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Addendum: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

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  1. Sandor Spisak & David Chen & Pornlada Likasitwatanakul & Paul Doan & Zhixin Li & Pratyusha Bala & Laura Vizkeleti & Viktoria Tisza & Pushpamali Silva & Marios Giannakis & Brian Wolpin & Jun Qi & Nilay, 2024. "Identifying regulators of aberrant stem cell and differentiation activity in colorectal cancer using a dual endogenous reporter system," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
  2. Kosuke Yamaguchi & Xiaoying Chen & Brianna Rodgers & Fumihito Miura & Pavel Bashtrykov & Frédéric Bonhomme & Catalina Salinas-Luypaert & Deis Haxholli & Nicole Gutekunst & Bihter Özdemir Aygenli & Lau, 2024. "Non-canonical functions of UHRF1 maintain DNA methylation homeostasis in cancer cells," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
  3. Sumana Srivatsa & Hesam Montazeri & Gaia Bianco & Mairene Coto-Llerena & Mattia Marinucci & Charlotte K. Y. Ng & Salvatore Piscuoglio & Niko Beerenwinkel, 2022. "Discovery of synthetic lethal interactions from large-scale pan-cancer perturbation screens," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
  4. Omar Alhalabi & Jianfeng Chen & Yuxue Zhang & Yang Lu & Qi Wang & Sumankalai Ramachandran & Rebecca Slack Tidwell & Guangchun Han & Xinmiao Yan & Jieru Meng & Ruiping Wang & Anh G. Hoang & Wei-Lien Wa, 2022. "MTAP deficiency creates an exploitable target for antifolate therapy in 9p21-loss cancers," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
  5. G. Gambardella & G. Viscido & B. Tumaini & A. Isacchi & R. Bosotti & D. di Bernardo, 2022. "A single-cell analysis of breast cancer cell lines to study tumour heterogeneity and drug response," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
  6. Adrià Fernández-Torras & Miquel Duran-Frigola & Martino Bertoni & Martina Locatelli & Patrick Aloy, 2022. "Integrating and formatting biomedical data as pre-calculated knowledge graph embeddings in the Bioteque," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
  7. Seungyeul Yoo & Abhilasha Sinha & Dawei Yang & Nasser K. Altorki & Radhika Tandon & Wenhui Wang & Deebly Chavez & Eunjee Lee & Ayushi S. Patel & Takashi Sato & Ranran Kong & Bisen Ding & Eric E. Schad, 2022. "Integrative network analysis of early-stage lung adenocarcinoma identifies aurora kinase inhibition as interceptor of invasion and progression," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
  8. Tanaz Sharifnia & Mathias J. Wawer & Amy Goodale & Yenarae Lee & Mariya Kazachkova & Joshua M. Dempster & Sandrine Muller & Joan Levy & Daniel M. Freed & Josh Sommer & Jérémie Kalfon & Francisca Vazqu, 2023. "Mapping the landscape of genetic dependencies in chordoma," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
  9. George Rosenberger & Wenxue Li & Mikko Turunen & Jing He & Prem S. Subramaniam & Sergey Pampou & Aaron T. Griffin & Charles Karan & Patrick Kerwin & Diana Murray & Barry Honig & Yansheng Liu & Andrea , 2024. "Network-based elucidation of colon cancer drug resistance mechanisms by phosphoproteomic time-series analysis," Nature Communications, Nature, vol. 15(1), pages 1-27, December.
