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FlashFry: a fast and flexible tool for large-scale CRISPR target design.
Published in:
BMC Biology, 2018, v. 16, n. 1, p. 1, doi. 10.1186/s12915-018-0545-0
By:
- McKenna, Aaron;
- Shendure, Jay
Publication type:
Article
Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain.
Published in:
Nature Biotechnology, 2018, v. 36, n. 5, p. 442, doi. 10.1038/nbt.4103
By:
- Raj, Bushra;
- Wagner, Daniel E;
- McKenna, Aaron;
- Pandey, Shristi;
- Klein, Allon M;
- Shendure, Jay;
- Gagnon, James A;
- Schier, Alexander F
Publication type:
Article
Absolute quantification of somatic DNA alterations in human cancer.
Published in:
Nature Biotechnology, 2012, v. 30, n. 5, p. 413, doi. 10.1038/nbt.2203
By:
- Carter, Scott L;
- Cibulskis, Kristian;
- Helman, Elena;
- McKenna, Aaron;
- Shen, Hui;
- Zack, Travis;
- Laird, Peter W;
- Onofrio, Robert C;
- Winckler, Wendy;
- Weir, Barbara A;
- Beroukhim, Rameen;
- Pellman, David;
- Levine, Douglas A;
- Lander, Eric S;
- Meyerson, Matthew;
- Getz, Gad
Publication type:
Article
Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine.
Published in:
Nature Medicine, 2014, v. 20, n. 6, p. 682, doi. 10.1038/nm.3559
By:
- Van Allen, Eliezer M;
- Wagle, Nikhil;
- Stojanov, Petar;
- Perrin, Danielle L;
- Cibulskis, Kristian;
- Marlow, Sara;
- Jane-Valbuena, Judit;
- Friedrich, Dennis C;
- Kryukov, Gregory;
- Carter, Scott L;
- McKenna, Aaron;
- Sivachenko, Andrey;
- Rosenberg, Mara;
- Kiezun, Adam;
- Voet, Douglas;
- Lawrence, Michael;
- Lichtenstein, Lee T;
- Gentry, Jeff G;
- Huang, Franklin W;
- Fostel, Jennifer
Publication type:
Article
Paired exome analysis of Barrett's esophagus and adenocarcinoma.
Published in:
Nature Genetics, 2015, v. 47, n. 9, p. 1047, doi. 10.1038/ng.3343
By:
- Taylor-Weiner, Amaro;
- Peng, Shouyong;
- Stojanov, Petar;
- Lin, Jules;
- Bass, Adam J;
- Stewart, Chip;
- Seepo, Sara;
- Odze, Robert D;
- Nason, Katie S;
- Stachler, Matthew D;
- Carter, Scott L;
- Lander, Eric S;
- Leshchiner, Ignaty;
- Lawrence, Michael S;
- McKenna, Aaron;
- Chang, Andrew C;
- Agoston, Agoston T;
- Beer, David G;
- Loda, Massimo;
- Davison, Jon M
Publication type:
Article
Somatic mutation of CDKN1B in small intestine neuroendocrine tumors.
Published in:
Nature Genetics, 2013, v. 45, n. 12, p. 1483, doi. 10.1038/ng.2821
By:
- Francis, Joshua M;
- Kiezun, Adam;
- Ramos, Alex H;
- Serra, Stefano;
- Pedamallu, Chandra Sekhar;
- Qian, Zhi Rong;
- Banck, Michaela S;
- Kanwar, Rahul;
- Kulkarni, Amit A;
- Karpathakis, Anna;
- Manzo, Veronica;
- Contractor, Tanupriya;
- Philips, Juliet;
- Nickerson, Elizabeth;
- Pho, Nam;
- Hooshmand, Susanne M;
- Brais, Lauren K;
- Lawrence, Michael S;
- Pugh, Trevor;
- McKenna, Aaron
Publication type:
Article
Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity.
Published in:
Nature Genetics, 2013, v. 45, n. 5, p. 478, doi. 10.1038/ng.2591
By:
- Dulak, Austin M;
- Stojanov, Petar;
- Peng, Shouyong;
- Lawrence, Michael S;
- Fox, Cameron;
- Stewart, Chip;
- Bandla, Santhoshi;
- Imamura, Yu;
- Schumacher, Steven E;
- Shefler, Erica;
- McKenna, Aaron;
- Carter, Scott L;
- Cibulskis, Kristian;
- Sivachenko, Andrey;
- Saksena, Gordon;
- Voet, Douglas;
- Ramos, Alex H;
- Auclair, Daniel;
- Thompson, Kristin;
- Sougnez, Carrie
Publication type:
Article
The genetic landscape of high-risk neuroblastoma.
