Awesome-CancerEvolution

Papers for studying cancer evolution.

No update since 30 Jul 2019. You can check related contents in published paper, Towards multi-omics characterization of tumor heterogeneity: a comprehensive review of statistical and machine learning approaches.

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Clonal evolution and Intratumor heterogeneity.

• 1976-10 | The clonal evolution of tumor cell populations. | PC Nowell | Science.

• 2006-10 | Cancer as an evolutionary and ecological process. | Lauren M.F. Merlo, John W. Pepper, Brian J. Reid & Carlo C. Maley | Nature Reviews Cancer.

• 2008-09 | Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing. | Peter J. Campbell, Erin D. Pleasance, Philip J. Stephens, Ed Dicks, Richard Rance, Ian Goodhead, George A. Follows, Anthony R. Green, P. Andy Futreal, and Michael R. Stratton | Proceedings of the National Academy of Sciences.

• 2011-02 | Cancer tumors as Metazoa 1.0: tapping genes of ancient ancestors. | P. C. W. Davies, C. H. Lineweaver | Physical Biology.

• 2011-04 | Tumour evolution inferred by single-cell sequencing. | Nicholas Navin, Jude Kendall, Jennifer Troge, Peter Andrews, Linda Rodgers, Jeanne McIndoo, Kerry Cook, Asya Stepansky, Dan Levy, Diane Esposito, Lakshmi Muthuswamy, Alex Krasnitz, W. Richard McCombie, James Hicks & Michael Wigler | Nature.

• 2012-01 | Clonal evolution in cancer. | Mel Greaves & Carlo C. Maley | Nature.

• 2012-03 | Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing. | Marco Gerlinger, M.D., Andrew J. Rowan, B.Sc., Stuart Horswell, M.Math., James Larkin, M.D., Ph.D., David Endesfelder, Dip.Math., Eva Gronroos, Ph.D., Pierre Martinez, Ph.D., Nicholas Matthews, B.Sc., Aengus Stewart, M.Sc., Patrick Tarpey, Ph.D., Ignacio Varela, Ph.D., Benjamin Phillimore, B.Sc., Sharmin Begum, M.Sc., Neil Q. McDonald, Ph.D., Adam Butler, B.Sc., David Jones, M.Sc., Keiran Raine, M.Sc., Calli Latimer, B.Sc., Claudio R. Santos, Ph.D., Mahrokh Nohadani, H.N.C., Aron C. Eklund, Ph.D., Bradley Spencer-Dene, Ph.D., Graham Clark, B.Sc., Lisa Pickering, M.D., Ph.D., Gordon Stamp, M.D., Martin Gore, M.D., Ph.D., Zoltan Szallasi, M.D., Julian Downward, Ph.D., P. Andrew Futreal, Ph.D., and Charles Swanton, M.D., Ph.D. | The New England Journal of Medicine.

• 2012-04 | Evolution of the cancer genome. | Yates, Lucy R., and Peter J. Campbell | Nature Reviews Genetics.

• 2013-02 | Variable clonal repopulation dynamics influence chemotherapy response in colorectal cancer. | Antonija Kreso, Catherine A. O'Brien, Peter van Galen, Olga I. Gan, Faiyaz Notta, Andrew M. K. Brown, Karen Ng, Jing Ma, Erno Wienholds, Cyrille Dunant, Aaron Pollett, Steven Gallinger, John McPherson, Charles G. Mullighan, Darryl Shibata, John E. Dick | Science.

• 2013-06 | Evolutionary dynamics of cancer in response to targeted combination therapy. | Ivana Bozic Johannes G Reiter Benjamin Allen Tibor Antal Krishnendu Chatterjee Preya Shah Yo Sup Moon Amin Yaqubie Nicole Kelly Dung T Le Evan J Lipson Paul B Chapman Luis A Diaz Jr Bert Vogelstein Martin A Nowak | eLife.

• 2013-09 | The causes and consequences of genetic heterogeneity in cancer evolution. | Rebecca A. Burrell, Nicholas McGranahan, Jiri Bartek & Charles Swanton | Nature.

