pypi: PyClone | Projects | Ecosyste.ms: Papers

10.1136/jitc-2020-000705

SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery
Cited by: 17
Author(s): Siwen Hu‐Lieskovan, Srabani Bhaumik, Kavita M. Dhodapkar, Jean‐Charles Grivel, Sumati Gupta, Brent A. Hanks, Sylvia Janetzki, Thomas O. Kleen, Yoshinobu Koguchi, Amanda W. Lund, Cristina Maccalli, Yolanda D. Mahnke, Ruslan D. Novosiadly, Senthamil R. Selvan, Tasha N. Sims, Yingdong Zhao, Holden T. Maecker
Software Mentions: 15
Published: about 4 years ago

10.1007/s00401-020-02226-7

Patient-derived organoids and orthotopic xenografts of primary and recurrent gliomas represent relevant patient avatars for precision oncology
Cited by: 69
Author(s): Anna Golebiewska, Ann-Christin Hau, Anaïs Oudin, Daniel Stieber, Yahaya A Yabo, Virginie Baus, Vanessa Barthelemy, Eliane Klein, Sébastien Bougnaud, Olivier Keunen, May Wantz, Alessandro Michelucci, Virginie Neirinckx, Arnaud Muller, Tony Kaoma, Petr V. Nazarov, Francisco Azuaje, Alfonso De Falco, Ben Flies, Lorraine Richart, Suresh Poovathingal, Thaís Arns, Kamil Grzyb, Andreas Möck, Christel Herold‐Mende, Anne Steinø, Dennis Brown, Patrick May, Hrvoje Miletić, Tathiane M. Malta, Houtan Noushmehr, Yong-Jun Kwon, Winnie Jahn, Barbara Klink, Georgette Tanner, Lucy F. Stead, Michel Mittelbronn, Alexander Skupin, Frank Hutter, Rolf Bjerkvig, Simone P. Niclou
Software Mentions: 12
Published: about 4 years ago

10.1016/j.cell.2016.08.041

A Biobank of Breast Cancer Explants with Preserved Intra-tumor Heterogeneity to Screen Anticancer Compounds
Cited by: 359
Author(s): Alejandra Bruna, Oscar M. Rueda, Wendy Greenwood, Ankita Batra, Maurizio Callari, R N Batra, Katherine Pogrebniak, José Luís Sandoval, John W. Cassidy, Ana Tufegdžić Vidaković, Stephen‐John Sammut, Linda Jones, Elena Provenzano, Richard D. Baird, Peter Eirew, James Hadfield, Matthew Eldridge, Anne McLaren-Douglas, Andrew Barthorpe, Howard Lightfoot, Mark J. O’Connor, Joe W. Gray, Javier Cortés, José Baselga, Elisabetta Marangoni, Alana L. Welm, Samuel Aparicio, Violeta Serra, Mathew J. Garnett, Carlos Caldas
Software Mentions: 11
Published: over 8 years ago

10.1371/journal.pcbi.1006596

Whole genomes define concordance of matched primary, xenograft, and organoid models of pancreas cancer
Cited by: 43
Author(s): Deena M.A. Gendoo, Robert E. Denroche, Amy Zhang, Nikolina Radulovich, Gun Ho Jang, Mathieu Lemire, Sandra E. Fischer, Dianne Chadwick, Ilinca M. Lungu, Emin Ibrahimov, Pinjiang Cao, Lincoln Stein, Julie M. Wilson, John M.S. Bartlett, Ming‐Sound Tsao, Neesha C. Dhani, David W. Hedley, Steven Gallinger, Benjamin Haibe‐Kains
Software Mentions: 9
Published: almost 6 years ago

10.1016/j.cell.2021.01.002

Meta-analysis of tumor- and T cell-intrinsic mechanisms of sensitization to checkpoint inhibition
Cited by: 412
Author(s): Kevin Litchfield, James L. Reading, Clare Puttick, Krupa Thakkar, Chris Abbosh, Robert Bentham, Thomas B.K. Watkins, Rachel Rosenthal, Dhruva Biswas, Andrew Rowan, Emilia L. Lim, Maise Al Bakir, Virginia Turati, José Afonso Guerra-Assunção, Lucía Conde, Andrew J.S. Furness, Sunil Kumar Saini, Sine Reker Hadrup, Javier Herrero, Se‐Hoon Lee, Peter Van Loo, Tariq Enver, James Larkin, Matthew D. Hellmann, Samra Turajlic, Sergio A. Quezada, Nicholas McGranahan, Charles Swanton
Software Mentions: 7
Published: almost 4 years ago

10.1186/1471-2105-16-S13-S7

Enhancing cancer clonality analysis with integrative genomics
Cited by: 6
Author(s): Erich A. Peterson, Michael Bauer, Shweta S. Chavan, Cody Ashby, Niels Weinhold, Christoph Heuck, Gareth J. Morgan, Donald J. Johann
Software Mentions: 7
Published: about 9 years ago

10.1002/cam4.2632

Serial ultra‐deep sequencing of circulating tumor DNA reveals the clonal evolution in non‐small cell lung cancer patients treated with anti‐PD1 immunotherapy
Cited by: 27
Author(s): Li Li, Yübo Wang, Weiwei Shi, Mengxiao Zhu, Zhulin Liu, Nuo Luo, Yanwu Zeng, Yong He
Software Mentions: 5
Published: about 5 years ago

10.1016/j.celrep.2019.04.098

The Genomic and Immune Landscapes of Lethal Metastatic Breast Cancer
Cited by: 85
Author(s): Leticia De Mattos-Arruda, Stephen‐John Sammut, Edith Ross, Rachael Bashford-Rogers, Erez Greenstein, Havell Markus, Sandro Morganella, Yvonne H. F. Teng, Yosef E. Maruvka, Bernard Pereira, Oscar M. Rueda, Suet-Feung Chin, Tania Contente-Cuomo, Regina Mayor, Alexandra Arias, H. Raza Ali, Wei Cope, Daniel Guimarães Tiezzi, Aliakbar Dariush, Tauanne Dias Amarante, Dan Reshef, Nikaoly Ciriaco, Elena Martinez-Saez, Vicente Peg, Santiago Ramón y Cajal, Javier Cortés, George S. Vassiliou, Gad Getz, Serena Nik-Zainal, Muhammed Murtaza, Nir Friedman, Florian Markowetz, Joan Seoane, Carlos Caldas
Software Mentions: 5
Published: over 5 years ago

10.1186/s13073-019-0679-x

pTuneos: prioritizing tumor neoantigens from next-generation sequencing data
Cited by: 36
Author(s): Chi Zhou, Zhiting Wei, Zhanbing Zhang, Biyu Zhang, Chenyu Zhu, Ke Chen, Guohui Chuai, Sheng Qu, Lu Xie, Yong Gao, Qi Liu
Software Mentions: 5
Published: about 5 years ago

