Application of Bioinformatics to Cancer Biology 3

• 2676 · PDF Subtyping cancer cachexia through automated body composition Sonia Boscenco, Venise Jan Castillon, Perry J. Pickhardt, John W. Garrett, Nathaniel C. Swinburne, Ed Reznik
• 2677 Identifying and analyzing clinicopathological features of uterine endometrial endometrioid tumors discordant by p53 and copy number status Sreekar B. Challa, Jessica D. St. Laurent, Zehra Ordulu, Alexander J. Neil, Melissa S. Gildenberg, Matthew L. Meyerson, Yvonne Y. Li, Andrew D. Cherniack, Elizabeth H. Stover
• 2678 · PDF A multimodal model to forecast prostate cancer metastasis from primary tumor transcriptomics and histopathology morphology Itzel Valencia, Priyanka Vasanthakumari, Pier V. Nuzzo, Edoardo Francini, Francesco Ravera, Giuseppe N. Fanelli, Sara Bleve, Cristian Scatena, Luigi Marchionni, Mohamed Omar
• 2679 · PDF Integrated Bulk and Single-Cell Transcriptomics Reveal Hepatocyte-Like Reprogramming in Metastatic Small Intestinal Neuroendocrine Tumors Sunanda Biswas Mukherjee, James P. Madigan, Samira M. Sadowski
• 2680 · PDF Dosage-dependent adaptations to Complex I mutations in cancer cell lines Neil Ruthen, Ziad El Bakouny, Amy Shepherd, Sonia Boscenco, Benan Nalbant, Caleb Lareau, Payam Gammage, Ed Reznik
• 2681 · PDF Past exposure to genotoxic cancer therapies is associated with elevated local mutagenesis at CTCF binding sites in metastatic tumors Kevin C. L. Cheng, Jigyansa Mishra, Juri Reimand
• 2682 · PDF Multiomic dissection of HBV-, HCV-, and non-viral HCC reveals distinct proliferation, interferon, and metabolic signatures Amerti Guta, Daniel O'Brien, Aditya V. Bhagwate, Jean-Pierre A. Kocher, Lewis R. Roberts
• 2683 · PDF Multi-omic analysis of patient and preclinical data highlights challenges in targeting tumor heterogeneity in glioblastoma Ha Dang, Verah Nyarige, Gonzalo Lopez, Ann Forslund, Wei Zhang, Bo Hu, Junfei Zhao, Maria Ortiz-Estevez, Alexandre Alloy, Romain Georges, Elizabeth Tindall, Josh Baughman, Kai Wang, Jorge Benitez-Hernandez, Celia Fontanillo
• 2684 Androgen receptor expression negatively correlates with immune infiltration and response to immune checkpoint inhibitors in ER-positive/HER2-negative breast cancer Jun Arima, Kohei Chida, Rongrong Wu, Takafumi Shima, Toru Kuramoto, Hiroki Hamamoto, Kohei Taniguchi, Nao Kawaguchi, Ryo Tanaka, Yoshiro Imai, Kosei Kimura, Mitsuhiko Iwamoto, Kenichi Hakamada, Takashi Ishikawa, Sang-Woong Lee, Kazuaki Takabe
• 2685 · PDF Analysis of long-read sequencing data with vmwhere reveals variation in microsatellite length and chromatin state in Ewing sarcoma Sara K. Peterson, A. McCauley Massie, Alex Rubinsteyn, Jeremy R. Wang, Ian J. Davis
• 2686 Extraction of cellular networks and microenvironmental characteristics in liver cancer tissues using geospatial approaches for therapeutic and diagnostic potential Kanae Echizen, Yoshiki Nonaka, Tomonori Kamiya, Maho Tsuda, Yoshimi Yukawa-Muto, Hideki Fujii, Kenichi Kohashi, Ryo Takahashi, Takahiro Kodama, Naoko Ohtani
• 2687 · PDF First single slide spatially resolved multiomic integration of pancreatic cancer: High-plex proteomic and whole transcriptome analysis Mari-Claire McGuigan, Luke McNickle, Assya Legrini, Ghazal Latifi, Claire Kennedy-Dietrich, Hannah Morgan, Olivia McCabe, Fraser Duthie, Tengyu Zhang, Michail Doukas, Andrea Gonzelz Cisar, Yoana Doncheva, Josefina Martinez Vasquez, Yi Cui, Sanghamithra korukonda, Ashley Heck, Kim Young, Joanne Edwards, Joseph Beechem, Nigel Jamieson
• 2688 · PDF A unified prostate cancer single-cell atlas reveals molecular subtypes and lineage plasticity across disease progression Hanbyul Cho, Yuping Zhang, Jiayi Zhou, Rahul Mannan, Saravana M. Dhanasekaran, Xuhong Cao, Arul M. Chinnaiyan
• 2689 · PDF Single-cell multiome sequencing reveals distinct transcriptional programs associated with ecDNA amplifications in medulloblastoma Hui Hui, Yan Yuen Lo, Jessica Wang, Rishaan Kenkre, Jon D. Larson, Sunita Sridhar, Owen Chapman, Lukas Chavez