• 2013-11 | Punctuated evolution of prostate cancer genomes. | Sylvan C. Baca, Davide Prandi, Michael S. Lawrence, Juan Miguel Mosquera, Alessandro Romanel, Yotam Drier, Kyung Park, Naoki Kitabayashi, Theresa Y. MacDonald, Mahmoud Ghandi, Eliezer Van Allen, Gregory V. Kryukov, Andrea Sboner, Jean-Philippe Theurillat, T. David Soong, Elizabeth Nickerson, Daniel Auclair, Ashutosh Tewari, Himisha Beltran, Robert C. Onofrio, Gunther Boysen, Candace Guiducci, Christopher E. Barbieri, Kristian Cibulskis, Andrey Sivachenko, Scott L. Carter, Gordon Saksena, Douglas Voet, Alex H. Ramos, Wendy Winckler, Michelle Cipicchio, Kristin Ardlie, Philip W. Kantoff, Michael F. Berger, Stacey B. Gabriel, Todd R. Golub, Matthew Meyerson, Eric S. Lander, Olivier Elemento, Gad Getz, Francesca Demichelis, Mark A. Rubin, Levi A. Garraway | Cell.

• 2013-11 | Life history trade-offs in cancer evolution. | C. Athena Aktipis, Amy M. Boddy, Robert A. Gatenby, Joel S. Brown & Carlo C. Maley | Nature Reviews Cancer.

• 2014-02 | Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of genetic and phenotypic cellular diversity. | Vanessa Almendro, Yu-Kang Cheng, Amanda Randles, Shalev Itzkovitz, Andriy Marusyk, Elisabet Ametller, Xavier Gonzalez-Farre, Montse Munoz, Hege G. Russnes, Aslaug Helland, Inga H. Rye, Anne-Lise Borresen-Dale, Reo Maruyama, Alexander van Oudenaarden, Mitchell Dowsett, Robin L. Jones, Jorge Reis-Filho, Pere Gascon, Mithat Gonen, Franziska Michor, Kornelia Polyak | Cell Reports.

• 2014-10 | Non-cell-autonomous driving of tumour growth supports sub-clonal heterogeneity. | Andriy Marusyk, Doris P. Tabassum, Philipp M. Altrock, Vanessa Almendro, Franziska Michor & Kornelia Polyak | Nature.

• 2014-10 | Cancer evolution: mathematical models and computational inference.| Niko Beerenwinkel, Roland F. Schwarz, Moritz Gerstung and Florian Markowetz | Systematic Biology.

• 2015-01 | Biological and Therapeutic Impact of Intratumor Heterogeneity in Cancer Evolution. | Nicholas McGranahan and Charles Swanton | Cancer Cell.

• 2015-02 | A Big Bang model of human colorectal tumor growth. | Andrea Sottoriva, Haeyoun Kang, Zhicheng Ma, Trevor A Graham, Matthew P Salomon, Junsong Zhao, Paul Marjoram, Kimberly Siegmund, Michael F Press, Darryl Shibata & Christina Curtis | Nature Genetics.

• 2015-02 | Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution. | Peter Eirew, Adi Steif, Jaswinder Khattra, Gavin Ha, Damian Yap, Hossein Farahani, Karen Gelmon, Stephen Chia, Colin Mar, Adrian Wan, Emma Laks, Justina Biele, Karey Shumansky, Jamie Rosner, Andrew McPherson, Cydney Nielsen, Andrew J. L. Roth, Calvin Lefebvre, Ali Bashashati, Camila de Souza, Celia Siu, Radhouane Aniba, Jazmine Brimhall, Arusha Oloumi, Tomo Osako, Alejandra Bruna, Jose L. Sandoval, Teresa Algara, Wendy Greenwood, Kaston Leung, Hongwei Cheng, Hui Xue, Yuzhuo Wang, Dong Lin, Andrew J. Mungall, Richard Moore, Yongjun Zhao, Julie Lorette, Long Nguyen, David Huntsman, Connie J. Eaves, Carl Hansen, Marco A. Marra, Carlos Caldas, Sohrab P. Shah & Samuel Aparicio |Nature.

