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A suspension technique for efficient large-scale cancer organoid culturing and perturbation screens.
Published in:
Scientific Reports, 2022, v. 12, n. 1, p. 1, doi. 10.1038/s41598-022-09508-y
By:
- Price, Stacey;
- Bhosle, Shriram;
- Gonçalves, Emanuel;
- Li, Xiaodun;
- McClurg, Dylan P.;
- Barthorpe, Syd;
- Beck, Alex;
- Hall, Caitlin;
- Lightfoot, Howard;
- Farrow, Luke;
- Ansari, Rizwan;
- Jackson, David A.;
- Allen, Laura;
- Roberts, Kirsty;
- Beaver, Charlotte;
- Francies, Hayley E.;
- Garnett, Mathew J.
Publication type:
Article
Inferred Ancestral Origin of Cancer Cell Lines Associates with Differential Drug Response.
Published in:
International Journal of Molecular Sciences, 2021, v. 22, n. 18, p. 10135, doi. 10.3390/ijms221810135
By:
- Nguyen, Phong B. H.;
- Ohnmacht, Alexander J.;
- Sharifli, Samir;
- Garnett, Mathew J.;
- Menden, Michael P.
Publication type:
Article
A statistical framework for assessing pharmacological responses and biomarkers using uncertainty estimates.
Published in:
eLife, 2020, p. 1, doi. 10.7554/eLife.60352
By:
- Dennis Wang;
- Hensman, James;
- Kutkaite, Ginte;
- Toh, Tzen S.;
- Galhoz, Ana;
- Dry, Jonathan R.;
- Saez-Rodriguez, Julio;
- Garnett, Mathew J.;
- Menden, Michael P.;
- Dondelinger, Frank
Publication type:
Article
Genome-wide CRISPR screens of oral squamous cell carcinoma reveal fitness genes in the Hippo pathway.
Published in:
eLife, 2020, p. 1, doi. 10.7554/eLife.57761
By:
- Annie Wai Yeeng Chai;
- Pei San Yee;
- Price, Stacey;
- Shi Mun Yee;
- Hui Mei Lee;
- Tiong, Vivian K. H.;
- Gonçalves, Emanuel;
- Behan, Fiona M.;
- Bateson, Jessica;
- Gilbert, James;
- Aik Choon Tan;
- McDermott, Ultan;
- Garnett, Mathew J.;
- Sok Ching Cheong
Publication type:
Article
Genome-wide CRISPR screens of oral squamous cell carcinoma reveal fitness genes in the Hippo pathway.
Published in:
eLife, 2020, p. 1
By:
- Annie Wai Yeeng Chai;
- Pei San Yee;
- Price, Stacey;
- Shi Mun Yee;
- Hui Mei Lee;
- Tiong, Vivian K. H.;
- Gonçalves, Emanuel;
- Behan, Fiona M.;
- Bateson, Jessica;
- Gilbert, James;
- Tan, Aik Choon;
- McDermott, Ultan;
- Garnett, Mathew J.;
- Sok Ching Cheong
Publication type:
Article
Cell Model Passports—a hub for clinical, genetic and functional datasets of preclinical cancer models.
Published in:
Nucleic Acids Research, 2019, v. 47, n. D1, p. D923, doi. 10.1093/nar/gky872
By:
- van der Meer, Dieudonne;
- Barthorpe, Syd;
- Yang, Wanjuan;
- Lightfoot, Howard;
- Hall, Caitlin;
- Gilbert, James;
- Francies, Hayley E;
- Garnett, Mathew J
Publication type:
Article
Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells.
Published in:
Nucleic Acids Research, 2013, v. 41, p. D955, doi. 10.1093/nar/gks1111
By:
- Wanjuan Yang;
- Soares, Jorge;
- Greninger, Patricia;
- Edelman, Elena J.;
- Lightfoot, Howard;
- Forbes, Simon;
- Bindal, Nidhi;
- Beare, Dave;
- Smith, James A.;
- Thompson, I. Richard;
- Ramaswamy, Sridhar;
- Futreal, P. Andrew;
- Haber, Daniel A.;
- Stratton, Michael R.;
- Benes, Cyril;
- McDermott, Ultan;
- Garnett, Mathew J.
Publication type:
Article
Integrated cross-study datasets of genetic dependencies in cancer.
Published in:
Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-21898-7
By:
- Pacini, Clare;
- Dempster, Joshua M.;
- Boyle, Isabella;
- Gonçalves, Emanuel;
- Najgebauer, Hanna;
- Karakoc, Emre;
- van der Meer, Dieudonne;
- Barthorpe, Andrew;
- Lightfoot, Howard;
- Jaaks, Patricia;
- McFarland, James M.;
- Garnett, Mathew J.;
- Tsherniak, Aviad;
- Iorio, Francesco
Publication type:
Article
CoRe: a robustly benchmarked R package for identifying core-fitness genes in genome-wide pooled CRISPR-Cas9 screens.