  10. Hao Wang & R. Alejandro Sica & Gurbakhash Kaur & Phillip M. Galbo & Zhixin Jing & Christopher D. Nishimura & Xiaoxin Ren & Ankit Tanwar & Bijan Etemad-Gilbertson & Britta Will & Deyou Zheng & David Fo, 2024. "TMIGD2 is an orchestrator and therapeutic target on human acute myeloid leukemia stem cells," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
  11. Jurica Levatić & Marina Salvadores & Francisco Fuster-Tormo & Fran Supek, 2022. "Mutational signatures are markers of drug sensitivity of cancer cells," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
  12. Cemal Erdem & Sean M. Gross & Laura M. Heiser & Marc R. Birtwistle, 2023. "MOBILE pipeline enables identification of context-specific networks and regulatory mechanisms," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
  13. Ozge Saatci & Metin Cetin & Meral Uner & Unal Metin Tokat & Ioulia Chatzistamou & Pelin Gulizar Ersan & Elodie Montaudon & Aytekin Akyol & Sercan Aksoy & Aysegul Uner & Elisabetta Marangoni & Mathew S, 2023. "Toxic PARP trapping upon cAMP-induced DNA damage reinstates the efficacy of endocrine therapy and CDK4/6 inhibitors in treatment-refractory ER+ breast cancer," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
  14. Philip East & Gavin P. Kelly & Dhruva Biswas & Michela Marani & David C. Hancock & Todd Creasy & Kris Sachsenmeier & Charles Swanton & Julian Downward & Sophie de Carné Trécesson, 2022. "RAS oncogenic activity predicts response to chemotherapy and outcome in lung adenocarcinoma," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
  15. Park, Seyoung & Kim, Hyunjin & Lee, Eun Ryung, 2023. "Regional quantile regression for multiple responses," Computational Statistics & Data Analysis, Elsevier, vol. 188(C).
  16. Yan Li & Chen Xu & Bing Wang & Fujiang Xu & Fahan Ma & Yuanyuan Qu & Dongxian Jiang & Kai Li & Jinwen Feng & Sha Tian & Xiaohui Wu & Yunzhi Wang & Yang Liu & Zhaoyu Qin & Yalan Liu & Jing Qin & Qi Son, 2022. "Proteomic characterization of gastric cancer response to chemotherapy and targeted therapy reveals potential therapeutic strategies," Nature Communications, Nature, vol. 13(1), pages 1-26, December.
  17. Guidantonio Malagoli Tagliazucchi & Anna J. Wiecek & Eloise Withnell & Maria Secrier, 2023. "Genomic and microenvironmental heterogeneity shaping epithelial-to-mesenchymal trajectories in cancer," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
  18. Aina Maria Mas & Enrique Goñi & Igor Ruiz de los Mozos & Aida Arcas & Luisa Statello & Jovanna González & Lorea Blázquez & Wei Ting Chelsea Lee & Dipika Gupta & Álvaro Sejas & Shoko Hoshina & Alexandr, 2023. "ORC1 binds to cis-transcribed RNAs for efficient activation of replication origins," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
  19. Liu, Jicai & Si, Yuefeng & Niu, Yong & Zhang, Riquan, 2022. "Projection quantile correlation and its use in high-dimensional grouped variable screening," Computational Statistics & Data Analysis, Elsevier, vol. 167(C).
  20. Ming Tang & Hussein A. Abbas & Marcelo V. Negrao & Maheshwari Ramineni & Xin Hu & Shawna Marie Hubert & Junya Fujimoto & Alexandre Reuben & Susan Varghese & Jianhua Zhang & Jun Li & Chi-Wan Chow & Xiz, 2021. "The histologic phenotype of lung cancers is associated with transcriptomic features rather than genomic characteristics," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
  21. Nicolae Sapoval & Amirali Aghazadeh & Michael G. Nute & Dinler A. Antunes & Advait Balaji & Richard Baraniuk & C. J. Barberan & Ruth Dannenfelser & Chen Dun & Mohammadamin Edrisi & R. A. Leo Elworth &, 2022. "Current progress and open challenges for applying deep learning across the biosciences," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
  22. Kelsy C. Cotto & Yang-Yang Feng & Avinash Ramu & Megan Richters & Sharon L. Freshour & Zachary L. Skidmore & Huiming Xia & Joshua F. McMichael & Jason Kunisaki & Katie M. Campbell & Timothy Hung-Po Ch, 2023. "Integrated analysis of genomic and transcriptomic data for the discovery of splice-associated variants in cancer," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
  23. Mariela Cortés-López & Laura Schulz & Mihaela Enculescu & Claudia Paret & Bea Spiekermann & Mathieu Quesnel-Vallières & Manuel Torres-Diz & Sebastian Unic & Anke Busch & Anna Orekhova & Monika Kuban &, 2022. "High-throughput mutagenesis identifies mutations and RNA-binding proteins controlling CD19 splicing and CART-19 therapy resistance," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
  24. Caterina Bartolacci & Cristina Andreani & Gonçalo Vale & Stefano Berto & Margherita Melegari & Anna Colleen Crouch & Dodge L. Baluya & George Kemble & Kurt Hodges & Jacqueline Starrett & Katerina Poli, 2022. "Targeting de novo lipogenesis and the Lands cycle induces ferroptosis in KRAS-mutant lung cancer," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
  25. Shi, Chengchun & Xu, Tianlin & Bergsma, Wicher & Li, Lexin, 2021. "Double generative adversarial networks for conditional independence testing," LSE Research Online Documents on Economics 112550, London School of Economics and Political Science, LSE Library.
