Application of Bioinformatics to Cancer Biology 1

• 39 · PDF Single-cell dissection of ESCC identifies targetable cells-of-origin and therapeutic vulnerabilities in early tumorigenesis Kyung Pil Ko, Jie Zhang, Sohee Jun, Jae-Il Park
• 40 · PDF Integrated transcriptomic and immune-clonal evolution defines stepwise molecular progression in lung adenocarcinoma Kang Qin, An Qin, John V. Heymach
• 41 · PDF Integrative analysis of genomic and transcriptomic data informs precancer progression in the pancreas Kathleen Noller, Jiaying Lai, Daniel Lesperance, Ricky S. Adkins, Ahmed M. Elhossiny, Paola A. Guerrera, Kimal Rajapakshe, Anirban Maitra, Anup Mahurkar, Owen White, Marina Pasca Di Magliano, Michael Ochs, Luciane Tsukamoto Kagohara, Laura Wood, Rachel Karchin, Elana Judith Fertig
• 42 · PDF Engineering antigen-dependent stability in nanobodies: A bioinformatics tool for tuning intracellular nanobody stability Alvin Fu, Rohith Leeladharan, Junhee Park, Shriya Kapila, Liuhan Ke, Amina Mohamed, Cynthia Zhao, Radha Manohar Kapgate, Anh Leith, Jonathan Tang
• 43 · PDF Epigenetic-neurotransmitter crosstalk between EZH2 and dopamine D1 receptor signaling in triple-negative breast cancer Maciej Pietrzak, Xilal Y. Rima, Gautam Sarathy, Shivani Dhekne, Lara Rizotto, Dario Palmieri, Sanjay Gupta, Daniel G. Stover, Giovanni Nigita, Eduardo Reátegui, Pierre Giglio, Christian Rolfo, Eswar Shankar
• 44 · PDF scSubtype2.0: Predictor of breast cancer molecular subtypes at single cell resolution Alexander V. Lobanov, Hani Jieun Kim, Sehrish Kanwal, Kate Harvey, John Reeves, Marcel Batten, Beata Kiedik, Daniel L. Roden, Mun N. Hui, Kym Pham Stewart, Oliver Hofmann, Sandra O’Toole, Elgene Lim, Sean M. Grimmond, Alexander Swarbrick, Charles M. Perou
• 45 · PDF Identification of germline AEN polymorphisms as risk factors in cervical cancer Golya Shahrokhi, Mari Kyllesø Halle, Vinodh Srinivasasaina­gendra, Jianqing Zhang, Aishwarya Sundaresan, Roshan Kumar, Shafiq Shaikh, Nichol He, Camilla Krakstad, Sadeep Shrestha, Paul Auer, Janet Rader, Hemant Tiwari, Akinyemi I. Ojesina
• 46 · PDF High-definition signatures of single-base substitutions in human cancer Jessica N. Au, Marcos Diaz-Gay, Raviteja Vangara, Pilar Gallego-Garcia, Mousumy Kundu, S.M Ashiqul Islam, Maria Zhivagui, Zichen Jiang, Christopher Steele, Sarah Moody, Michael R. Stratton, Paul J. Brennan, Ludmil B. Alexandrov
• 47 · PDF Identifying noncanonical sources of cancer neoepitopes using PEPMatch and CEDAR Daniel Marrama, Ibel Carri, Nina Blazeska, Randi Vita, Hannah K. Carter, Morten Nielsen, Alessandro Sette, Zeynep Kosaloglu-Yalcin, Bjoern Peters
• 48 · PDF Somatic NFKBIZ v ariant modulates inflammation at single-cell resolution Catherine H. Feng, Andrew R. D'Avino, Anders W. Rasmussen, Dan Landau
• 49 · PDF The PER3-RORB axis defines a tumor-suppressive circadian state associated with improved survival in head and neck squamous cell carcinoma Harold Nathan Tan, Oriol Mirallas, Paul Selvadurai, Michael Wotman, Luana Sousa, Neal Akhave, Khaled Sanber, Renata Ferrarotto, George R. Blumenschein, Maura L. Gillison, Faye M. Johnson, Timothy A. Yap