• 2015-04 | Therapy-induced tumour secretomes promote resistance and tumour progression. | Anna C. Obenauf, Yilong Zou, Andrew L. Ji, Sakari Vanharanta, Weiping Shu, Hubing Shi, Xiangju Kong, Marcus C. Bosenberg, Thomas Wiesner, Neal Rosen, Roger S. Lo & Joan Massagué | Nature.

• 2015-06 | Solutions to Peto’s paradox revealed by mathematical modelling and cross-species cancer gene analysis. | Aleah F. Caulin, Trevor A. Graham, Li-San Wang, Carlo C. Maley | Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences.

• 2015-06 | Cancer across the tree of life: cooperation and cheating in multicellularity. | C. Athena Aktipis, Amy M. Boddy, Gunther Jansen, Urszula Hibner, Michael E. Hochberg, Carlo C. Maley, Gerald S. Wilkinson | Philosophical Transactions of the Royal Society of London. Series B, Biological sciences.

• 2015-11 | Extremely high genetic diversity in a single tumor points to prevalence of non-Darwinian cell evolution. | Shaoping Ling, Zheng Hu, Zuyu Yang, Fang Yang, Yawei Li, Pei Lin, Ke Chen, Lili Dong, Lihua Cao, Yong Tao, Lingtong Hao, Qingjian Chen, Qiang Gong, Dafei Wu, Wenjie Li, Wenming Zhao, Xiuyun Tian, Chunyi Hao, Eric A. Hungate, Daniel V. T. Catenacci, Richard R. Hudson, Wen-Hsiung Li, Xuemei Lu, and Chung-I Wu | Proceedings of the National Academy of Sciences.

• 2015-12 | Clock-like mutational processes in human somatic cells. | Ludmil B Alexandrov, Philip H Jones, David C Wedge, Julian E Sale, Peter J Campbell, Serena Nik-Zainal & Michael R Stratton | Nature Genetics.

• 2015-05 | The evolutionary history of lethal metastatic prostate cancer. | Gunes Gundem, Peter Van Loo, Barbara Kremeyer, Ludmil B. Alexandrov, Jose M. C. Tubio, Elli Papaemmanuil, Daniel S. Brewer, Heini M. L. Kallio, Gunilla Högnäs, Matti Annala, Kati Kivinummi, Victoria Goody, Calli Latimer, Sarah O'Meara, Kevin J. Dawson, William Isaacs, Michael R. Emmert-Buck, Matti Nykter, Christopher Foster, Zsofia Kote-Jarai, Douglas Easton, Hayley C. Whitaker, ICGC Prostate UK Group, David E. Neal, Colin S. Cooper, Rosalind A. Eeles, Tapio Visakorpi, Peter J. Campbell, Ultan McDermott, David C. Wedge & G. Steven Bova | Nature.

• 2016-01 | Identification of neutral tumor evolution across cancer types. | Marc J Williams, Benjamin Werner, Chris P Barnes, Trevor A Graham & Andrea Sottoriva | Nature Genetics.

• 2016-01 | Pan-cancer analysis of the extent and consequences of intratumor heterogeneity | Noemi Andor, Trevor A Graham, Marnix Jansen, Li C Xia, C Athena Aktipis, Claudia Petritsch, Hanlee P Ji & Carlo C Maley | Nature Medicine.

• 2016-01 | Pan-cancer analysis of intratumor heterogeneity as a prognostic determinant of survival. | Luc G.T. Morris, Nadeem Riaz, Alexis Desrichard, Yasin Şenbabaoğlu, A. Ari Hakimi, Vladimir Makarov, Jorge S. Reis-Filho and Timothy A. Chan | Oncotarget.

• 2016-03 | Identification of neutral tumor evolution across cancer types. | Marc J Williams, Benjamin Werner, Chris P Barnes, Trevor A Graham & Andrea Sottoriva | Nature Genetics.