10.1016/j.cell.2017.07.025

Heterogeneous Tumor-Immune Microenvironments among Differentially Growing Metastases in an Ovarian Cancer Patient
Cited by: 338
Author(s): 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, Martin L. Miller
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pcbi.1003703

Inferring Clonal Composition from Multiple Sections of a Breast Cancer
Cited by: 104
Author(s): Habil Zare, Junfeng Wang, Alex Hu, Kris Weber, Joshua D. Smith, Deborah A. Nickerson, Chang Woo Song, Daniela Witten, C. Anthony Blau, William Stafford Noble
Software Mentions: 5
Published: over 10 years ago

10.1186/s13059-020-02175-0

Multiomics profiling of primary lung cancers and distant metastases reveals immunosuppression as a common characteristic of tumor cells with metastatic plasticity
Cited by: 32
Author(s): Won‐Chul Lee, Alexandre Reuben, Xin Hu, Nicholas McGranahan, Runzhe Chen, Ali Jalali, Marcelo V. Negrão, Shawna M. Hubert, Chad Tang, Chia-Chin Wu, Anthony San Lucas, Whijae Roh, Kenichi Suda, Jihye Kim, Aik-Choon Tan, David H. Peng, Wei Lü, Ximing Tang, Chi-Wan Chow, Junya Fujimoto, Carmen Behrens, Neda Kalhor, Kazutaka Fukumura, Marcus Coyle, Rebecca Thornton, Curtis Gumbs, Jun Li, Chang-Jiun Wu, Latasha Little, Emily Roarty, Xingzhi Song, J. Jack Lee, Erik P. Sulman, Ganesh Rao, Stephen G. Swisher, Lixia Diao, Jing Wang, John V. Heymach, Jason T. Huse, Paul Scheet, Ignacio I. Wistuba, Don L. Gibbons, P. Andrew Futreal, Jianhua Zhang, Daniel R. Gomez, Jianjun Zhang
Software Mentions: 5
Published: about 4 years ago

10.1186/s13059-016-0945-9

Application of single-cell RNA sequencing in optimizing a combinatorial therapeutic strategy in metastatic renal cell carcinoma
Cited by: 163
Author(s): Kyu‐Tae Kim, Hye Won Lee, Hae‐Ock Lee, Hye Jin Song, Da Eun Jeong, Sang Hyun Shin, Hyunho Kim, Yoojin Shin, Do‐Hyun Nam, Byong Chang Jeong, David G. Kirsch, Kyeung Min Joo, Woong-Yang Park
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0224143

Assessing reliability of intra-tumor heterogeneity estimates from single sample whole exome sequencing data
Cited by: 14
Author(s): J. Abecassis, Anne-Sophie Hamy, Cécile Laurent, Benjamin Sadacca, Hélène Bonsang-Kitzis, Fabien Reyal, Jean-Philippe Vert
Software Mentions: 4
Published: about 5 years ago

10.1038/s42003-021-01959-9

Genomic profiling reveals heterogeneous populations of ductal carcinoma in situ of the breast
Cited by: 31
Author(s): Satoi Nagasawa, Yuta Kuze, Ichiro Maeda, Yasuyuki Kojima, Ai Motoyoshi, Tatsuya Onishi, Tsuguo Iwatani, Takamichi Yokoe, Junki Koike, Motohiro Chosokabe, Manabu Kubota, Hibiki Seino, Ayako Suzuki, Masahide Seki, Katsuya Tsuchihara, Eisuke Inoue, Koichiro Tsugawa, Tomohiko Ohta, Yutaka Suzuki
Software Mentions: 4
Published: over 3 years ago

10.1038/s42003-021-02637-6

DEVOLUTION—A method for phylogenetic reconstruction of aneuploid cancers based on multiregional genotyping data
Cited by: 6
Author(s): Natalie Andersson, Subhayan Chattopadhyay, Anders Valind, Jenny Karlsson, David Gisselsson
Software Mentions: 4
Published: about 3 years ago

10.1016/j.cell.2018.03.043

Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal
Cited by: 436
Author(s): Samra Turajlic, Hang Xu, Kevin Litchfield, Andrew Rowan, Stuart Horswell, Tim Chambers, Tim O’Brien, José I. López, Thomas B.K. Watkins, David Nicol, Mark Stares, Ben Challacombe, Steve Hazell, Ashish Chandra, Thomas J. Mitchell, Lewis Au, Claudia Eichler-Jonsson, Faiz Jabbar, Aspasia Soultati, Simon Chowdhury, Sarah Rudman, Joanna Lynch, A. Fernando, Gordon Stamp, Emma Nye, Aengus Stewart, Xing Wei, Jonathan C. Smith, Mickael Escudero, Adam Huffman, Nik Matthews, Greg Elgar, Ben Phillimore, Marta Costa, Sharmin Begum, Sophia Ward, Max Salm, Stefan Boeing, Rosalie Fisher, Lavinia Spain, Carolina Navas, Eva Grönroos, Sebastijan Hobor, Sarkhara Sharma, Ismaeel Aurangzeb, Sharanpreet Lall, Alexander Polson, Mary Varia, Catherine Horsfield, Nicos Fotiadis, Lisa Pickering, Roland F. Schwarz, Bruno Silva, Javier Herrero, Nick M. Luscombe, Mariam Jamal‐Hanjani, Rachel Rosenthal, Nicolai J. Birkbak, Gareth A. Wilson, Orsolya Pipek, Dezső Ribli, Marcin Krzystanek, István Csabai, Zoltan Szállási, Martin Gore, Nicholas McGranahan, Peter Van Loo, Peter J. Campbell, James Larkin, Charles Swanton
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-020-76025-1

Prediction of survival and recurrence in patients with pancreatic cancer by integrating multi-omics data
Cited by: 33
Author(s): Bin Baek, Hyunju Lee
Software Mentions: 4
Published: about 4 years ago

10.18632/oncotarget.24365

New therapeutic targets for pulmonary sarcomatoid carcinomas based on their genomic and phylogenetic profiles
Cited by: 40
Author(s): Takahiro Nakagomi, Taichiro Goto, Yosuke Hirotsu, Daichi Shikata, Yujiro Yokoyama, Rumi Higuchi, Kenji Amemiya, Kenichiro Okimoto, Toshio Oyama, Hitoshi Mochizuki, Masao Omata
Software Mentions: 4
Published: almost 7 years ago

10.1093/bioinformatics/btaa672

A statistical approach for tracking clonal dynamics in cancer using longitudinal next-generation sequencing data
Cited by: 6
Author(s): Dimitrios V Vavoulis, Anthony Cutts, Jenny C. Taylor, Anna Schuh
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-020-59006-2

Power and pitfalls of computational methods for inferring clone phylogenies and mutation orders from bulk sequencing data
Cited by: 19
Author(s): Sayaka Miura, Tracy Vu, Jiamin Deng, Tiffany Buturla, Olumide Oladeinde, Joongdae Choi, Sudhir Kumar
Software Mentions: 4
Published: almost 5 years ago