Published in:
BMC Genomics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12864-021-08129-5
By:
- Vinceti, Alessandro;
- Karakoc, Emre;
- Pacini, Clare;
- Perron, Umberto;
- De Lucia, Riccardo Roberto;
- Garnett, Mathew J.;
- Iorio, Francesco
Publication type:
Article
Logic models to predict continuous outputs based on binary inputs with an application to personalized cancer therapy.
Published in:
Scientific Reports, 2016, p. 36812, doi. 10.1038/srep36812
By:
- Knijnenburg, Theo A.;
- Klau, Gunnar W.;
- Iorio, Francesco;
- Garnett, Mathew J.;
- McDermott, Ultan;
- Shmulevich, Ilya;
- Wessels, Lodewyk F. A.
Publication type:
Article
Minimal genome-wide human CRISPR-Cas9 library.
Published in:
Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02268-4
By:
- Gonçalves, Emanuel;
- Thomas, Mark;
- Behan, Fiona M.;
- Picco, Gabriele;
- Pacini, Clare;
- Allen, Felicity;
- Vinceti, Alessandro;
- Sharma, Mamta;
- Jackson, David A.;
- Price, Stacey;
- Beaver, Charlotte M.;
- Dovey, Oliver;
- Parry-Smith, David;
- Iorio, Francesco;
- Parts, Leopold;
- Yusa, Kosuke;
- Garnett, Mathew J.
Publication type:
Article
Combinations of PARP Inhibitors with Temozolomide Drive PARP1 Trapping and Apoptosis in Ewing’s Sarcoma.
Published in:
PLoS ONE, 2015, v. 10, n. 10, p. 1, doi. 10.1371/journal.pone.0140988
By:
- Gill, Sonja J.;
- Travers, Jon;
- Pshenichnaya, Irina;
- Kogera, Fiona A.;
- Barthorpe, Syd;
- Mironenko, Tatiana;
- Richardson, Laura;
- Benes, Cyril H.;
- Stratton, Michael R.;
- McDermott, Ultan;
- Jackson, Stephen P.;
- Garnett, Mathew J.
Publication type:
Article
A Semi-Supervised Approach for Refining Transcriptional Signatures of Drug Response and Repositioning Predictions.
Published in:
PLoS ONE, 2015, v. 10, n. 10, p. 1, doi. 10.1371/journal.pone.0139446
By:
- Iorio, Francesco;
- Shrestha, Roshan L.;
- Levin, Nicolas;
- Boilot, Viviane;
- Garnett, Mathew J.;
- Saez-Rodriguez, Julio;
- Draviam, Viji M.
Publication type:
Article
ETV6-NTRK3 transformation requires insulin-like growth factor 1 receptor signaling and is associated with constitutive IRS-1 tyrosine phosphorylation.
Published in:
Oncogene, 2002, v. 21, n. 37, p. 5684, doi. 10.1038/sj.onc.1205669
By:
- Morrison, Kevin B.;
- Tognon, Cristina E.;
- Garnett, Mathew J.;
- Deal, Cheri;
- Sorensen, Poul HB
Publication type:
Article
Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen.
Published in:
Nature Communications, 2019, v. 10, n. 1, p. 1, doi. 10.1038/s41467-019-09799-2
By:
- Menden, Michael P.;
- Wang, Dennis;
- Mason, Mike J.;
- Szalai, Bence;
- Bulusu, Krishna C.;
- Yuanfang Guan;
- Yu, Thomas;
- Jaewoo Kang;
- Minji Jeon;
- Wolfinger, Russ;
- Tin Nguyen;
- Zaslavskiy, Mikhail;
- Ghazoui, Zara;
- Ahsen, Mehmet Eren;
- Vogel, Robert;
- Neto, Elias Chaibub;
- Norman, Thea;
- Tang, Eric K. Y.;
- Garnett, Mathew J.;
- Di Veroli, Giovanni Y.
Publication type:
Article
Functional linkage of gene fusions to cancer cell fitness assessed by pharmacological and CRISPR-Cas9 screening.
Published in:
Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-09940-1
By:
- Picco, Gabriele;
- Chen, Elisabeth D.;
- Alonso, Luz Garcia;
- Behan, Fiona M.;
- Gonçalves, Emanuel;
- Bignell, Graham;
- Matchan, Angela;
- Fu, Beiyuan;
- Banerjee, Ruby;
- Anderson, Elizabeth;
- Butler, Adam;
- Benes, Cyril H.;
- McDermott, Ultan;
- Dow, David;
- Iorio, Francesco;
- Stronach, Euan;
- Yang, Fengtang;
- Yusa, Kosuke;
- Saez-Rodriguez, Julio;
- Garnett, Mathew J.
