Application of Bioinformatics to Cancer Biology 2

• 1407 · PDF Single-cell long-read transcriptomics reveals isoform centric molecular features of rare pseudomyxoma peritonei disease Kyungtae Lee, Anuja Sathe, Raegan Wood, Dongin Lee, Billy Lau, Hanlee P. Ji
• 1408 · PDF MicroNucML: A machine learning approach for micronuclei segmentation and the refinement of nuclei-micronuclei relationships Nadejda B. Boev, Yukai Wang, Ulises O. Garcia, Kate M. MacDonald, Shane M. Harding, Sushant Kumar
• 1409 · PDF Fusion epigenotyping using cell‑free DNA methylation improves detection of actionable ALK fusions in non-small cell lung cancer Laura Tung, Anton Valouev, Justin Odegaard, Lauren Lawrence, Nicole Zhang, Martina Lefterova, Matthew Ellis, Tingting Jiang, Sheila Solomon, Darya Chudova
• 1410 · PDF Transcriptional silencing of homologous recombination defines a functional HRD in invasive lobular carcinoma Yona Kim, Yeseul Kim, Harim Oh, Sung Hak Lee, Sangjeong Ahn, You-Na Sung
• 1411 · PDF Extrachromosomal DNA amplification defines a high-risk subgroup and unique molecular features in gastric cancer Jieun Lee, Donghyeok Seol, Seunghyun Kang, Chanmi Bang, Mira Yoo, Soyeon Kim, Hyeongjin Cho, So Hyun Kang, Young Suk Park, Sang-Hoon Ahn, Hyung-Ho Kim, Eunhee YI, Sanghyun Kim, Hoon Kim, Yun-Suhk Suh
• 1412 · PDF Informatics-driven spatial-omics for cancer immunotherapy discovery in gynecologic cancers Rongting Huang, Diane Libert, Arslan Kasimov, Leandra Kingsley, Sahar Nasr, Reem Al-Humadi, Lindsey A. Finch, Elisabeth Diver, Ravali A. Reddy, Babak Litkouhi, Kristin Bixel, Sizun Jiang, Brooke Howitt
• 1413 · PDF Targetable gene dependencies in Ewing sarcoma subtypes Dusan Pesic, Josh Nash, Timmy Wen, Pedro Lemos Ballester, Livia Garzia, Olivier Delattre, David Malkin, Adam Shlien
• 1414 · PDF Shared gut virome profiles highlight potential early colorectal cancer markers in HIV-helminth co-infection Botle Precious Damane, Thanyani V. Mulaudzi, Jonathan Featherston, Sayed Shakeel Kader, Pragalathan Naidoo, Zodwa Dlamini, Zilungile Lynette Mkhize-Kwitshana
• 1415 1415 A comprehensive computational study of PARP1 isoforms and their interactions with nucleolin: Structural insights and implications for breast cancer Nathaniel Zimmerman, Grela Jerliu, Naomi Hutchinson, Anjana Saxena, Shaneen M. Singh
• 1416 · PDF Stress-responsive glucocorticoid receptor signaling shapes the immune tumor microenvironment in lung cancer Sabrina Akter, Aiman Soliman, Robert A. Winn, Zeynep Madak-Erdogan, Sage J. Kim
• 1417 · PDF Bulk RNA-seq atlas guided annotation of tumor transcriptomes Timmy T. Wen, Dusan Pesic, Pedro L. Ballester, Josh Nash, Adam Shlien
• 1418 · PDF Uncovering novel splice junctions in prostate cancer using DeepSAP Pankaj Vats, Fadel Berakdar, Thomas D. Wu, Tong Zhu, Mehrzad Samadi
• 1419 · PDF Integrated spatial and genetic lineage tracing uncovers cell state plasticity underlying recurrence in group3 and group4 medulloblastoma Bohyeon Yu, Emanuele Filiberto Rosatti, Jangham Jung, Abhinav Jain, Joanna Phillips, Aaron Antonio Diaz
• 1420 1420 Image-based ROI selection for spatial transcriptomic experiments using immune checkpoint inhibitor treatment outcome prediction in gastric cancer Sunho Park, Minji Kim, Jean R. Clemenceau, Seock-Jin Chung, Eric F. Sha, Changjin Hong, Soyoung Im, Hwanil Choi, Soonyoung Lee, Jongseong Jang, Kohei Shitara, Sung Hak Lee, Jae-Ho Cheong, Tae Hyun Hwang
