CellNEST reveals cell-cell relay networks using attention mechanisms on spatial transcriptomics
Authors: Fatema Tuz Zohora, Deisha Paliwal, Eugenia Flores-Figueroa, Joshua Li, Tingxiao Gao, Faiyaz Notta, Gregory W Schwartz.
Reference: Nature Methods
DOI: 10.1038/s41592-025-02721-3
Year: 2025
Metastatic medulloblastoma remodels the local leptomeningeal microenvironment to promote further metastatic colonization and growth
Authors: Namal Abeysundara, Alexandra Rasnitsyn, Vernon Fong, Alexander Bahcheli, Randy Van Ommeren, Kyle Juraschka, Maria Vladoiu, Winnie Ong, Bryn Livingston, Pasqualino de Antonellis, Michelle Ly, Borja López Holgado, Olga Sirbu, Shahrzad Bahrampour, Hyun-Kee Min, Jerry Fan, Carolina Nor, Abhirami Visvanathan, Jiao Zhang, Hao Wang, Lei Qin, Ning Huang, Jonelle Pallotta, Tajana Douglas, Esta Mak, Haipeng Su, Karen Ng, Kevin Yang Zhang, Craig Daniels, Calixto-Hope G. Lucas, Charles G. Eberhart, Hailong Liu, Tao Jiang, Faiyaz Notta, Vijay Ramaswamy, Jüri Reimand, Marco Gallo, Jeremy N. Rich, Xiaochong Wu, Xi Huang & Michael D. Taylor.
Reference: Nature Cell Biology
DOI: 10.1038/s41556-025-01660-7
Year: 2025
Transcription phenotypes of pancreatic cancer are driven by genomic events during tumour evolution
Authors: Michelle Chan-Seng-Yue, Jaeseung C. Kim, Gavin W. Wilson, Karen Ng, Eugenia Flores Figueroa, Grainne M. O’Kane, Ashton A. Connor, Robert E. Denroche, Robert C. Grant, Jessica McLeod, Julie M. Wilson, Gun Ho Jang, Amy Zhang, Anna Dodd, Sheng-Ben Liang, Ayelet Borgida, Dianne Chadwick, Sangeetha Kalimuthu, Ilinca Lungu, John M. S. Bartlett, Paul M. Krzyzanowski, Vandana Sandhu, Hervé Tiriac, Fieke E. M. Froeling, Joanna M. Karasinska, James T. Topham, Daniel J. Renouf, David F. Schaeffer, Steven J. M. Jones, Marco A. Marra, Janessa Laskin, Runjan Chetty, Lincoln D. Stein, George Zogopoulos, Benjamin Haibe-Kains, Peter J. Campbell, David A. Tuveson, Jennifer J. Knox, Sandra E. Fischer, Steven Gallinger & Faiyaz Notta.
Reference: Nature
DOI: 10.1038/s41588-019-0566-9
Year: 2020
Cryptic genomic lesions in adverse-risk acute myeloid leukemia identified by integrated whole genome and transcriptome sequencing
Authors: Jaeseung C. Kim, Philip C. Zuzarte, Tracy Murphy, Michelle Chan-Seng-Yue, Andrew M. K. Brown, Paul M. Krzyzanowski, Adam C. Smith, Faiyaz Notta, Mark D. Minden & John D. McPherson.
Reference: Leukemia - Nature
DOI: 10.1038/s41375-019-0546-1
Year: 2020
A genetic roadmap of pancreatic cancer: still evolving
Authors: Faiyaz Notta, Stephan A Hahn, Francisco X Real.
Reference: Gut
DOI: 10.1136/gutjnl-2016-313317
Year: 2019
A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns
Authors: Faiyaz Notta, Michelle Chan-Seng-Yue, Mathieu Lemire, Yilong Li, Gavin W. Wilson, Ashton A. Connor, Robert E. Denroche, Sheng-Ben Liang, Andrew M. K. Brown, Jaeseung C. Kim, Tao Wang, Jared T. Simpson, Timothy Beck, Ayelet Borgida, Nicholas Buchner, Dianne Chadwick, Sara Hafezi-Bakhtiari, John E. Dick, Lawrence Heisler, Michael A. Hollingsworth, Emin Ibrahimov, Gun Ho Jang, Jeremy Johns, Lars G. T. Jorgensen, Calvin Law, Olga Ludkovski, Ilinca Lungu, Karen Ng, Danielle Pasternack, Gloria M. Petersen, Liran I. Shlush, Lee Timms, Ming-Sound Tsao, Julie M. Wilson, Christina K. Yung, George Zogopoulos, John M. S. Bartlett, Ludmil B. Alexandrov, Francisco X. Real, Sean P. Cleary, Michael H. Roehrl, John D. McPherson, Lincoln D. Stein, Thomas J. Hudson, Peter J. Campbell & Steven Gallinger.
Reference: Nature
DOI: 10.1038/nature19823
Year: 2016
Distinct routes of lineage development reshape the human blood hierarchy across ontogeny
Authors: Faiyaz Notta, Sasan Zandi, Naoya Takayama, Stephanie Dobson, Olga I. Gan, Gavin Wilson, Kerstin B. Kaufmann, Jessica McLeod, Elisa Laurenti, Cyrille F. Dunant, John D. McPherson, Lincoln D. Stein, Yigal Dror, & John E. Dick.
Reference: Science
Year: 2015
Evolution of human BCR–ABL1 lymphoblastic leukaemia-initiating cells
Authors: Faiyaz Notta, Charles G. Mullighan, Jean C. Y. Wang, Armando Poeppl, Sergei Doulatov, Letha A. Phillips, Jing Ma, Mark D. Minden, James R. Downing & John E. Dick.
Reference: Nature
Year: 2011