Publication type:
Article
Highlights from the 1st European cancer dependency map symposium and workshop.
Published in:
FEBS Letters, 2023, v. 597, n. 15, p. 1921, doi. 10.1002/1873-3468.14699
By:
- Trastulla, Lucia;
- Savino, Aurora;
- Beltrao, Pedro;
- Ciriano, Isidro Cortés;
- Fenici, Peter;
- Garnett, Mathew J.;
- Guerini, Ilaria;
- Bigas, Nuria Lòpez;
- Mattaj, Iain;
- Petsalaki, Evangelia;
- Riva, Laura;
- Tape, Christopher J.;
- Leeuwen, Jolanda Van;
- Sharma, Sumana;
- Vazquez, Francisca;
- Iorio, Francesco
Publication type:
Article
UBE2S elongates ubiquitin chains on APC/C substrates to promote mitotic exit.
Published in:
Nature Cell Biology, 2009, v. 11, n. 11, p. 1363, doi. 10.1038/ncb1983
By:
- Garnett, Mathew J.;
- Mansfeld, Jörg;
- Godwin, Colin;
- Matsusaka, Takahiro;
- Wu, Jiahua;
- Russell, Paul;
- Pines, Jonathon;
- Venkitaraman, Ashok R.
Publication type:
Article
Patient‐specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies.
Published in:
Molecular Systems Biology, 2020, v. 16, n. 6, p. 1, doi. 10.15252/msb.209690
By:
- Eduati, Federica;
- Jaaks, Patricia;
- Wappler, Jessica;
- Cramer, Thorsten;
- Merten, Christoph A;
- Garnett, Mathew J;
- Saez‐Rodriguez, Julio
Publication type:
Article
Patient‐specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies.
Published in:
Molecular Systems Biology, 2020, v. 16, n. 2, p. 1, doi. 10.15252/msb.20188664
By:
- Eduati, Federica;
- Jaaks, Patricia;
- Wappler, Jessica;
- Cramer, Thorsten;
- Merten, Christoph A;
- Garnett, Mathew J;
- Saez‐Rodriguez, Julio
Publication type:
Article
scSNV-seq: high-throughput phenotyping of single nucleotide variants by coupled single-cell genotyping and transcriptomics.
Published in:
Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03169-y
By:
- Cooper, Sarah E.;
- Coelho, Matthew A.;
- Strauss, Magdalena E.;
- Gontarczyk, Aleksander M.;
- Wu, Qianxin;
- Garnett, Mathew J.;
- Marioni, John C.;
- Bassett, Andrew R.
Publication type:
Article
Mutations of the BRAF gene in human cancer.
Published in:
Nature, 2002, v. 417, n. 6892, p. 949, doi. 10.1038/nature00766
By:
- Davies, Helen;
- Bignell, Graham R.;
- Cox, Charles;
- Stephens, Philip;
- Edkins, Sarah;
- Clegg, Sheila;
- Teague, Jon;
- Woffendin, Hayley;
- Garnett, Mathew J.;
- Bottomley, William;
- Davis, Neil;
- Dicks, Ed;
- Ewing, Rebecca;
- Floyd, Yvonne;
- Gray, Kristian;
- Hall, Sarah;
- Hawes, Rachel;
- Hughes, Jaime;
- Kosmidou, Vivian
Publication type:
Article
SLFN11 informs on standard of care and novel treatments in a wide range of cancer models.
Published in:
2021
By:
- Winkler, Claudia;
- Armenia, Joshua;
- Jones, Gemma N.;
- Tobalina, Luis;
- Sale, Matthew J.;
- Petreus, Tudor;
- Baird, Tarrion;
- Serra, Violeta;
- Wang, Anderson T.;
- Lau, Alan;
- Garnett, Mathew J.;
- Jaaks, Patricia;
- Coker, Elizabeth A.;
- Pierce, Andrew J.;
- O'Connor, Mark J.;
- Leo, Elisabetta
Publication type:
journal article
Systematic identification of genomic markers of drug sensitivity in cancer cells.
Published in:
Nature, 2012, v. 483, n. 7391, p. 570, doi. 10.1038/nature11005
By:
- Garnett, Mathew J.;
- Edelman, Elena J.;
- Heidorn, Sonja J.;
- Greenman, Chris D.;
- Dastur, Anahita;
- Lau, King Wai;
- Greninger, Patricia;
- Thompson, I. Richard;
- Luo, Xi;
- Soares, Jorge;
- Liu, Qingsong;
- Iorio, Francesco;
- Surdez, Didier;
- Chen, Li;
- Milano, Randy J.;
- Bignell, Graham R.;
- Tam, Ah T.;
- Davies, Helen;
- Stevenson, Jesse A.;
- Barthorpe, Syd
Publication type:
Article
The germline genetic component of drug sensitivity in cancer cell lines.