• 50 · PDF Spatial transcriptomics uncovers patterns of transcriptional reprogramming and immune evasion in small cell lung cancer Emmanuel S. Spanos, Meng Wang, Amin Sabet, Esther Redin, Charles M. Rudin, Joseph Chan
• 51 · PDF RAS(ON) multi-selective inhibition remodels cancer-associated fibroblast subtypes and extracellular matrix in pancreatic cancer Lorenzo Tomassoni, Allison C. Hess, Kevin Munoz Forti, Hun Jin Jeong, Deanna J. Besart, Tanner C. Dalton, Urszula N. Wasko, Carmine F. Palermo, Stephen A. Sastra, Chang H. Lee, Andrea Califano, Simon Schworer, Marie C. Hasselluhn, Kenneth P. Olive
• 52 · PDF Quantifying the selective advantage of copy number amplifications to reveal therapeutic targets in ovarian cancer Meng Liu, Jeff Mandell, Jeffrey Peter Townsend
• 53 · PDF RNA fusions: An untapped source of neoantigens for immune based breast cancer prevention and treatment across all subtypes of breast cancers Anjana Bhardwaj, Chathurani Ranathunge, Shiyanth Thevasagayampillai, Aaranyah Kandasamy, Brandon H. Than, Constance T. Albarracin, Isabelle Bedrosian
• 54 Integrating connectivity mapping resources to prioritize and personalize drug candidates for individual triple negative breast cancer patients Lily D. Taub, Anna Byrd, Daniel J. Clarke, Ido Diamant, Criseyda Martinez, Elisa Port, Hanna Y. Irie, Avi Maayan
• 55 · PDF Differentiation state and immune interaction contribute to drug response in AML Natasha R. A. Black, Dharani Thirumalaisamy, Mira Rajagopalan, Trevor Enright, Melissa Stewart, Evan Lind, Elie A. Traer, Jeffrey W. Tyner, Olga H. Nikolova
• 56 · PDF COSMIC: Advancing the cancer genomics knowledgebase of somatic mutations Madhumita Madhumita, Madiha Ahmed, Joanna Argasinska, David Armstrong, Nidhi Bindal Dhir, Denise Carvalho-Silva, Lucie Chadelle, Patrick Dao, Stephen Duke, Giovanna Fasanella, Muhammad Fouzan, Abishekraj Gnanasambandam, Avirup Guha Neogi, Susan Haller, Bhavana Harsha, Balazs Hetenyi, Leonie Hodges, Steven Jupe, Rachel Lyne, Thomas Maurel, Karen McLaren, Thomas Mutimer, Sumodh Nair, Hanna Najgebauer, Helder Pedro, Sophie Poole, Amaia Sangrador-Vegas, Zoe Sheard, Manpreet Singh Chawla, Michael Starkey, Rebecca Steele, Sari Ward, Ellen Wiedemann, Jennifer Wilding, Siew Yit Yong, Jon Teague
• 57 · PDF Functional pathway analysis reveals discordance between clinical HER2 status and downstream effector activation in breast cancer Salim Arslan, Julian Schmidt, Cher Bass, Foivos Ntelemis, J Carl Barrett, Oscar Maiques, Jakob Nikolas Kather, Pahini Pandya
• 58 · PDF Characterizing tumor-stroma interfaces in chemotherapy-treated ovarian cancer via spatial transcriptomics Po-Yuan Chen, Tyler M. Yasaka, Tzu-Hung Hsiao, Tai-Ming Ko, Yu-Chiao Chiu
• 59 · PDF Mutational signatures in cancer genomes alter short linear protein motifs involved in cellular signaling networks Jigyansa Mishra, Masroor Bayati, Nina Adler, Zoe P. Klein, Kevin C. L. Cheng, Juri Reimand
