. Li, Wanding Zhou
• 1515 · PDF Doublet removal enhances single-cell resolution and uncovers malignant transcriptional programs in NSCLC Benjamin Jin, Eva Liu, Amy Lei, Qian Wang

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