  26. Jun Lu, 2022. "Bayesian Low-Rank Interpolative Decomposition for Complex Datasets," Studies in Engineering and Technology, Redfame publishing, vol. 9(1), pages 112-112, December.
  27. Junyi Chen & Xiaoying Wang & Anjun Ma & Qi-En Wang & Bingqiang Liu & Lang Li & Dong Xu & Qin Ma, 2022. "Deep transfer learning of cancer drug responses by integrating bulk and single-cell RNA-seq data," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
  28. Kerryn Elliott & Vinod Kumar Singh & Martin Boström & Erik Larsson, 2023. "Base-resolution UV footprinting by sequencing reveals distinctive damage signatures for DNA-binding proteins," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
  29. Sanju Sinha & Karina Barbosa & Kuoyuan Cheng & Mark D. M. Leiserson & Prashant Jain & Anagha Deshpande & David M. Wilson & Bríd M. Ryan & Ji Luo & Ze’ev A. Ronai & Joo Sang Lee & Aniruddha J. Deshpand, 2021. "A systematic genome-wide mapping of oncogenic mutation selection during CRISPR-Cas9 genome editing," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
  30. Abdurrahman Elbasir & Ying Ye & Daniel E. Schäffer & Xue Hao & Jayamanna Wickramasinghe & Konstantinos Tsingas & Paul M. Lieberman & Qi Long & Quaid Morris & Rugang Zhang & Alejandro A. Schäffer & Noa, 2023. "A deep learning approach reveals unexplored landscape of viral expression in cancer," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
  31. Qiwei Jiang & Xiaomei Zhang & Xiaoming Dai & Shiyao Han & Xueji Wu & Lei Wang & Wenyi Wei & Ning Zhang & Wei Xie & Jianping Guo, 2022. "S6K1-mediated phosphorylation of PDK1 impairs AKT kinase activity and oncogenic functions," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
  32. Alon Stern & Mariam Fokra & Boris Sarvin & Ahmad Abed Alrahem & Won Dong Lee & Elina Aizenshtein & Nikita Sarvin & Tomer Shlomi, 2023. "Inferring mitochondrial and cytosolic metabolism by coupling isotope tracing and deconvolution," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
  33. Yanli Liu & Zhong Wu & Jin Zhou & Dinesh K. A. Ramadurai & Katelyn L. Mortenson & Estrella Aguilera-Jimenez & Yifei Yan & Xiaojun Yang & Alison M. Taylor & Katherine E. Varley & Jason Gertz & Peter S., 2021. "A predominant enhancer co-amplified with the SOX2 oncogene is necessary and sufficient for its expression in squamous cancer," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
  34. Xiao-Song Wang & Sanghoon Lee & Han Zhang & Gong Tang & Yue Wang, 2022. "An integral genomic signature approach for tailored cancer therapy using genome-wide sequencing data," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
  35. Caitlin E. Mills & Kartik Subramanian & Marc Hafner & Mario Niepel & Luca Gerosa & Mirra Chung & Chiara Victor & Benjamin Gaudio & Clarence Yapp & Ajit J. Nirmal & Nicholas Clark & Peter K. Sorger, 2022. "Multiplexed and reproducible high content screening of live and fixed cells using Dye Drop," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
  36. Min Pan & William C. Wright & Richard H. Chapple & Asif Zubair & Manbir Sandhu & Jake E. Batchelder & Brandt C. Huddle & Jonathan Low & Kaley B. Blankenship & Yingzhe Wang & Brittney Gordon & Payton A, 2021. "The chemotherapeutic CX-5461 primarily targets TOP2B and exhibits selective activity in high-risk neuroblastoma," Nature Communications, Nature, vol. 12(1), pages 1-20, December.
