Vineet Bafna
Active 1990–2025
- 178
- Papers
- 23,646
- Citations
- 77
- h-index
- 157
- i10-index
Citations
Citation sources
Countries
Institutions
Fields
- Biochemistry, Genetics and Molecular Biology58.4%
- Computer Science10.8%
- Medicine9.7%
- Chemistry8.2%
- Immunology and Microbiology3.6%
- Agricultural and Biological Sciences2.6%
- Other6.7%
Topics
- Genomics and Phylogenetic Studies7.5%
- Advanced Proteomics Techniques and Applications3.2%
- Cancer Genomics and Diagnostics3.2%
- Chromosomal and Genetic Variations2.7%
- Genome Rearrangement Algorithms2.7%
- Algorithms and Data Compression2.5%
- Other78.2%
Coauthors
- Paul S. Mischel34
- Jens Luebeck32
- Howard Y. Chang20
- Pavel A. Pevzner14
- King L. Hung13
- Utkrisht Rajkumar13
- Vikas Bansal13
- Ivy Tsz-Lo Wong11
- Sihan Wu10
- Kristen M. Turner9
- Joshua T. Lange8
- Siavash Mirarab8
- Sorin Istrail8
- Viraj Deshpande8
- Bjarni V. Halldórsson7
- Mehrdad Bakhtiari7
- Roel G.W. Verhaak7
- Shahab Sarmashghi7
- Siavash R. Dehkordi7
- Stephen Tanner7
- Ali Bashir6
- Jun Tang6
- Kathryn E. Yost6
- Kelly A. Frazer6
All papers
- Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers
Authors: Hoon Kim, Nam Nguyen, Kristen M. Turner, Sihan Wu, Amit D. Gujar, Jens Luebeck, Jihe Liu, Viraj Deshpande, Utkrisht Rajkumar, Sandeep Namburi, Samirkumar B. Amin, Eunhee Yi, Francesca Menghi, Johannes H. Schulte, Anton G. Henssen, Howard Y. Chang, Christine R. Beck, Paul S. Mischel, Vineet Bafna, Roel G.W. Verhaak - Nature Genetics 2020 cited by 635
- Circular ecDNA promotes accessible chromatin and high oncogene expression
Authors: Sihan Wu, Kristen M. Turner, Nam Nguyen, Ramya Raviram, Marcella L. Erb, Jennifer Santini, Jens Luebeck, Utkrisht Rajkumar, Yarui Diao, Bin Li, Wenjing Zhang, Nathan M. Jameson, M. Ryan Corces, Jeffrey M. Granja, Xingqi Chen, Ceyda Çoruh, Armen Abnousi, Jack Houston, Zhen Ye, Rong Hu, Miao Yu, Hoon Kim, Julie A. Law, Roel G.W. Verhaak, Ming Hu, Frank B. Furnari, Howard Y. Chang, Bing Ren, Vineet Bafna, Paul S. Mischel - Nature 2019 cited by 721
- Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity
Authors: Kristen M. Turner, Viraj Deshpande, Doruk Beyter, Tomoyuki Koga, Jessica M. Rusert, Catherine Lee, Bin Li, Karen C. Arden, Bing Ren, David A. Nathanson, Harley I. Kornblum, Michael D. Taylor, Sharmeela Kaushal, Webster K. Cavenee, Robert J. Wechsler‐Reya, Frank B. Furnari, Scott R. VandenBerg, P. Nagesh Rao, Geoffrey M. Wahl, Vineet Bafna, Paul S. Mischel - Nature 2017 cited by 923
- Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer
Authors: Hui Zhang, Tao Liu, Zhen Zhang, Samuel Payne, Bai Zhang, Jason McDermott, Jianying Zhou, Vladislav Petyuk, Li Chen, Debjit Ray, Shisheng Sun, Feng Yang, Lijun Chen, Jing Wang, Punit Shah, Seong Won, Paul Aiyetan, Sunghee Woo, Yuan Tian, Marina A. Gritsenko, Therese RW Clauss, Caitlin H. Choi, Matthew Monroe, Stefani N. Thomas, Song Nie, Chaochao Wu, Ronald Moore, Kun‐Hsing Yu, David L. Tabb, David Fenyö, Vineet Bafna, Yue Wang, Henry Rodriguez, Emily S. Boja, Tara Hiltke, Robert Rivers, Lori J. Sokoll, Heng Zhu, Ie‐Ming Shih, Leslie Cope, Akhilesh Pandey, Bing Zhang, M Snyder, Douglas A. Levine, Richard Smith, Daniel W. Chan, Karin Rodland, Steven A. Carr, Michael A. Gillette, Karl R. Klauser, Eric Kuhn, D.R. Mani, Philipp Mertins, Karen A. Ketchum, Ratna R. Thangudu, Shuang