• 2016-03 | Exploiting Temporal Collateral Sensitivity in Tumor Clonal Evolution. | Boyang Zhao, Joseph C. Sedlak, Raja Srinivas, Pau Creixell, Justin R. Pritchard, Bruce Tidor, Douglas A. Lauffenburger, Michael T. Hemann | Nature Genetics.

• 2016-03 | Tumor cells can follow distinct evolutionary paths to become resistant to epidermal growth factor receptor inhibition. | Aaron N Hata, Matthew J Niederst, Hannah L Archibald, Maria Gomez-Caraballo, Faria M Siddiqui, Hillary E Mulvey, Yosef E Maruvka, Fei Ji, Hyo-eun C Bhang, Viveksagar Krishnamurthy Radhakrishna, Giulia Siravegna, Haichuan Hu, Sana Raoof, Elizabeth Lockerman, Anuj Kalsy, Dana Lee, Celina L Keating, David A Ruddy, Leah J Damon, Adam S Crystal, Carlotta Costa, Zofia Piotrowska, Alberto Bardelli, Anthony J Iafrate, Ruslan I Sadreyev, Frank Stegmeier, Gad Getz, Lecia V Sequist, Anthony C Faber, Jeffrey A Engelman | Nature Medicine.

• 2016-07 | Clonal evolution of glioblastoma under therapy. | Jiguang Wang, Emanuela Cazzato, Erik Ladewig, Veronique Frattini, Daniel I S Rosenbloom, Sakellarios Zairis, Francesco Abate, Zhaoqi Liu, Oliver Elliott, Yong-Jae Shin, Jin-Ku Lee, In-Hee Lee, Woong-Yang Park, Marica Eoli, Andrew J Blumberg, Anna Lasorella, Do-Hyun Nam, Gaetano Finocchiaro, Antonio Iavarone & Raul Rabadan | Nature Genetics.

• 2016-10 | Natural Selection in Cancer Biology: From Molecular Snowflakes to Trait Hallmarks. | Angelo Fortunato, Amy Boddy, Diego Mallo, Athena Aktipis, Carlo C. Maley and John W. Pepper | Cold Spring Harbor Perspectives in Medicine.

• 2017-01 | Tumor Evolution: Linear, Branching, Neutral or Punctuated?. | Alexander Davis, Ruli Gao, Nicholas Navin | Biochimica et Biophysica Acta (BBA) - Reviews on Cancer.

• 2017-01 | Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer. | Alvin P Makohon-Moore, Ming Zhang, Johannes G Reiter, Ivana Bozic, Benjamin Allen, Deepanjan Kundu, Krishnendu Chatterjee, Fay Wong, Yuchen Jiao, Zachary A Kohutek, Jungeui Hong, Marc Attiyeh, Breanna Javier, Laura D Wood, Ralph H Hruban, Martin A Nowak, Nickolas Papadopoulos, Kenneth W Kinzler, Bert Vogelstein, Christine A Iacobuzio-Donahue | Nature Genetics.

• 2017-02 | Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity. | Kristen M. Turner, Viraj Deshpande, Doruk Beyter, Tomoyuki Koga, Jessica Ruser/, Catherine Lee, Bin Li, Karen Arden, Bing Ren, David A. Nathanson, Harley I. Kornblum, Michael D. Taylor, Sharmeela Kaushal, Webster K. Cavenee, Robert Wechsler-Reya, Frank B. Furnari, Scott R. Vandenberg, P. Nagesh Rao, Geoffrey M. Wahl, Vineet Bafna, Paul S. Mischel | Nature.

• 2017-02 | Clonal Heterogeneity and Tumor Evolution: Past, Present, and the Future. | Nicholas McGranahan, Charles Swanton | Cell.

• 2017-03 | A population genetics perspective on the determinants of intra-tumor heterogeneity. | Zheng Hu, Ruping Sun, Christina Curtis | Biochimica et Biophysica Acta (BBA) - Reviews on Cancer.

• 2017-06 | MicroRNA-Mediated Dynamic Bidirectional Shift between the Subclasses of Glioblastoma Stem-like Cells. | Arun K. Rooj, Franz Ricklefs, Marco Mineo, Ichiro Nakano, E. Antonio Chiocca, Agnieszka Bronisz, Jakub Godlewski | Cell Reports.