10.1038/srep37767

Measuring intratumor heterogeneity by network entropy using RNA-seq data
Cited by: 49
Author(s): Youngjun Park, Sangsoo Lim, Jin Wu Nam, Sun Kim
Software Mentions: 4
Published: about 8 years ago

10.1172/jci.insight.150203

Genomic and epigenomic evolution of acquired resistance to combination therapy in esophageal squamous cell carcinoma
Cited by: 6
Author(s): Qingjie Min, Yan Wang, Qingnan Wu, Xianfeng Li, Huajing Teng, Jingyuan Fan, Yiren Cao, Pingsheng Fan, Qimin Zhan
Software Mentions: 4
Published: over 3 years ago

10.1093/gigascience/giab036

MesKit: a tool kit for dissecting cancer evolution of multi-region tumor biopsies through somatic alterations
Cited by: 10
Author(s): Mengni Liu, Jianyu Chen, Xin Wang, Chengwei Wang, Xiaolong Zhang, Yubin Xie, Zhixiang Zuo, Qi Zhao
Software Mentions: 4
Published: over 3 years ago

10.1186/s13073-019-0643-9

Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time
Cited by: 8
Author(s): Paul Little, Danyu Lin, Wei Sun
Software Mentions: 4
Published: over 5 years ago

10.1186/s40425-019-0609-x

Paired whole exome and transcriptome analyses for the Immunogenomic changes during concurrent chemoradiotherapy in esophageal squamous cell carcinoma
Cited by: 22
Author(s): Sehhoon Park, Je‐Gun Joung, Min Ye, Jae‐Yong Nam, Daeun Ryu, Dongryul Oh, Woong-Yang Park, Sehoon Lee, Yoon La Choi, Jin Seok Ahn, Myung‐Ju Ahn, Keunchil Park, Jong‐Mu Sun
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1007603

SuperFreq: Integrated mutation detection and clonal tracking in cancer
Cited by: 34
Author(s): Christoffer Flensburg, Tobias Sargeant, Alicia Oshlack, Ian J. Majewski
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pmed.1002204

The Subclonal Architecture of Metastatic Breast Cancer: Results from a Prospective Community-Based Rapid Autopsy Program “CASCADE”
Cited by: 111
Author(s): Peter Savas, Zhi L. Teo, Christophe Lefèvre, Christoffer Flensburg, Franco Caramia, Kathryn Alsop, Mariam Mansour, Prudence A. Francis, Heather Thorne, Maria João Silva, Nnennaya Kanu, Michelle Dietzen, Andrew Rowan, Maik Kschischo, Stephen B. Fox, David D.L. Bowtell, Sarah-Jane Dawson, Terence P. Speed, Charles Swanton, Sherene Loi
Software Mentions: 4
Published: almost 8 years ago

10.1002/1878-0261.12456

Clinical factors associated with circulating tumor <scp>DNA</scp> (ct <scp>DNA</scp> ) in primary breast cancer
Cited by: 29
Author(s): Yidong Zhou, Yaping Xu, Yuhua Gong, Yanyan Zhang, Yaping Lu, Changjun Wang, Ru Yao, Peng Li, Yanfang Guan, Jiayin Wang, Xuefeng Xia, Ling Yang, Xin Yi, Qiang Sun
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12859-021-04338-7

Conifer: clonal tree inference for tumor heterogeneity with single-cell and bulk sequencing data
Cited by: 1
Author(s): Leila Baghaarabani, Sama Goliaei, Mohammad-Hadi Foroughmand-Araabi, Seyed Peyman Shariatpanahi, Bahram Goliaei
Software Mentions: 3
Published: over 3 years ago

10.1016/j.cell.2017.10.001

Allele-Specific HLA Loss and Immune Escape in Lung Cancer Evolution
Cited by: 848
Author(s): Nicholas McGranahan, Rachel Rosenthal, Crispin Hiley, Andrew Rowan, Thomas B.K. Watkins, Gareth A. Wilson, Nicolai J. Birkbak, Selvaraju Veeriah, Peter Van Loo, Javier Herrero, Charles Swanton, Mariam Jamal‐Hanjani, Seema Shafi, Justyna Czyzewska-Khan, Diana Johnson, Joanne Laycock, Leticia Bosshard‐Carter, Pat Gorman, Robert E. Hynds, Gareth A. Wilson, Stuart Horswell, Richard Mitter, Mickael Escudero, Aengus Stewart, Andrew Rowan, Hang Xu, Samra Turajlic, Crispin Hiley, Christopher Abbosh, Jacki Goldman, Richard Stone, Tamara Denner, Nik Matthews, Greg Elgar, Sophia Ward, Marta Costa, Sharmin Begum, Ben Phillimore, Tim Chambers, Emma Nye, Sofia Graca, Maise Al Bakir, Kroopa Joshi, Andrew Furness, Assma Ben Aissa, Yien Ning Sophia Wong, Andy Georgiou, Sergio A. Quezada, John A. Hartley, Helen Lowe, David Lawrence, Martin Hayward, Νικόλαος Παναγιωτόπουλος, Shyam Kolvekar, Mary Falzon, Elaine Borg, Teresa Marafioti, Celia Simeon, Gemma Hector, Amy M. Smith, Marie Aranda, Marco Novelli, Dahmane Oukrif, Sam M. Janes, Ricky Thakrar, Martin Förster, Tanya Ahmad, Siow Ming Lee, Dionysis Papadatos-Pastos, Dawn Carnell, R. Mendes, Jeremy George, Neal Navani, Asia Ahmed, Magali Taylor, Junaid Choudhary, Yvonne Summers, Raffaele Califano, Paul Taylor, Rajesh Shah, Piotr Krysiak, Kendadai Rammohan, Eustace Fontaine, Richard Booton, Matthew Evison, Philip Crosbie, Stuart B. Moss, Faiza Idries, Leena Dennis Joseph, Paul Bishop, Anshuman Chaturved, Anne Marie Quinn, Helen Doran, Angela Leek, Phil Harrison, Katrina Moore, Rachael Waddington, Juliette Novasio, Fiona Blackhall, Jane Rogan, Elaine Smith, Caroline Dive, Jonathan Tugwood, Ged Brady, Dominic G. Rothwell, Francesca Chemi, Jackie Pierce, Sakshi Gulati, Babu Naidu, Gerald Langman, Simon Trotter, Mary Bellamy, Hollie Bancroft, Amy Kerr, Salma Kadiri, Joanne Webb, Gary Middleton, Madava Djearaman, Dean A. Fennell, Jacqui A. Shaw, John Le Quesne, David A. Moore, Apostolos Nakas, Sridhar Rathinam, William Monteiro, Hilary Marshall, Louise Nelson, Jonathan Bennett, Joan Riley, Lindsay Primrose, Luke Martinson, Girija Anand, Sajid Khan, Anita Amadi, Marianne Nicolson, Keith M. Kerr, Shirley Palmer, Hardy Remmen, J. Richard Miller, Keith Buchan, Mahendran Chetty, Lesley Gomersall, J.F. Lester, Alison L. Edwards, Fiona J. E. Morgan, Haydn Adams, Helen Davies, Malgorzata Kornaszewska, Richard Attanoos, S. Löck, Azmina Verjee, Mairead MacKenzie, Maggie Wilcox, Harriet Bell, Allan Hackshaw, Yenting Ngai, Sean Smith, Nicole Gower, Christian Ottensmeier, Serena Chee, Benjamin Johnson, Aiman Alzetani, Emily Shaw, Eric Lim, Paulo De Sousa, Monica Tavares Barbosa, Alex Bowman, Simon Jordan, Alexandra Rice, Hilgardt Raubenheimer, Chiara Proli, Maria Elena Cufari, John Carlo Ronquillo, Angela Kwayie, Harshil Bhayani, Morag Hamilton, Yusura Bakar, Natalie Mensah, Lyn Ambrose, Anand Devaraj, Silviu Buderi, Jonathan Finch, Leire Azcarate, Hema Chavan, Sophie M. Green, Hillaria Mashinga, Andrew G. Nicholson, Kelvin Lau, Michael Sheaff, Peter Schmid, John Conibear, Veni Ezhil, Babikir Ismail, Melanie Irvin-Sellers, Vineet Prakash, Peter Russell, Teresa Light, Tracey Horey, Sarah Danson, Jonathan Bury, John F. Edwards, Jennifer Hill, Sue Matthews, Yota Kitsanta, Kim Suvarna, Patricia Fisher, Allah Dino Keerio, Michael Shackcloth, John R. Gosney, Pieter E. Postmus, Sarah Feeney, Julius Asante-Siaw, Hugo J.W.L. Aerts, Stefan C. Dentro, Christophe Dessimoz
Software Mentions: 3
Published: about 7 years ago