• 1421 · PDF Pediatric pan-cancer characterization of transposable elements and their modulation by germline TP53 variants Brianne Laverty, Shilpa Yadahalli, Safa Majeed, Ashby Kissoondoyal, Laura Raiti, Ann Gong, Noa Alon, Kashif Daud, Alexander Solovyov, Scott Davidson, Yisu Li, Mehdi Layeghifard, Adam Shlien, David Malkin, Vallijah Subasri
• 1422 · PDF Characterizing clinical toxicity in cancer combination therapies Alexandra M. Wong, Cecile Meier-Scherling, Lorin Crawford
• 1423 · PDF Aneuploidy detection from FFPE archived tissues: A computational approach for FFPE-CUTAC data Aditya T. Parmar, Yiyang Niu, Kami Ahmad, Steven Henikoff, Ye Zheng
• 1424 · PDF Unique tumor ecosystems in metaplastic breast cancer identified through single nucleus RNA sequencing Aatish Thennavan, Tuan M Tran, Jianzhuo Li, Clinton Yam, Nicholas E. Navin
• 1425 1425 Identifying tumor-specific membrane targets, therapeutics, and matching cell lines for experimental validation with the Multiomics2Targets2 workflow Anna I. Byrd, Lily D. Taub, Avi Ma'ayan
• 1426 · PDF A single-cell tumor atlas defines robust pathway and gene signatures enabling cancer cell-line fidelity assessment Rosyli F. Reveron-Thornton, Chuner Guo, James P. Agolia, Maria Moozhiyil Korah, Peter Yuxin Xie, Andrea Delitto, Amanda Gonçalves, Angela Tabora, Biren Reddy, Wesley Bobst, Amanda R. Kirane, Monica Dua, Brendan Visser, Byrne Lee, George Poultsides, Jeffrey A. Norton, Derrick C. Wan, Michael T. Longaker, Deshka Foster, Daniel Delitto
• 1427 · PDF Exploring high-resolution subtypes for pancreatic ductal adenocarcinoma via a meta-clustering approach Nick Boos Peterson, Jieqiong Wang, Shibiao Wan
• 1428 · PDF Single cell RNA-seq analysis of osteosarcoma reveals conserved and distinct ecosystems across sites and species Yogesh Budhathoki, Matthew Cannon, Troy A. Mceachron, Anand G. Patel, Matthew Gust, Jaime F. Modiano, Dylan T. Ammons, Kathryn Cronise, Daniel Regan, Heather Gardner, Ryan D. Roberts
• 1429 1429 Stress-responsive genomic alterations reveal a bi-directional relationship between PTSD biology and breast cancer aggressiveness Alakesh Bera, Meera Srivastava
• 1430 · PDF Conserved tumor imprinted T cell states across cancers revealed by pan cancer single cell atlases Yan Zong, Hongru Shen, Yajing Bi, Xiangchun Li
• 1431 · PDF Functional heterogeneity of neutrophils in hepatocarcinogenesis in animal models and human patients Zhihao Huang, Wang Xiaopeng, Wei Dai, Xin-Yuan Guan, Feng Gen-Sheng
• 1432 · PDF Single-cell-derived gene-pair classifiers for prostate cancer prognostication Lucio Queiroz, Karnika Singh, Wikum Dinalankara, Luigi Marchionni
• 1433 1433 Evidence of noncontiguous haplotype patterns at chromosome band 13q12 associated with prostate cancer risk in men of African ancestry in the All of Us Research Program William Peter Letsou, Daniel Galvin Gusmano, Meet Boghani, Ifti M. Gazi, Ashwin Nori
• 1434 · PDF Scalable, unsupervised deep learning frameworks for rare event detection and single cell phenotyping in enrichment free liquid biopsies Dean Tessone, Amin Naghdloo, Javier Murgoitio-Esandi, Jeremy Mason, Assad Oberai, James B. Hicks, Peter Kuhn

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