Published in:
Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-05811-3
By:
- Menden, Michael P.;
- Casale, Francesco Paolo;
- Stephan, Johannes;
- Bignell, Graham R.;
- Iorio, Francesco;
- McDermott, Ultan;
- Garnett, Mathew J.;
- Saez-Rodriguez, Julio;
- Stegle, Oliver
Publication type:
Article
Perturbation-response genes reveal signaling footprints in cancer gene expression.
Published in:
Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-017-02391-6
By:
- Schubert, Michael;
- Saez-Rodriguez, Julio;
- Klinger, Bertram;
- Klünemann, Martina;
- Sieber, Anja;
- Uhlitz, Florian;
- Blüthgen, Nils;
- Sauer, Sascha;
- Garnett, Mathew J.
Publication type:
Article
Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting.
Published in:
BMC Genomics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12864-018-4989-y
By:
- Iorio, Francesco;
- Behan, Fiona M.;
- Gonçalves, Emanuel;
- Bhosle, Shriram G.;
- Chen, Elisabeth;
- Shepherd, Rebecca;
- Beaver, Charlotte;
- Ansari, Rizwan;
- Pooley, Rachel;
- Wilkinson, Piers;
- Harper, Sarah;
- Butler, Adam P.;
- Stronach, Euan A.;
- Saez-Rodriguez, Julio;
- Yusa, Kosuke;
- Garnett, Mathew J.
Publication type:
Article
Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects.
Published in:
Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1637-z
By:
- Gonçalves, Emanuel;
- Behan, Fiona M.;
- Louzada, Sandra;
- Arnol, Damien;
- Stronach, Euan A.;
- Yang, Fengtang;
- Yusa, Kosuke;
- Stegle, Oliver;
- Iorio, Francesco;
- Garnett, Mathew J.
Publication type:
Article
GDSCTools for mining pharmacogenomic interactions in cancer.
Published in:
Bioinformatics, 2018, v. 34, n. 7, p. 1226, doi. 10.1093/bioinformatics/btx744
By:
- Cokelaer, Thomas;
- Chen, Elisabeth;
- Iorio, Francesco;
- Menden, Michael P;
- Lightfoot, Howard;
- Saez-Rodriguez, Julio;
- Garnett, Mathew J
Publication type:
Article
Fast randomization of large genomic datasets while preserving alteration counts.
Published in:
Bioinformatics, 2014, v. 30, n. 17, p. i617, doi. 10.1093/bioinformatics/btu474
By:
- Gobbi, Andrea;
- Iorio, Francesco;
- Dawson, Kevin J.;
- Wedge, David C.;
- Tamborero, David;
- Alexandrov, Ludmil B.;
- Lopez-Bigas, Nuria;
- Garnett, Mathew J.;
- Jurman, Giuseppe;
- Saez-Rodriguez, Julio
Publication type:
Article
Combinatorial CRISPR screen identifies fitness effects of gene paralogues.
Published in:
Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-21478-9
By:
- Thompson, Nicola A.;
- Ranzani, Marco;
- van der Weyden, Louise;
- Iyer, Vivek;
- Offord, Victoria;
- Droop, Alastair;
- Behan, Fiona;
- Gonçalves, Emanuel;
- Speak, Anneliese;
- Iorio, Francesco;
- Hewinson, James;
- Harle, Victoria;
- Robertson, Holly;
- Anderson, Elizabeth;
- Fu, Beiyuan;
- Yang, Fengtang;
- Zagnoli-Vieira, Guido;
- Chapman, Phil;
- Del Castillo Velasco-Herrera, Martin;
- Garnett, Mathew J.
Publication type:
Article
Cancer stem cell-related gene expression as a potential biomarker of response for first-in-class imipridone ONC201 in solid tumors.
Published in:
PLoS ONE, 2017, v. 12, n. 8, p. 1, doi. 10.1371/journal.pone.0180541
By:
- Prabhu, Varun V.;
- Lulla, Amriti R.;
- Madhukar, Neel S.;
- Ralff, Marie D.;
- Zhao, Dan;
- Kline, Christina Leah B.;
- Van den Heuvel, A. Pieter J.;
- Lev, Avital;
- Garnett, Mathew J.;
- McDermott, Ultan;
- Benes, Cyril H.;
- Batchelor, Tracy T.;
- Chi, Andrew S.;
- Elemento, Olivier;
- Allen, Joshua E.;
- El-Deiry, Wafik S.
Publication type:
Article

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