10.1016/j.cell.2021.03.009

Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes
Cited by: 210
Author(s): Stefan C. Dentro, Ignaty Leshchiner, Kerstin Haase, Maxime Tarabichi, Jeff Wintersinger, Amit G. Deshwar, Kaixian Yu, Yulia Rubanova, Geoff Macintyre, Jonas Demeulemeester, Ignacio Vázquez-García, Kortine Kleinheinz, Dimitri Livitz, Salem Malikić, Nilgun Donmez, Subhajit Sengupta, Pavana Anur, Clemency Jolly, Marek Cmero, Daniel Rosebrock, Steven E. Schumacher, Yu Fan, Matthew Fittall, Ruben M. Drews, Xiaotong Yao, Thomas B.K. Watkins, Ju Hee Lee, Matthias Schlesner, Hongtu Zhu, David J. Adams, Nicholas McGranahan, Charles Swanton, Gad Getz, Paul C. Boutros, Marcin Imieliński, Rameen Beroukhim, S. Cenk Şahinalp, Yuan Ji, Martin Peifer, Iñigo Martincorena, Florian Markowetz, Ville Mustonen, Ke Yuan, Moritz Gerstung, Paul T. Spellman, Wenyi Wang, Quaid Morris, David C. Wedge, Peter Van Loo, Santiago González, David D.L. Bowtell, Peter J. Campbell, Shaolong Cao, Elizabeth L. Christie, Yupeng Cun, Kevin J. Dawson, Roland Eils, Dale W. Garsed, Gavin Ha, Lara Jerman, Henry Lee-Six, Thomas J. Mitchell, Layla Oesper, Myron Peto, Benjamin J. Raphael, Adriana Salcedo, Ruian Shi, Seung Jun Shin, Lincoln Stein, Oliver Spiro, Shankar Vembu, David A. Wheeler, Tsun-Po Yang
Software Mentions: 3
Published: over 3 years ago

10.1038/s42003-021-01973-x

Genomic landscape of extraordinary responses in metastatic breast cancer
Cited by: 2
Author(s): Sun Min Lim, Eun Young Kim, Kyung Hae Jung, Sora Kim, Ja Seung Koo, Kyung Sik Kim, Seho Park, Hyung Seok Park, Byoung Woo Park, Young Up Cho, Jee Ye Kim, Soonmyung Paik, Nak‐Jung Kwon, Gun Min Kim, Ji Hyoung Kim, Min Hwan Kim, Min Hyok Jeon, Sang Woo Kim, Joohyuk Sohn
Software Mentions: 3
Published: over 3 years ago

10.1186/s13059-015-0592-6

BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies
Cited by: 110
Author(s): Ke Yuan, Thomas Sakoparnig, Florian Markowetz, Niko Beerenwinkel
Software Mentions: 3
Published: almost 10 years ago

10.1038/s41392-020-00448-5

Personalized neoantigen pulsed dendritic cell vaccine for advanced lung cancer
Cited by: 94
Author(s): Zhenyu Ding, Qing Li, Rui Zhang, Li Xie, Yang Shu, Song Gao, Peipei Wang, Xianwei Su, Yun Qin, Yuelan Wang, Jun Fang, Zhongzheng Zhu, Xuyang Xia, Guochao Wei, Hui Wang, Hong Qian, Xianling Guo, Zhibo Gao, Yu Wang, Yuquan Wei, Qing Xu, Hong‐Xi Xu, Li Yang
Software Mentions: 3
Published: almost 4 years ago

10.1002/path.4230

Distinct evolutionary trajectories of primary high‐grade serous ovarian cancers revealed through spatial mutational profiling
Cited by: 351
Author(s): Ali Bashashati, Gavin Ha, Alicia A. Tone, Jiarui Ding, Leah M Prentice, Andrew Roth, Jamie Rosner, Karey Shumansky, Steve E. Kalloger, Janine Senz, Winnie Yang, Melissa K. McConechy, Nataliya Melnyk, Michael S. Anglesio, Margaret Luk, Kane Tse, Thomas Zeng, Richard A. Moore, Yongjun Zhao, Marco A. Marra, Blake Gilks, Stephen Yip, David G. Huntsman, Jessica N. McAlpine, Sohrab P. Shah
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pmed.1002136

Clonal Evolutionary Analysis during HER2 Blockade in HER2-Positive Inflammatory Breast Cancer: A Phase II Open-Label Clinical Trial of Afatinib +/- Vinorelbine
Cited by: 25
Author(s): Gerald Goh, RM Schmid, Kelly Guiver, Wichit Arpornwirat, Imjai Chitapanarux, Vinod Ganju, Seock‐Ah Im, Sung‐Bae Kim, Arunee Dechaphunkul, Jedzada Maneechavakajorn, Neil L. Spector, Thomas Yau, Mehdi Afrit, Slim Ben Ahmed, Stephen Johnston, Neil Gibson, Martina Uttenreuther-Fischer, Javier Herrero, Charles Swanton
Software Mentions: 3
Published: about 8 years ago

10.3389/fmed.2021.620988

Clonal Evolution Dynamics in Primary and Metastatic Lesions of Pancreatic Neuroendocrine Neoplasms
Cited by: 3
Author(s): Zhou Tong, Lin Wang, Weiwei Shi, Yanwu Zeng, Hangyu Zhang, Lulu Liu, Yi Zheng, Chunlei Chen, Weiliang Xia, Weijia Fang, Peng Zhao
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-021-95109-0