• 2017-07 | The role of tumour heterogeneity and clonal cooperativity in metastasis, immune evasion and clinical outcome. | Deborah R. Caswell, Charles Swanton | BMC Medicine.

• 2017-08 | Multiregional Tumor Trees Are Not Phylogenies. | João M.Alves, Tamara Prieto, David Posada | Trends in Cancer.

• 2017-08 | Genomic Evolution of Breast Cancer Metastasis and Relapse. | Yates LR, Knappskog S, Wedge D, Farmery JHR, Gonzalez S, Martincorena I, Alexandrov LB, Van Loo P, Haugland HK, Lilleng PK, Gundem G, Gerstung M, Pappaemmanuil E, Gazinska P, Bhosle SG, Jones D, Raine K, Mudie L, Latimer C, Sawyer E, Desmedt C, Sotiriou C, Stratton MR, Sieuwerts AM, Lynch AG, Martens JW, Richardson AL, Tutt A, Lønning PE, Campbell PJ. | Cancer Cell.

• 2017-08 | Heterogeneous Tumor-Immune Microenvironments among Differentially Growing Metastases in an Ovarian Cancer Patient. | Alejandro Jiménez-Sánchez, Danish Memon, Stephane Pourpe, Harini Veeraraghavan, Yanyun Li, Hebert Alberto Vargas, Michael B. Gill, Kay J. Park, Oliver Zivanovic, Jason Konner, Jacob Ricca, Dmitriy Zamarin, Tyler Walther, Carol Aghajanian, Jedd D. Wolchok, Evis Sala, Taha Merghoub, Alexandra Snyder, Alexandra Snyder, Martin L. Miller | Cell.

• 2017-09 | Biology and evolution of poorly differentiated neuroendocrine tumors. | David S Rickman, Himisha Beltran, Francesca Demichelis & Mark A Rubin | Nature Medicine.

• 2017-10 | Cooperation and cheating as innovation: insights from cellular societies. | Athena Aktipis, Carlo C. Maley | Philosophical Transactions of the Royal Society of London. Series B, Biological sciences.

• 2017-11 | Universal Patterns of Selection in Cancer and Somatic Tissues. | IñigoMartincorena, Keiran M.Raine, MoritzGerstung, Kevin J.Dawson, KerstinHaase, PeterVan Loo, HelenDavies, Michael R.Stratton, Peter J.Campbell | Cell.

• 2017-11 | Comprehensive Analysis of Hypermutation in Human Cancer. | Campbell BB, Light N, Fabrizio D, Zatzman M, Fuligni F, de Borja R, Davidson S, Edwards M, Elvin JA, Hodel KP, Zahurancik WJ, Suo Z, Lipman T, Wimmer K, Kratz CP, Bowers DC, Laetsch TW, Dunn GP, Johanns TM, Grimmer MR, Smirnov IV, Larouche V, Samuel D, Bronsema A, Osborn M, Stearns D, Raman P, Cole KA, Storm PB, Yalon M, Opocher E, Mason G, Thomas GA, Sabel M, George B, Ziegler DS, Lindhorst S, Issai VM, Constantini S, Toledano H, Elhasid R, Farah R, Dvir R, Dirks P, Huang A, Galati MA, Chung J, Ramaswamy V, Irwin MS, Aronson M, Durno C, Taylor MD, Rechavi G, Maris JM, Bouffet E, Hawkins C, Costello JF, Meyn MS, Pursell ZF, Malkin D, Tabori U, Shlien A. | Cell.

• 2017-11 | Between-region genetic divergence reflects the mode and tempo of tumor evolution. | Ruping Sun, Zheng Hu, Andrea Sottoriva, Trevor A Graham, Arbel Harpak, Zhicheng Ma, Jared M Fischer, Darryl Shibata & Christina Curtis | Nature Genetics.

• 2018-04 | Overview on Clinical Relevance of Intra-Tumor Heterogeneity. | Giorgio Stanta, imageSerena Bonin | Frontiers in Medicine.