Cai, Mauricio Oberti, Amanda G. Paulovich, Jeffrey R. Whiteaker, Nathan Edwards, Peter B. McGarvey, Subha Madhavan, Pei Wang, Daniel W. Chan, Akhilesh Pandey, Ie‐Ming Shih, Hui Zhang, Zhen Zhang, Heng Zhu, Leslie Cope, Gordon A. Whiteley, Steven J. Skates, Forest M. White, Douglas A. Levine, Emily S. Boja, Christopher R. Kinsinger, Tara Hiltke, Mehdi Mesri, Robert Rivers, Henry Rodriguez, Kenna M. Shaw, Stephen E. Stein, David Fenyö, Tao Liu, Jason McDermott, Samuel Payne, Karin Rodland, Richard Smith, Paul A. Rudnick, M Snyder, Yingming Zhao, Xian Chen, David F. Ransohoff, Andrew N. Hoofnagle, D.C. Liebler, Melinda E. Sanders, Zhiao Shi, Robbert J.C. Slebos, David L. Tabb, Bing Zhang and 10 more - Cell 2016 cited by 1,126
- Exploring the landscape of focal amplifications in cancer using AmpliconArchitect
Authors: Viraj Deshpande, Jens Luebeck, Nam Nguyen, Mehrdad Bakhtiari, Kristen M. Turner, Richard B. Schwab, Hannah Carter, Paul S. Mischel, Vineet Bafna - Nature Communications 2019 cited by 368
- ecDNA hubs drive cooperative intermolecular oncogene expression
Authors: King L. Hung, Kathryn E. Yost, Liangqi Xie, Quanming Shi, Konstantin Helmsauer, Jens Luebeck, Robert Schöpflin, Joshua T. Lange, Rocío Chamorro González, Natasha E. Weiser, Celine Chen, Maria E. Valieva, Ivy Tsz-Lo Wong, Sihan Wu, Siavash R. Dehkordi, Connor V. Duffy, Katerina Kraft, Jun Tang, Julia A. Belk, John C. Rose, M. Ryan Corces, Jeffrey M. Granja, Rui Li, Utkrisht Rajkumar, Jordan Friedlein, Anindya Bagchi, Ansuman T. Satpathy, Robert Tjian, Stefan Mundlos, Vineet Bafna, Anton G. Henssen, Paul S. Mischel, Zhe Liu, Howard Y. Chang - Nature 2021 cited by 337
- The evolutionary dynamics of extrachromosomal DNA in human cancers
Authors: Joshua T. Lange, John C. Rose, Celine Chen, Yuriy Pichugin, Liangqi Xie, Jun Tang, King L. Hung, Kathryn E. Yost, Quanming Shi, Marcella L. Erb, Utkrisht Rajkumar, Sihan Wu, Sabine Taschner‐Mandl, Marie Bernkopf, Charles Swanton, Zhe Liu, Weini Huang, Howard Y. Chang, Vineet Bafna, Anton G. Henssen, Benjamin Werner, Paul S. Mischel - Nature Genetics 2022 cited by 195
- Extrachromosomal DNA in the cancerous transformation of Barrett’s oesophagus
Authors: Jens Luebeck, Alvin Wei Tian Ng, Patricia C. Galipeau, Xiaohong Li, Carissa A. Sanchez, Annalise Katz‐Summercorn, Hoon Kim, Sriganesh Jammula, Yudou He, Scott M. Lippman, Roel G.W. Verhaak, Carlo C. Maley, Ludmil B. Alexandrov, Brian J. Reid, Rebecca C. Fitzgerald, Thomas G. Paulson, Howard Y. Chang, Sihan Wu, Vineet Bafna, Paul S. Mischel - Nature 2023 cited by 190
- HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
Authors: Peter Edge, Vineet Bafna, Vikas Bansal - Genome Research 2016 cited by 466
- Epigenetic dysregulation from chromosomal transit in micronuclei
Authors: Albert S. Agustinus, Duaa H. Al-Rawi, Bhargavi Dameracharla, Ramya Raviram, Bailey S.C.L. Jones, Stephanie Stransky, Lorenzo Scipioni, Jens Luebeck, Melody Di Bona, Danguolė Norkūnaitė, Robert M. Myers, Mercedes A. Duran Paez, Seongmin Choi, Britta Weigelt, Shira Yomtoubian, Andrew McPherson, Eléonore Toufektchan, Kristina Keuper, Paul S. Mischel, Vivek Mittal, Sohrab P. Shah, John Maciejowski, Zuzana Štorchová, Enrico Gratton, Peter Ly, Dan A. Landau, Mathieu F. Bakhoum, Richard P. Koche, Simone Sidoli, Vineet Bafna, Yael David, Samuel F. Bakhoum - Nature 2023 cited by 115
- Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH
Authors: King L. Hung, Jens Luebeck, Siavash R. Dehkordi, Caterina I. Colón, Rui Li, Ivy Tsz-Lo Wong, Ceyda Çoruh, Prashanthi Dharanipragada, Shirley H. Lomeli, Natasha E. Weiser, Gatien Moriceau, Xiao Zhang, Chris Bailey, Kathleen E. Houlahan, Wenting Yang, Rocío Chamorro González, Charles Swanton, Christina Curtis, Mariam Jamal‐Hanjani, Anton G. Henssen, Julie A. Law, William J. Greenleaf, Roger S. Lo, Paul S. Mischel, Vineet Bafna, Howard Y. Chang - Nature Genetics 2022 cited by 123
- Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA
Authors: Erik N. Bergstrom, Jens Luebeck, Mia Petljak, Azhar Khandekar, Mark Barnes, Tongwu Zhang, Christopher D. Steele, Nischalan Pillay, Maria Teresa Landi, Vineet Bafna, Paul S. Mischel, Reuben S. Harris, Ludmil B. Alexandrov - Nature 2022 cited by 165
- Extrachromosomal oncogene amplification in tumour pathogenesis and evolution
Authors: Roel G.W. Verhaak, Vineet Bafna, Paul S. Mischel - Nature reviews. Cancer 2019 cited by 346
- Extrachromosomal DNA: An Emerging Hallmark in Human Cancer
Authors: Sihan Wu, Vineet Bafna, Howard Y. Chang, Paul S. Mischel - Annual Review of Pathology Mechanisms of Disease 2021 cited by 120
- NAD metabolic dependency in cancer is shaped by gene amplification and enhancer remodelling
Authors: Sudhir Chowdhry, Ciro Zanca, Utkrisht Rajkumar, Tomoyuki Koga, Yarui Diao, Ramya Raviram, Feng Liu, Kristen M. Turner, Huijun Yang, Elizabeth Brunk, Junfeng Bi, Frank B. Furnari, Vineet Bafna, Bing Ren, Paul S. Mischel - Nature 2019 cited by 223
- A deep population reference panel of tandem repeat variation
Authors: Helyaneh Ziaei Jam, Yang Li, Ross DeVito, Nima Mousavi, Nichole Ma, Ibra Lujumba, Yagoub Adam, Mikhail O. Maksimov, Bonnie Huang, Egor Dolzhenko, Yunjiang Qiu, Fredrick Elishama Kakembo, Habi Joseph, Blessing Onyido, Jumoke Adeyemi, Mehrdad Bakhtiari, Jonghun Park, Sara Javadzadeh, Daudi Jjingo, Ezekiel Adebiyi, Vineet Bafna, Melissa Gymrek - Nature Communications 2023 cited by 76
- Origins and impact of extrachromosomal DNA
Authors: Chris Bailey, Oriol Pich, Kerstin Thol, Thomas B. K. Watkins, Jens Luebeck, Andrew Rowan, Georgia Stavrou, Natasha E. Weiser, Bhargavi Dameracharla, Robert B. Bentham, Wei-Ting Lu, Jeanette Kittel, S.Y. Cindy Yang, Brooke E. Howitt, N. Sharma, Maria Litovchenko, Roberto Salgado, King L. Hung, Alex J. Cornish, David A. Moore, Richard S. Houlston, Vineet Bafna, Howard Y. Chang, Serena Nik‐Zainal, Nnennaya Kanu, Nicholas McGranahan, J. C. Ambrose, Paramasivam Arumugam, R. Bevers, Marta Bleda, F. Boardman-Pretty, C. R. Boustred, Helen Brittain, Matthew A. Brown, M. J. Caulfield, G. C. Chan, Adam Giess, John N. Griffin, Angela Hamblin, Seton Henderson, Tim Hubbard, Robert W. Jackson, L. J. Jones, D. Kasperaviciute, Melis Kayikci, A. Kousathanas, L. Lahnstein, A. Lakey, S. E. A. Leigh, Ivone Leong, F. J. Lopez, F. Maleady-Crowe, Meriel McEntagart, Federico Minneci, Jonathan S. Mitchell, L. Moutsianas, Melanie Mueller, Nirupa Murugaesu, Anna C. Need, Peter O’Donovan, Christopher A. Odhams, Christine Patch, D. Perez-Gil, M. B. Pereira, J. Pullinger, T. Rahim, A. Rendon, Tim Rogers, K. Savage, K. Sawant, Richard H. Scott, Afshan Siddiq, A. Sieghart, Sean Smith, A. Sosinsky, A. Stuckey, M. Tanguy, Ana Lisa Taylor Tavares, Elaine Thomas, S. R. Thompson, Arianna Tucci, M. J. Welland, Eric O. Williams, Kate Witkowska, S. M. Wood, Magdalena Zarowiecki, Adrienne M. Flanagan, Paul S. Mischel, Mariam Jamal‐Hanjani, Charles Swanton - Nature 2024 cited by 142