Mutational patterns and clonal evolution from diagnosis to relapse in pediatric acute lymphoblastic leukemia
Cited by: 4
Author(s): Shumaila Sayyab, Anders Lundmark, Malin Larsson, Markus Ringnér, Sara Nystedt, Yanara Marincevic-Zuniga, Katja Pokrovskaja Tamm, Jonas Abrahamsson, Linda Fogelstrand, Mats Heyman, Ulrika Norén‐Nyström, Gudmar Lönnerholm, Arja Harila‐Saari, Eva Berglund, Jessica Nordlund, Ann‐Christine Syvänen
Software Mentions: 3
Published: over 3 years ago

10.1186/s13073-021-00958-z

Profiling diverse sequence tandem repeats in colorectal cancer reveals co-occurrence of microsatellite and chromosomal instability involving Chromosome 8
Cited by: 6
Author(s): Giwon Shin, Stephanie Greer, Erik Hopmans, Susan M. Grimes, HoJoon Lee, Liang Zhao, Laura Miotke, Carlos J. Suarez, Alison Almeda, Sigurdís Haraldsdóttir, Hanlee P. Ji
Software Mentions: 3
Published: over 3 years ago

10.1186/s13059-014-0443-x

SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization
Cited by: 58
Author(s): Yi Qiao, Aaron R. Quinlan, Amir A. Jazaeri, Roeland Verhaak, David A. Wheeler, Gábor Marth
Software Mentions: 3
Published: over 10 years ago

10.1038/s41418-019-0384-8

A functional genetic screen defines the AKT-induced senescence signaling network
Cited by: 31
Author(s): Keefe T. Chan, Shaun Blake, Haoran Zhu, Jian Kang, Anna S Trigos, Piyush B. Madhamshettiwar, Jeannine Diesch, Lassi Paavolainen, Péter Horváth, Ross D. Hannan, Amee J. George, Elaine Sanij, Katherine M. Hannan, Kaylene J. Simpson, Richard B. Pearson
Software Mentions: 3
Published: over 5 years ago

10.1002/advs.202101230

<i>IDH</i> Mutation Subgroup Status Associates with Intratumor Heterogeneity and the Tumor Microenvironment in Intrahepatic Cholangiocarcinoma
Cited by: 18
Author(s): Xiao Xiang, Ziyang Liu, Chong Zhang, Li Zhao, Jie Gao, Shun Zhang, Qi Cao, Jinghui Cheng, Hengkang Liu, Dingbao Chen, Cheng Qian, Ning Zhang, Ruidong Xue, Fan Bai, Jinmin Zhu
Software Mentions: 3
Published: over 3 years ago

10.3389/fonc.2021.726034

Activity of Wnt/PCP Regulation Pathway Classifies Patients of Low-Grade Glioma Into Molecularly Distinct Subgroups With Prognostic Difference
Cited by: 1
Author(s): Meng Zhang, Dan Wang, Lan Su, Jingjiao Ma, Sizhen Wang, Meng Cui, Shunming Hong, Bing Guan, Xiaodong Ma
Software Mentions: 2
Published: over 3 years ago

10.18632/aging.202888

Genetic landscape of breast cancer and mutation tracking with circulating tumor DNA in Chinese women
Cited by: 6
Author(s): Yinghao Wang, Lizhi Lin, Linhong Li, Jialiang Wen, Yili Chi, Rutian Hao, Xuanxuan Dai, Yizuo Chen, Du-Ping Huang, Yi-Li Zhou, Jie You, Zhiqiang Ye, Hao Chen, Liping Jin, Danxiang Chen, Fan Yang, Erjie Xia, Xueyan Ma, Fengyu Guo, Yunguang Tong, Min Zheng, Ouchen Wang
Software Mentions: 2
Published: over 3 years ago

10.1186/s13015-019-0155-6

Implications of non-uniqueness in phylogenetic deconvolution of bulk DNA samples of tumors
Cited by: 12
Author(s): Yuanyuan Qi, Dikshant Pradhan, Mohammed El-Kebir
Software Mentions: 2
Published: over 5 years ago

10.1186/s12859-015-0694-x

A simplicial complex-based approach to unmixing tumor progression data
Cited by: 10
Author(s): Theodore Roman, Amir Nayyeri, Brittany Terese Fasy, Russell Schwartz
Software Mentions: 2
Published: over 9 years ago

10.1186/s12885-017-3815-2

Intra-tumor heterogeneity in breast cancer has limited impact on transcriptomic-based molecular profiling
Cited by: 9
Author(s): Govindasamy-Muralidharan Karthik, Mattias Rantalainen, Gustav Stålhammar, John Lövrot, Ikram Ullah, Amjad Alkodsi, Ran Ma, Lena Wedlund, Johan Lindberg, Jan Frisell, Jonas Bergh, Johan Hartman
Software Mentions: 2
Published: about 7 years ago

10.1186/1471-2164-16-S8-S7

Computational methods and resources for the interpretation of genomic variants in cancer
Cited by: 18
Author(s): Rui Tian, Malay Kumar Basu, Emidio Capriotti
Software Mentions: 2
Published: over 9 years ago

10.1186/s12920-018-0457-4

A graph-based algorithm for estimating clonal haplotypes of tumor sample from sequencing data
Cited by: 4
Author(s): Yixuan Wang, Xuanping Zhang, Shuai Ding, Yushui Geng, Jianye Liu, Zhongmeng Zhao, Rong Zhang, Xiao Xiao, Jiayin Wang
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41375-018-0043-y

Genomic profiling reveals spatial intra-tumor heterogeneity in follicular lymphoma
Cited by: 80
Author(s): Shamzah Araf, Jun Wang, Koorosh Korfi, Céline Pangault, Eleni Kotsiou, Ana Río-Machín, T. Rahim, James A. Heward, Andrew Clear, Sameena Iqbal, Jeff Davies, Peter Johnson, Maria Calaminici, Silvia Montoto, Rebecca Auer, Claude Chelala, John G. Gribben, Trevor A. Graham, Thierry Fest, Jude Fitzgibbon, Jessica Okosun
Software Mentions: 2
Published: almost 7 years ago

10.1093/molbev/msz182

NUQA: Estimating Cancer Spatial and Temporal Heterogeneity and Evolution through Alignment-Free Methods
Cited by: 1
Author(s): Aideen C. Roddy, Anna Jurek-Loughrey, José Ivanildo de Souza, Alan Gilmore, Paul G. O’Reilly, Alexey Stupnikov, David González de Castro, Kevin M. Prise, Manuel Salto-Tellez, Darragh G. McArt
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pcbi.1008400

Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine
Cited by: 5
Author(s): Linda K. Sundermann, Jeff Wintersinger, Gunnar Rätsch, Jens Stoye, Quaid Morris
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pcbi.1008240