• 2019-05 | Monogenic and polygenic inheritance become instruments for clonal selection. | Po-Ru Loh, Giulio Genovese, Steven A McCarroll | BioRxiv.

Algorithms for inference clonal structure.

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• 2012-05 | Absolute quantification of somatic DNA alterations in human cancer. | Scott L Carter, Kristian Cibulskis, Elena Helman, Aaron McKenna, Hui Shen, Travis Zack, Peter W Laird, Robert C Onofrio, Wendy Winckler, Barbara A Weir, Rameen Beroukhim, David Pellman, Douglas A Levine, Eric S Lander, Matthew Meyerson & Gad Getz | Nature Biotechnology.

• 2014-01 | EXPANDS: expanding ploidy and allele frequency on nested subpopulations. | Noemi Andor, Julie V. Harness, Sabine Müller, Hans W. Mewes and Claudia Petritsch | Bioinformatics.

• 2014-02 | Inferring clonal evolution of tumors from single nucleotide somatic mutations. | Wei Jiao, Shankar Vembu, Amit G Deshwar, Lincoln Stein and Quaid Morris | BMC Bioinformatics.

• 2014-04 | PyClone: statistical inference of clonal population structure in cancer. | Andrew Roth, Jaswinder Khattra, Damian Yap, Adrian Wan, Emma Laks, Justina Biele, Gavin Ha, Samuel Aparicio, Alexandre Bouchard-Côté & Sohrab P Shah | Nature Methods.

• 2014-07 | TITAN: Inference of copy number architectures in clonal cell populations from tumor whole genome sequence data. | Gavin Ha, Andrew Roth, Jaswinder Khattra, Julie Ho, Damian Yap, Leah M Prentice, Nataliya Melnyk, Andrew McPherson, Ali Bashashati, Emma Laks, Justina Biele, Jiarui Ding, Alan Le, Jamie Rosner, Karey Shumansky, Marco A Marra, C Blake Gilks, David G Huntsman, Jessica N McAlpine, Samuel Aparicio and Sohrab P Shah | Genome research.

• 2014-08 | SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution. | Christopher A. Miller , Brian S. White , Nathan D. Dees, Malachi Griffith, John S. Welch, Obi L. Griffith, Ravi Vij, Michael H. Tomasson, Timothy A. Graubert, Matthew J. Walter, Matthew J. Ellis, William Schierding, John F. DiPersio, Timothy J. Ley, Elaine R. Mardis, Richard K. Wilson, Li Ding | PLoS Computational Biology.

• 2014-10 | Quantifying tumor heterogeneity in whole-genome and whole-exome sequencing data. | Layla Oesper, Gryte Satas and Benjamin J. Raphael | Bioinformatics.

• 2015-02 | PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors. | Amit G Deshwar, Shankar Vembu, Christina K Yung, Gun Ho Jang, Lincoln Stein and Quaid Morris | Genome Biology.

• 2015-02 | BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies. | Ke Yuan, Thomas Sakoparnig, Florian Markowetz, Niko Beerenwinkel | Genome Biology.

• 2016-09 | FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing. | Ronglai Shen and Venkatraman E. Seshan | Nucleic Acids Research.

• 2016-12 | SiFit: A Method for Inferring Tumor Trees from Single-Cell Sequencing Data under Finite-site Models. | Hamim Zafar, Anthony Tzen, Nicholas Navin, Ken Chen, Luay Nakhleh | BioRxiv.

• 2019-03 | Cell composition analysis of bulk genomics using single-cell data. | Amit Frishberg, Naama Peshes-Yaloz, Ofir Cohn, Diana Rosentul, Yael Steuerman, Liran Valadarsky, Gal Yankovitz, Michal Mandelboim, Fuad A. Iraqi, Ido Amit, Lior Mayo, Eran Bacharach, Irit Gat-Viks | Nature Methods

Review in inference methods for reconstructing population of genomic clones

• 2018-07 | Distribution-based measures of tumor heterogeneity are sensitive to mutation calling and lack strong clinical predictive power. | Javad Noorbakhsh, Hyunsoo Kim, Sandeep Namburi, Jeffrey H. Chuang | Scientific Reports.