• 60 · PDF CpGene: a DNA methylation-based biomarker discovery platform Konstantinos Lazaros, Vasiliki Tzelepi, Christopher J. Logothetis, Aristidis G. Vrahatis, Susan (Souzana) Logotheti
• 61 · PDF Defining spatial biomarkers of survival across solid tumors using a pan-cancer proteomics atlas Khoa Huynh, Joaquin Reyna, Bruno Matuck, KEVIN BYRD, Jinze Liu
• 62 · PDF Comprehensive characterization of m 6 A RNA methylation across human cancers Yining Zhao, Ke Chen, Hu Chen, Yizhe Song, Kamalika Mojumdar, Wei Liu, Stephanie H Ting, Ayush Semwal, Hui Shen, Li Ding, Genomic Data Analysis Network, Katherine Hoadley, Han Liang
• 63 · PDF Intratumoral Candida albicans associates with hypoxia and poor outcomes in non small cell lung cancer (NSCLC) Dipankor Chatterjee, Dennis J. Grencewicz, Alexander Loncar, Ruohan Wu, Alex Samouilov, Sylvain Ferrandon, McKenzie Kreamer, Yogita Mehra, Aspen Carson, Rebecca Hoyd, Shiva Jahanbakhshi, Fouad Choueiry, Matthew Anderson, Martin Benej, Dustin Bosch, Jiangjiang (Chris) Zhu, Jinghai Wu, Thèrése Bocklage, Martin McCarter, Ahmad Tarhini, Bodour Salhia, Christopher A. Moskaluk, Gregory Riedlinger, Song Yao, Ashiq Masood, Sheetal Hardikar, Mmadili N. Ilozumba, Cornelia M. Ulrich, Abdul Rafeh Naqash, Carlos H.F. Chan, Craig D. Shriver, Dinesh Pal Mudaranthakam, Aaditya Pallerla, Michelle Churchman, Robert J. Rounbehler, Laura Chambers, Matthew F. Kalady, Nicholas C. Denko, David P. Carbone, Dan Spakowicz
• 64 · PDF Mechanisms of resistance to CDK4/6 inhibitors: Insights from single-cell nucleus sequencing and spatial transcriptomics Seung-eun Bang, EunChae Kim, Won-Ji Ryu, Hyein Jung, Yoonjin Cha, Joohyuk Sohn, Gun Min Kim, Kyoo Hyun Kim, Byungjin Hwang, Min Hwan Kim
• 65 Integrating spatial transcriptomics and digital pathology with whole-genome data from Genomics England to characterise the tumour and it's microenvironment in colorectal cancer Luke McNickle, Assya Legrini, Yoana Doncheva, Mari-Claire McGuigan, Ghazal Latifi, Claire Kennedy Dietrich, Molly McKenzie, Phimmada Hatthakarnkul, Tom Wright, Leonor Patricia Schubert Santana, Emma McCargow, Cong Chen, Henry M. Wood, Jon Laye, Gemma Hemmings, Caroline Cartlidge, Derek Magee, Phil Quirke, Joanne Edwards, Nigel Jamieson
• 66 · PDF Gene co-amplification and structural patterns reveal principles of extrachromosomal DNA in cancer Jens Luebeck, Ted Liefeld, Edwin Huang, Forrest Kim, Bhargavi Dameracharla, Michael A. Chan, Dhruv Khatri, Kyra Fetter, Kaiyuan Zhu, Thorin Tabor, Soyeon Kim, Hoon Kim, Roel Verhaak, Michael M. Reich, Paul S. Mischel, Jill P. Mesirov, Vineet Bafna
• 67 · PDF Validation of a gene pair-based machine learning model for treatment prioritization in breast cancer Rishi Nair, Nicholas R. Mistry, Roy Khalife, Anthony M. Magliocco
• 68 YAP-TEAD-dependent VASP expression increases cell stiffness and migration in TNBC cells under high extracellular glucose conditions Wonkyung Lee, Seeun Oh, Tae-Hyung Kim

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