PhyDOSE: Design of follow-up single-cell sequencing experiments of tumors
Cited by: 2
Author(s): Leah L. Weber, Nuraini Aguse, Nicholas Chia, Mohammed El-Kebir
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pcbi.1007451

Uncovering the subtype-specific temporal order of cancer pathway dysregulation
Cited by: 5
Author(s): Sahand Khakabimamaghani, Dujian Ding, Oliver Snow, Martin Ester
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pcbi.1005815

Automated deconvolution of structured mixtures from heterogeneous tumor genomic data
Cited by: 8
Author(s): Theodore Roman, Lu Xie, Russell Schwartz
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pgen.1006853

Integrative analysis of genomic alterations in triple-negative breast cancer in association with homologous recombination deficiency
Cited by: 35
Author(s): Masahito Kawazu, Shinya Kojima, Toshihide Ueno, Yasushi Totoki, Hiromi Nakamura, Akiko Kunita, Wei Qü, Junichi Yoshimura, Manabu Soda, Takahiko Yasuda, Natsuko Hama, Mihoko Saito‐Adachi, Kazuhito Sato, Shinji Kohsaka, Eirin Sai, Masako Ikemura, Shigeru Yamamoto, Tomoko Ogawa, Masashi Fukayama, Keiichiro Tada, Yasuyuki Seto, Shinichi Morishita, Shoichi Hazama, Tatsuhiro Shibata, Yuichi Yamashita, Hiroyuki Mano
Software Mentions: 2
Published: over 7 years ago

10.1038/s41419-021-03410-7

Genomic profiles and tumor immune microenvironment of primary lung carcinoma and brain oligo-metastasis
Cited by: 13
Author(s): Zhengbo Song, Ling Yang, Zhipeng Zhou, Pansong Li, Wenxian Wang, Guoping Cheng, Rongrong Chen, Lianpeng Chang, Yiping Zhang, Yanfang Guan, Xuefeng Xia, Xin Yi, Rongrong Zhou, Ming Chen
Software Mentions: 2
Published: almost 4 years ago

10.3389/fbioe.2020.01021

GeTallele: A Method for Analysis of DNA and RNA Allele Frequency Distributions
Cited by: 2
Author(s): Piotr Słowiński, Muzi Li, Paula Restrepo, Nawaf Alomran, Liam F. Spurr, C. Ryan Miller, Krasimira Tsaneva-Atanasova, Anélia Horvath
Software Mentions: 2
Published: over 4 years ago

10.3389/fonc.2020.571545

Integration of the Tumor Mutational Burden and Tumor Heterogeneity Identify an Immunological Subtype of Melanoma With Favorable Survival
Cited by: 11
Author(s): Yanmei Gao, Chunhe Yang, Ning He, Guodong Zhao, Jianfei Wang, Yadong Yang
Software Mentions: 2
Published: about 4 years ago

10.1186/s13059-014-0420-4

Biased estimates of clonal evolution and subclonal heterogeneity can arise from PCR duplicates in deep sequencing experiments
Cited by: 24
Author(s): Erin N. Smith, Kristen Jepsen, Mahdieh Khosroheidari, Laura Z. Rassenti, Matteo D’Antonio, Emanuela M. Ghia, Dennis A. Carson, Catriona Jamieson, Thomas J. Kipps, Kelly A. Frazer
Software Mentions: 2
Published: over 10 years ago

10.1186/s13059-014-0453-8

Deciphering intratumor heterogeneity and temporal acquisition of driver events to refine precision medicine
Cited by: 172
Author(s): Crispin Hiley, Elza C. de Bruin, Nicholas McGranahan, Charles Swanton
Software Mentions: 2
Published: over 10 years ago

10.1186/s13059-015-0620-6

Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy
Cited by: 401
Author(s): Mihaela Angelova, Pornpimol Charoentong, Hubert Hackl, M. Fischer, René Snajder, Anne Krogsdam, Maximilian J. Waldner, Gabriela Bindea, Bernhard Mlecnik, Jérôme Galon, Zlatko Trajanoski
Software Mentions: 2
Published: over 9 years ago

10.1186/s13059-017-1169-3

ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data
Cited by: 52
Author(s): Sohrab Salehi, Adi Steif, Andrew Roth, Samuel Aparicio, Alexandre Bouchard‐Côté
Software Mentions: 2
Published: almost 8 years ago

10.1186/s13073-021-00895-x

Modeling clonal structure over narrow time frames via circulating tumor DNA in metastatic breast cancer
Cited by: 7
Author(s): Zachary Weber, Katharine A. Collier, David Tallman, Juliet Forman, Sachet A. Shukla, Sarah Asad, Justin Rhoades, Samuel S. Freeman, Heather A. Parsons, Nicole Williams, Romualdo Barroso‐Sousa, Elizabeth H. Stover, Haider Mahdi, Carrie Cibulskis, Niall J. Lennon, Gavin Ha, Viktor A. Adalsteinsson, Sara M. Tolaney, Daniel G. Stover
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-017-13338-8

Engineered in-vitro cell line mixtures and robust evaluation of computational methods for clonal decomposition and longitudinal dynamics in cancer
Cited by: 4
Author(s): Hossein Farahani, Camila P. E. de Souza, Raewyn Billings, Damian Yap, Karey Shumansky, Adrian Wan, Daniel Lai, Anne-Marie Mes-Masson, Samuel Aparicio, Sohrab P. Shah
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-018-37389-7

Clonal dynamics monitoring during clinical evolution in chronic lymphocytic leukaemia
Cited by: 8
Author(s): Julia González-Rincón, Sagrario Gómez, Nerea Martinez, Kevin Troulé, Javier Perales-Patón, Sophia Derdak, Sergi Beltrán, Belén Fernández-Cuevas, Nuria Pérez-Sanz, Sara Nova-Gurumeta, Marta Gut, Fátima Al‐Shahrour, Miguel Á. Piris, José A. García-Marco, Margarita Sánchez‐Beato
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0208002

TargetClone: A multi-sample approach for reconstructing subclonal evolution of tumors
Cited by: 6
Author(s): Marleen M. Nieboer, Lambert C. J. Dorssers, Roy Straver, Leendert H. J. Looijenga, Jeroen de Ridder
Software Mentions: 1
Published: about 6 years ago

10.3389/fonc.2021.657483

Circulating Tumor DNA Analyses Predict Disease Recurrence in Non-Muscle-Invasive Bladder Cancer
Cited by: 8
Author(s): Jinghua Zhang, Daofeng Dai, Junqiang Tian, Lifeng Li, Jing Bai, Yaping Xu, Zhiping Wang, Aifa Tang
Software Mentions: 1
Published: over 3 years ago

10.1136/jitc-2019-000367

Efficacy and biomarker analysis of nivolumab plus gemcitabine and cisplatin in patients with unresectable or metastatic biliary tract cancers: results from a phase II study
Cited by: 68
Author(s): Kang Feng, Yang Liu, Yongtian Zhao, Qingming Yang, Liang Dong, Jiejie Liu, Xiang Li, Zhikun Zhao, Qian Mei, Weidong Han
Software Mentions: 1
Published: over 4 years ago