Algorithms for inference tumor microenvironment.

• 2010-10 | Probabilistic analysis of gene expression measurements from heterogeneous tissues. | Timo Erkkilä, Saara Lehmusvaara, Pekka Ruusuvuori, Tapio Visakorpi, Ilya Shmulevich and Harri Lähdesmäki | Bioinformatics.

• 2011-11 | Population-specific expression analysis (PSEA) reveals molecular changes in diseased brain. | Alexandre Kuhn, Doris Thu, Henry J Waldvogel, Richard L M Faull & Ruth Luthi-Carter | Nature Methods.

• 2013-03 | Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction. | Gerald Quon, Syed Haider, Amit G Deshwar, Ang Cui, Paul C Boutros & Quaid Morris | Genome medicine.

• 2013-04 | A mixture model for expression deconvolution from RNA-seq in heterogeneous tissues. | Yi Li, Xiaohui Xie | BMC bioinformatics.

• 2013-07 | DeMix: deconvolution for mixed cancer transcriptomes using raw measured data. | Jaeil Ahn, Ying Yuan, Giovanni Parmigiani, Milind B. Suraokar, Lixia Diao, Ignacio I. Wistuba and Wenyi Wang | Bioinformatics.

• 2013-10 | Inferring tumour purity and stromal and immune cell admixture from expression data. | Kosuke Yoshihara, Maria Shahmoradgoli, Emmanuel Martínez, Rahulsimham Vegesna, Hoon Kim, Wandaliz Torres-Garcia, Victor Trevin˜o, Hui Shen, Peter W. Laird, Douglas A. Levine, Scott L. Carter, Gad Getz, Katherine Stemke-Hale, Gordon B. Mills & Roel G.W. Verhaak | Nature Communications.

• 2015-01 | UNDO: A Bioconductor R package for unsupervised deconvolution of mixed gene expressions in tumor samples. | Niya Wang, Ting Gong, Robert Clarke, Lulu Chen, Ie-Ming Shih, Zhen Zhang, Douglas A. Levine, Jianhua Xuan1 and Yue Wang | Bioinformatics.

• 2015-03 | Robust enumeration of cell subsets from tissue expression profiles. | Aaron M Newman, Chih Long Liu, Michael R Green, Andrew J Gentles, Weiguo Feng, Yue Xu, Chuong D Hoang, Maximilian Diehn & Ash A Alizadeh | Nature Methods.

• 2016-03 | contamDE: differential expression analysis of RNA-seq data for contaminated tumor samples. | Qi Shen, Jiyuan Hu, Ning Jiang, Xiaohua Hu, Zewei Luo and Hong Zhang | Bioinformatics.

• 2016-12 | Pathway-based dissection of the genomic heterogeneity of cancer hallmarks with SLAPenrich. | Francesco Iorio, Luz Garcia-Alonso, Jonathan Brammeld, Inigo Martincorena, David R Wille, Ultan McDermott, Julio Saez-Rodriguez | BioRxiv.

• 2017-01 | Estimating and accounting for tumor purity in the analysis of DNA methylation data from cancer studies. | Xiaoqi Zheng, Naiqian Zhang, Hua-Jun Wu, Hao Wu | Genome Biology.

• 2019-01 | Bulk tissue cell type deconvolution with multi-subject single-cell expression reference. | Xuran Wang, Jihwan Park, Katalin Susztak, Nancy R. Zhang, Mingyao Li | Nature Communications.

Review in deconvolution method for transcriptome

• 2018-06 | Computational deconvolution of transcriptomics data from mixed cell populations. | Francisco Avila Cobos, Jo Vandesompele, Pieter Mestdagh, Katleen De Preter | Bioinformatics.

• 2019-01 | Comprehensive evaluation of computational cell-type quantification methods for immuno-oncology. | Gregor Sturm, Francesca Finotello, Florent Petitprez, Jitao David Zhang, Jan Baumbach, Wolf H Fridman, Markus List, Tatsiana Aneichyk | BioRxiv.

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