- Plasticity of Extrachromosomal and Intrachromosomal BRAF Amplifications in Overcoming Targeted Therapy Dosage Challenges
Authors: Kai Song, Jenna K. Minami, Arthur Huang, Siavash R. Dehkordi, Shirley H. Lomeli, Jens Luebeck, Mark H. Goodman, Gatien Moriceau, Oscar Krijgsman, Prashanthi Dharanipragada, Trevor Ridgley, William P. Crosson, Jesus Salazar, Eli Pazol, Gabriel Karin, Rachana Jayaraman, Nikolas G. Balanis, Salwan Alhani, Kyle Sheu, Johanna ten Hoeve, Amelia Palermo, Stephen E. Motika, T. Niroshi Senaratne, Kim H. Paraiso, Paul J. Hergenrother, P. Nagesh Rao, Asha S. Multani, Daniel S. Peeper, Vineet Bafna, Roger S. Lo, Thomas G. Graeber - Cancer Discovery 2021 cited by 77
- Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer
Authors: Gary C. Hon, R. David Hawkins, Otávia L. Caballero, Christine Lo, Ryan Lister, Mattia Pelizzola, Armand Valsesia, Zhen Ye, Samantha Kuan, Lee Edsall, Anamaria A. Camargo, Brian J. Stevenson, Joseph R. Ecker, Vineet Bafna, Robert L. Strausberg, Andrew J.G. Simpson, Bing Ren - Genome Research 2011 cited by 620
- AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplifications
Authors: Jens Luebeck, Ceyda Çoruh, Siavash R. Dehkordi, Joshua T. Lange, Kristen M. Turner, Viraj Deshpande, Dave A. Pai, Chao Zhang, Utkrisht Rajkumar, Julie A. Law, Paul S. Mischel, Vineet Bafna - Nature Communications 2020 cited by 98
- Variable number tandem repeats mediate the expression of proximal genes
Authors: Mehrdad Bakhtiari, Jonghun Park, Yuan-Chun Ding, Sharona Shleizer-Burko, Susan L. Neuhausen, Bjarni V. Halldórsson, Kāri Stefánsson, Melissa Gymrek, Vineet Bafna - Nature Communications 2021 cited by 107
- Coordinated inheritance of extrachromosomal DNAs in cancer cells
Authors: King L. Hung, Matthew G. Jones, Ivy Tsz-Lo Wong, Ellis J. Curtis, Joshua T. Lange, Britney Jiayu He, Jens Luebeck, Rachel Schmargon, Elisa Scanu, Lotte Brückner, Xiaowei Yan, Rui Li, Aditi Gnanasekar, Rocío Chamorro González, Julia A. Belk, Zhonglin Liu, Bruno Melillo, Vineet Bafna, Jan R. Dörr, Benjamin Werner, Weini Huang, Benjamin F. Cravatt, Anton G. Henssen, Paul S. Mischel, Howard Y. Chang - Nature 2024 cited by 77
- De novo somatic mutations in components of the PI3K-AKT3-mTOR pathway cause hemimegalencephaly
Authors: Jeong Ho Lee, My N. Huynh, Jennifer L. Silhavy, Sangwoo Kim, Tracy Dixon‐Salazar, Andrew Heiberg, Eric Scott, Vineet Bafna, Kiley J. Hill, Adrienne Collazo, Vincent Funari, Carsten Russ, Stacey B. Gabriel, Gary W. Mathern, Joseph G. Gleeson - Nature Genetics 2012 cited by 696
- Enhancing transcription–replication conflict targets ecDNA-positive cancers
Authors: Jun Tang, Natasha E. Weiser, Guiping Wang, Sudhir Chowdhry, Ellis J. Curtis, Yanding Zhao, Ivy Tsz-Lo Wong, Georgi K. Marinov, Rui Li, Philip Hanoian, Edison Tse, Salvador Garcia Mojica, Ryan J. Hansen, Joshua Plum, Auzon Steffy, Snezana Milutinovic, S. Todd Meyer, Jens Luebeck, Yanbo Wang, Shu Zhang, Nicolas Altemose, Christina Curtis, William J. Greenleaf, Vineet Bafna, Stephen J. Benkovic, Anthony B. Pinkerton, Shailaja Kasibhatla, Christian A. Hassig, Paul S. Mischel, Howard Y. Chang - Nature 2024 cited by 88