10.3389/fonc.2021.732071

Case Report: Systemic Treatment and Serial Genomic Sequencing of Metastatic Prostate Adenocarcinoma Progressing to Small Cell Carcinoma
Cited by: 2
Author(s): Xiaojun Lu, Wenwen Gao, Yu Zhang, Tao Wang, Hongliang Gao, Qing Chen, Xiaolei Shi, Bijun Lian, Wenhui Zhang, Xu Gao, Jing Li
Software Mentions: 1
Published: about 3 years ago

10.3389/fonc.2020.00729

Co-Occurring Alterations of ERBB2 Exon 20 Insertion in Non-Small Cell Lung Cancer (NSCLC) and the Potential Indicator of Response to Afatinib
Cited by: 9
Author(s): Bo Yuan, Jun Zhao, Chengzhi Zhou, Xiumei Wang, Bo Zhu, Minglei Zhuo, Xia Dong, Jian Feng, Cuihua Yi, Yunpeng Yang, Hua Zhang, Wangyan Zhou, Zhengtang Chen, Sheng Yang, Xinghao Ai, Kehe Chen, Xuefan Cui, Di-fa Liu, Shi Chen, Wei Wu, Yanjun Zhang, Lianpeng Chang, Jin Li, Rongrong Chen, Shuanying Yang
Software Mentions: 1
Published: over 4 years ago

10.3389/fonc.2021.634920

Durable Response to the Combination of Atezolizumab With Platinum-Based Chemotherapy in an Untreated Non-Smoking Lung Adenocarcinoma Patient With BRAF V600E Mutation: A Case Report
Cited by: 5
Author(s): Xiaomin Niu, Yingjia Sun, David Planchard, Luting Chiu, Jian Bai, Xinghao Ai, Shun Lü
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0223520

SpliceHetero: An information theoretic approach for measuring spliceomic intratumor heterogeneity from bulk tumor RNA-seq
Cited by: 10
Author(s): Minsu Kim, Sangseon Lee, Sangsoo Lim
Software Mentions: 1
Published: about 5 years ago

10.1007/s10911-020-09470-3

Methodological Advancements for Investigating Intra-tumoral Heterogeneity in Breast Cancer at the Bench and Bedside
Cited by: 5
Author(s): Mokryun Baek, Jeffrey T. Chang, Gloria V. Echeverria
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pone.0219682

Assessment of intratumoral heterogeneity with mutations and gene expression profiles
Cited by: 9
Author(s): Ji‐Yong Sung, Hyun-Tae Shin, Kyung-Ah Sohn, Soo-Yong Shin, Woong-Yang Park, Je‐Gun Joung
Software Mentions: 1
Published: over 5 years ago

10.1186/s13059-014-0473-4

A general framework for analyzing tumor subclonality using SNP array and DNA sequencing data
Cited by: 68
Author(s): Bo Li, Jun Z. Li
Software Mentions: 1
Published: over 10 years ago

10.1186/s13059-014-0470-7

Deciphering clonality in aneuploid breast tumors using SNP array and sequencing data
Cited by: 10
Author(s): Ingrid Im Lönnstedt, Franco Caramia, Jason J Li, Debora Fumagalli, Roberto Salgado, Andrew Rowan, Max Salm, Nnennaya Kanu, Peter Savas, Stuart Horswell, Stephan Gade, Sibylle Loibl, Patrick Neven, Christos Sotiriou, Charles Swanton, Sherene Loi, Terence P. Speed
Software Mentions: 1
Published: over 10 years ago

10.18632/oncotarget.7067

Pan-cancer analysis of intratumor heterogeneity as a prognostic determinant of survival
Cited by: 220
Author(s): Luc G.T. Morris, Nadeem Riaz, Alexis Desrichard, Yasin Şenbabaoğlu, A. Ari Hakimi, Vladimir Makarov, Jorge S. Reis‐Filho, Timothy A. Chan
Software Mentions: 1
Published: almost 9 years ago

10.1186/s13059-015-0602-8

PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors
Cited by: 351
Author(s): Amit G. Deshwar, Shankar Vembu, Christina K. Yung, Gun Ho Jang, Lincoln Stein, Quaid Morris
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pmed.1002197

Histological Transformation and Progression in Follicular Lymphoma: A Clonal Evolution Study
Cited by: 171
Author(s): Robert Kridel, Fong Chun Chan, Anja Mottok, Merrill Boyle, Pedro Farinha, King Tan, Barbara Meissner, Ali Bashashati, Andrew McPherson, Andrew Roth, Karey Shumansky, Damian Yap, Susana Ben-Neriah, Jamie Rosner, Maia A. Smith, Cydney B. Nielsen, Eva Giné, Adèle Telenius, Daisuke Ennishi, Andrew J. Mungall, Richard A. Moore, Ryan D. Morin, Nathalie A. Johnson, Laurie H. Sehn, Thomas Tousseyn, Ahmet Doğan, Joseph M. Connors, David W. Scott, Christian Steidl, Marco A. Marra, Randy D. Gascoyne, Sohrab P. Shah
Software Mentions: 1
Published: about 8 years ago

10.18632/oncotarget.19975

Concurrent somatic mutations in driver genes were significantly correlated with lymph node metastasis and pathological types in solid tumors
Cited by: 6
Author(s): Yanan Cheng, Shaojing Wang, Lei Han, Pengpeng Liu, Hui Li, Xiubao Ren, Jinpu Yu, Xishan Hao
Software Mentions: 1
Published: over 7 years ago

10.1186/s13059-015-0647-8

Fast and scalable inference of multi-sample cancer lineages
Cited by: 182
Author(s): Victoria Popic, Raheleh Salari, Iman Hajirasouliha, Dorna Kashef-Haghighi, Robert B. West, Serafim Batzoglou
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pcbi.1004416

SubClonal Hierarchy Inference from Somatic Mutations: Automatic Reconstruction of Cancer Evolutionary Trees from Multi-region Next Generation Sequencing
Cited by: 63
Author(s): Noushin Niknafs, Violeta Beleva-Guthrie, Daniel Q. Naiman, Rachel Karchin
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2105-15-35

Inferring clonal evolution of tumors from single nucleotide somatic mutations
Cited by: 222
Author(s): Wei Jiao, Shankar Vembu, Amit G. Deshwar, Lincoln Stein, Quaid Morris
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pcbi.1003665

SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution
Cited by: 381
Author(s): Christopher A. Miller, Brian S. White, Nathan D. Dees, Obi L. Griffith, John S. Welch, 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, Ding Li
Software Mentions: 1
Published: over 10 years ago