  37. Felix J. Metzner & Simon J. Wenzl & Michael Kugler & Stefan Krebs & Karl-Peter Hopfner & Katja Lammens, 2022. "Mechanistic understanding of human SLFN11," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
  38. Zheqi Li & Olivia McGinn & Yang Wu & Amir Bahreini & Nolan M. Priedigkeit & Kai Ding & Sayali Onkar & Caleb Lampenfeld & Carol A. Sartorius & Lori Miller & Margaret Rosenzweig & Ofir Cohen & Nikhil Wa, 2022. "ESR1 mutant breast cancers show elevated basal cytokeratins and immune activation," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
  39. Julia Joung & Paul C. Kirchgatterer & Ankita Singh & Jang H. Cho & Suchita P. Nety & Rebecca C. Larson & Rhiannon K. Macrae & Rebecca Deasy & Yuen-Yi Tseng & Marcela V. Maus & Feng Zhang, 2022. "CRISPR activation screen identifies BCL-2 proteins and B3GNT2 as drivers of cancer resistance to T cell-mediated cytotoxicity," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
  40. Cemal Erdem & Arnab Mutsuddy & Ethan M. Bensman & William B. Dodd & Michael M. Saint-Antoine & Mehdi Bouhaddou & Robert C. Blake & Sean M. Gross & Laura M. Heiser & F. Alex Feltus & Marc R. Birtwistle, 2022. "A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
  41. Hyeong-Min Lee & William C. Wright & Min Pan & Jonathan Low & Duane Currier & Jie Fang & Shivendra Singh & Stephanie Nance & Ian Delahunty & Yuna Kim & Richard H. Chapple & Yinwen Zhang & Xueying Liu , 2023. "A CRISPR-drug perturbational map for identifying compounds to combine with commonly used chemotherapeutics," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
  42. Atanu Paul & Stefano Annunziato & Bo Lu & Tianliang Sun & Olivera Evrova & Lara Planas-Paz & Vanessa Orsini & Luigi M. Terracciano & Olga Charlat & Zinger Yang Loureiro & Lei Ji & Raffaella Zamponi & , 2022. "Cell adhesion molecule KIRREL1 is a feedback regulator of Hippo signaling recruiting SAV1 to cell-cell contact sites," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
  43. Vincenzo Salemme & Mauro Vedelago & Alessandro Sarcinella & Federico Moietta & Alessio Piccolantonio & Enrico Moiso & Giorgia Centonze & Marta Manco & Andrea Guala & Alessia Lamolinara & Costanza Ange, 2023. "p140Cap inhibits β-Catenin in the breast cancer stem cell compartment instructing a protective anti-tumor immune response," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
  44. Noha A. M. Shendy & Melissa Bikowitz & Logan H. Sigua & Yang Zhang & Audrey Mercier & Yousef Khashana & Stephanie Nance & Qi Liu & Ian M. Delahunty & Sarah Robinson & Vanshita Goel & Matthew G. Rees &, 2024. "Group 3 medulloblastoma transcriptional networks collapse under domain specific EP300/CBP inhibition," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
  45. Guoshu Bi & Jiaqi Liang & Yunyi Bian & Guangyao Shan & Yiwei Huang & Tao Lu & Huan Zhang & Xing Jin & Zhencong Chen & Mengnan Zhao & Hong Fan & Qun Wang & Boyi Gan & Cheng Zhan, 2024. "Polyamine-mediated ferroptosis amplification acts as a targetable vulnerability in cancer," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
  46. Bingzhen Chen & Wenjuan Zhai & Lingchen Kong, 2022. "Variable selection and collinearity processing for multivariate data via row-elastic-net regularization," AStA Advances in Statistical Analysis, Springer;German Statistical Society, vol. 106(1), pages 79-96, March.
  47. Han Jin & Cheng Zhang & Martin Zwahlen & Kalle Feilitzen & Max Karlsson & Mengnan Shi & Meng Yuan & Xiya Song & Xiangyu Li & Hong Yang & Hasan Turkez & Linn Fagerberg & Mathias Uhlén & Adil Mardinoglu, 2023. "Systematic transcriptional analysis of human cell lines for gene expression landscape and tumor representation," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
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  49. Smriti Chawla & Anja Rockstroh & Melanie Lehman & Ellca Ratther & Atishay Jain & Anuneet Anand & Apoorva Gupta & Namrata Bhattacharya & Sarita Poonia & Priyadarshini Rai & Nirjhar Das & Angshul Majumd, 2022. "Gene expression based inference of cancer drug sensitivity," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
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