• 2690 · PDF Leveraging linked-reads to predict extrachromosomal DNA in advanced prostate cancer Alexander Fortuna, Natalie Fredriksson, Mital Bhakta, Rahul Mannan, Fengyun Su, Rui Wang, Dan Robinson, Yi-Mi Wu, Xuhong Cao, Arul M. Chinnaiyan, Lisa Munding, J. Zachary Sanborn
• 2691 Logic-gated Switch-DARPin-based immune cell engagers guided by data-driven tumor-antigen profiling: A computational workflow for the development of cancer immunotherapies Albulena Toska, Ana Maria Florescu, Eleni Tselempi, Alexander Link, Martin Steegmaier, Marcela Guzman Ayala
• 2692 · PDF EpiGuide: Tracking epigenetic plasticity in circulating tumor DNA to monitor tumor progression Edoardo Giuili, Renske Imschoot, Sam Kint, Maisa Renata Ferro dos Santos, Lotte Cornelli, Jef Haerinck, Joachim Taminau, Kathleen Schoofs, Ruben Van Paemel, Leander Meuris, Sofie Roelandt, Robin Van Belle, Sofie Van de Velde, Eva De Smet, Nicolas Debusschere, Celine Everaert, Geert Berx, Katleen De Preter
• 2693 · PDF Elucidating the role of specific cancer testis antigens in the progression and development of hepatocellular carcinoma Frida Mariana Delgadillo, Barbara Yang, Sabrina Stogoski, Shrikanth S. Gadad, Enrique I. Ramos
• 2694 · PDF Dissecting the mechanisms of drug resistance development post neoadjuvant osimertinib treatment in EGFR-mutant non-small lung cancer Su-Jin Choi, Jii Bum Lee, Hyuk Jee, Hyo Sup Shim, Byung Jo Park, Chang Young Lee, Min Hee Hong, Byoung Chul Cho, Sun Min Lim
• 2695 HELP-TCR: A harmonized and explainable language processing framework for functional analysis of t-cell receptor repertoires Yulyana Kalesnik, Dawid Krawczyk, Maciej Pietrzak, Michal Seweryn
• 2696 · PDF Unlocking novel gene-based biomarkers using an explainable deep learning framework for precision oncology Sydney Grant, Aritro Nath
• 2697 Single-cell transcriptomic characterisation reveals pathway determinants of bipolar androgen therapy response in prostate cancer Rosalia Quezada Urban, Shivakumar Keerthikumar, Peter Lau, Georgia Cuffe, Linda Teng, Ashlee K. Clark, Gail P. Risbridger, Renea A. Taylor, Megan Crumbaker, ANTHONY JOSHUA, Mitchell G. Lawrence
• 2698 · PDF MicroRNA expression can detect canine multicentric lymphoma in golden retrievers in serum samples taken pre-diagnosis Heather Treleaven, Latasha Ludwig, Alicia M. Viloria-Petit, R. Darren Wood, R. Ayesha Ali, Geoffrey Wood
• 2699 · PDF Accumulation of somatic mutation and clonal architecture of fallopian tube epithelium Seoyihl Kim, Wonjune Seo, Soyeon Kim, Taekeun Park, Miso Kim, Bhumsuk Keam, Tae Min Kim, Dong-Wan Kim, Se Ik Kim, Jeonghwan Youk
• 2700 · PDF SpaceMarkers 2.0: A framework for spatially aware cell-cell communication in spatial transcriptomic data Orian Stapleton, Dmitrijs Lvovs, Luciane Tsukamoto Kagohara, Elana Judith Fertig, Atul Deshpande
• 2701 · PDF A transcriptomic framework to predict response and prioritize indications for p53 restoration therapy Hosun Lee, Seunghwan Jung, Boram Kim, Seung-Hyun Shin, Yong Ho Heo, Yu-Yon Kim, Daejin Kim, Haemin Chon, In Young Choi
• 2702 · PDF Integrative Computational Pipeline for Tracking Neoantigen Retention Across PDX Passages in Genitourinary Cancers Md Imran Khan, Tyler Gross, Christian Migliarese, Ian Shea, Jonathan F. Lovell, Roberto Pili
• 2703 · PDF PTMax: An AI-enabled platform integrating literature mining and multi-omics for functional interpretation of phosphorylation in cancer Yanling Sun, Sara S. Savage, John M. Elizarraras, Eric Jaehnig, Bing Zhang
• 2704 · PDF NCI's childhood cancer data initiative: Advancing pediatric cancer research Subhashini Jagu, Jaime Guidry Auvil, Mark Cunningham, Bahar Sayoldin, Patrick Dunn, Sean Burke, Catherine Bullen, Hayley Dingerdissen, Rebecca Steck, Martin Ferguson, Johanna Lucinda Goderre, Gregory Reaman, Warren A. Kibbe

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