10.1002/cam4.3905

Comprehensive mutational analysis of background mucosa in patients with Lugol‐voiding lesions
Cited by: 1
Author(s): Naoki Akizue, Kenichiro Okimoto, Makoto Arai, Yosuke Hirotsu, Kenji Amemiya, Hirotaka Oura, Tatsuya Kaneko, Mamoru Tokunaga, Kentaro Ishikawa, Yuki Ohta, Takashi Taida, Keiko Saito, Daisuke Maruoka, Tomoaki Matsumura, Tomoo Nakagawa, Motoi Nishimura, Tetsuhiro Chiba, Kazuhiro Matsushita, Hitoshi Mochizuki, Osamu Yokosuka, Masao Omata, Naoya Kato
Software Mentions: 1
Published: over 3 years ago

10.1002/cam4.950

Touch imprint cytology with massively parallel sequencing (TIC-seq): a simple and rapid method to snapshot genetic alterations in tumors
Cited by: 34
Author(s): Kenji Amemiya, Yosuke Hirotsu, Taichiro Goto, Hiroshi Nakagomi, Hitoshi Mochizuki, Toshio Oyama, Masao Omata
Software Mentions: 1
Published: about 8 years ago

10.1093/annonc/mdx687

Differential binding affinity of mutated peptides for MHC class I is a predictor of survival in advanced lung cancer and melanoma
Cited by: 88
Author(s): Ehsan Ghorani, Rachel Rosenthal, Nicholas McGranahan, James L. Reading, Miranda L. Lynch, Karl S. Peggs, Charles Swanton, Sergio A. Quezada
Software Mentions: 1
Published: almost 7 years ago

10.1002/cam4.3541

Revealing the subtyping of non‐small cell lung cancer based on genomic evolutionary patterns by multi‐region sequencing
Cited by: 0
Author(s): Gaoming Liao, Xin Liang, Yanyan Ping, Yong Zhang, Jianlong Liao, Yihan Wang, Xiaobo Hou, Ze D. Jiang, Dong Xiao, Chaohan Xu, Yun Xiao
Software Mentions: 1
Published: about 4 years ago

10.1186/s13073-021-00963-2

The genomic architecture of EBV and infected gastric tissue from precursor lesions to carcinoma
Cited by: 7
Author(s): Zhang-Hua Chen, Shumei Yan, Xi-Xi Chen, Qi Zhang, Shangxin Liu, Yang Liu, Yiling Luo, Chao Zhang, Miao Xu, Yifan Zhao, Liyun Huang, Bin‐Liu Liu, Tian-Liang Xia, Dazhi Xu, Yao Liang, Yongming Chen, Wei Wang, Shuqiang Yuan, Huizhong Zhang, Jing‐Ping Yun, Weiwei Zhai, Mu‐Sheng Zeng, Fan Bai, Qian Zhong
Software Mentions: 1
Published: over 3 years ago

10.1186/s12935-020-01373-x

Genomic profiling of colorectal cancer with isolated lung metastasis
Cited by: 6
Author(s): Nan Zhang, Jiabo Di, Zaozao Wang, Pin Gao, Beihai Jiang, Xiangqian Su
Software Mentions: 1
Published: over 4 years ago

10.1186/bcr3658

Breast cancer intra-tumor heterogeneity
Cited by: 253
Author(s): Luciano G. Martelotto, Charlotte K.Y. Ng, Salvatore Piscuoglio, Britta Weigelt, Jorge S. Reis‐Filho
Software Mentions: 1
Published: over 10 years ago

10.1200/PO.20.00337

Loss of <i>SNAI2</i> in Prostate Cancer Correlates With Clinical Response to Androgen Deprivation Therapy
Cited by: 6
Author(s): Marek Cmero, Natalie Kurganovs, Ryan Stuchbery, Patrick McCoy, Corrina Grima, A. Ngyuen, Ken Chow, Stefano Mangiola, Geoff Macintyre, Nicholas Howard, Michael Kerger, Philip Dundee, Paul Ruljancich, David Clarke, Jeremy Grummet, Justin Peters, Anthony J. Costello, Sam Norden, Andrew Ryan, Phillip Parente, Christopher M. Hovens, Niall M. Corcoran
Software Mentions: 1
Published: about 3 years ago

10.1111/jcmm.14565

Co‐mutational assessment of circulating tumour DNA (ctDNA) during osimertinib treatment for T790M mutant lung cancer
Cited by: 11
Author(s): Puyuan Xing, Xiaohong Han, Sha Wang, Yutao Liu, Sheng Yang, Xuezhi Hao, Yan Wang, Peng Liu, Junling Li, Lin Wang, Lianpeng Chang, Yanfang Guan, Zhishang Zhang, Di Wu, Jiarui Yao, Xin Yi, Yuankai Shi
Software Mentions: 1
Published: over 5 years ago

10.1038/s41416-020-0933-4

Examining treatment responses of diagnostic marrow in murine xenografts to predict relapse in children with acute lymphoblastic leukaemia
Cited by: 1
Author(s): Abdulmohsen M. Alruwetei, Katerina Bendak, Babasaheb D. Yadav, Hernán Carol, Kathryn Evans, Chelsea Mayoh, Rosemary Sutton, Glenn M. Marshall, Richard B. Lock
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-017-12888-1

Signatures of positive selection reveal a universal role of chromatin modifiers as cancer driver genes
Cited by: 17
Author(s): Luís Zapata, Hana Sušak, Oliver Drechsel, Marc R. Friedländer, Xavier Estivill, Stephan Ossowski
Software Mentions: 1
Published: about 7 years ago

10.1002/path.5040

Mixed ductal‐lobular carcinomas: evidence for progression from ductal to lobular morphology
Cited by: 28
Author(s): Amy E. McCart Reed, Jamie R. Kutasovic, Kátia Nones, Jodi M. Saunus, Leonard Da Silva, Felicity Newell, Stephen H. Kazakoff, Lewis Melville, Janani Jayanthan, Ana Cristina Vargas, Lynne Reid, Jonathan Beesley, Xiao Qing Chen, Anne-Marie Patch, David Clouston, Alan Porter, Elizabeth Evans, John V. Pearson, Georgia Chenevix-Trench, Margaret C. Cummings, Nicola Waddell, Sunil R. Lakhani, Peter T. Simpson
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-018-29154-7

Distribution-based measures of tumor heterogeneity are sensitive to mutation calling and lack strong clinical predictive power
Cited by: 17
Author(s): Javad Noorbakhsh, Hyunsoo Kim, Sandeep Namburi, Jeffrey H. Chuang
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-018-36184-8

High-resolution deconstruction of evolution induced by chemotherapy treatments in breast cancer xenografts
Cited by: 14
Author(s): Hyunsoo Kim, Pooja Kumar, Francesca Menghi, Javad Noorbakhsh, Eliza Cerveira, Mallory Ryan, Qihui Zhu, Guruprasad Ananda, Joshy George, Henry C. Chen, Susan M. Mockus, Chengsheng Zhang, Yan Yang, James Keck, R. Krishna Murthy Karuturi, Carol J. Bult, Charles Lee, Edison T. Liu, Jeffrey H. Chuang
Software Mentions: 1
Published: about 6 years ago

Projects: pypi: PyClone

Papers Mentioning PyClone 119