Published in:
Nature Genetics, 2013, v. 45, n. 3, p. 279, doi. 10.1038/ng.2529
By:
- Pugh, Trevor J;
- Morozova, Olena;
- Attiyeh, Edward F;
- Asgharzadeh, Shahab;
- Wei, Jun S;
- Auclair, Daniel;
- Carter, Scott L;
- Cibulskis, Kristian;
- Hanna, Megan;
- Kiezun, Adam;
- Kim, Jaegil;
- Lawrence, Michael S;
- Lichenstein, Lee;
- McKenna, Aaron;
- Pedamallu, Chandra Sekhar;
- Ramos, Alex H;
- Shefler, Erica;
- Sivachenko, Andrey;
- Sougnez, Carrie;
- Stewart, Chip
Publication type:
Article
Genomic sequencing of meningiomas identifies oncogenic SMO and AKT1 mutations.
Published in:
Nature Genetics, 2013, v. 45, n. 3, p. 285, doi. 10.1038/ng.2526
By:
- Brastianos, Priscilla K;
- Horowitz, Peleg M;
- Santagata, Sandro;
- Jones, Robert T;
- McKenna, Aaron;
- Getz, Gad;
- Ligon, Keith L;
- Palescandolo, Emanuele;
- Van Hummelen, Paul;
- Ducar, Matthew D;
- Raza, Alina;
- Sunkavalli, Ashwini;
- MacConaill, Laura E;
- Stemmer-Rachamimov, Anat O;
- Louis, David N;
- Hahn, William C;
- Dunn, Ian F;
- Beroukhim, Rameen
Publication type:
Article
Whole-exome sequencing identifies a recurrent NAB2-STAT6 fusion in solitary fibrous tumors.
Published in:
Nature Genetics, 2013, v. 45, n. 2, p. 131, doi. 10.1038/ng.2522
By:
- Chmielecki, Juliann;
- Crago, Aimee M;
- Rosenberg, Mara;
- O'Connor, Rachael;
- Walker, Sarah R;
- Ambrogio, Lauren;
- Auclair, Daniel;
- McKenna, Aaron;
- Heinrich, Michael C;
- Frank, David A;
- Meyerson, Matthew
Publication type:
Article
A framework for variation discovery and genotyping using next-generation DNA sequencing data.
Published in:
Nature Genetics, 2011, v. 43, n. 5, p. 491, doi. 10.1038/ng.806
By:
- DePristo, Mark A.;
- Banks, Eric;
- Poplin, Ryan;
- Garimella, Kiran V.;
- Maguire, Jared R.;
- Hartl, Christopher;
- Philippakis, Anthony A.;
- del Angel, Guillermo;
- Rivas, Manuel A.;
- Hanna, Matt;
- McKenna, Aaron;
- Fennell, Tim J.;
- Kernytsky, Andrew M.;
- Sivachenko, Andrey Y.;
- Cibulskis, Kristian;
- Gabriel, Stacey B.;
- Altshuler, David;
- Daly, Mark J.
Publication type:
Article
Temporal stability and community assembly mechanisms in healthy broiler cecum.
Published in:
Frontiers in Microbiology, 2023, p. 1, doi. 10.3389/fmicb.2023.1197838
By:
- Ameer, Aqsa;
- Youqi Cheng;
- Saleem, Farrukh;
- Uzma;
- McKenna, Aaron;
- Richmond, Anne;
- Gundogdu, Ozan;
- Sloan, William T.;
- Javed, Sundus;
- Ijaz, Umer Zeeshan
Publication type:
Article
Genome Report: chromosome-scale genome assembly of the African spiny mouse (Acomys cahirinus).
Published in:
G3: Genes | Genomes | Genetics, 2023, v. 13, n. 10, p. 1, doi. 10.1093/g3journal/jkad177
By:
- Nguyen, Elizabeth Dong;
- Fard, Vahid Nikoonejad;
- Kim, Bernard Y.;
- Collins, Sarah;
- Galey, Miranda;
- Nelson, Branden R.;
- Wakenight, Paul;
- Gable, Simone M.;
- McKenna, Aaron;
- Bammler, Theo K.;
- MacDonald, Jim;
- Okamura, Daryl M.;
- Shendure, Jay;
- Beier, David R.;
- Ramirez, Jan Marino;
- Majesky, Mark W.;
- Millen, Kathleen J.;
- Tollis, Marc;
- Miller, Danny E.
Publication type:
Article
Comprehensive Longitudinal Microbiome Analysis of the Chicken Cecum Reveals a Shift From Competitive to Environmental Drivers and a Window of Opportunity for Campylobacter.
Published in:
Frontiers in Microbiology, 2018, p. N.PAG, doi. 10.3389/fmicb.2018.02452
By:
- Ijaz, Umer Zeeshan;
- Sivaloganathan, Lojika;
- McKenna, Aaron;
- Richmond, Anne;
- Kelly, Carmel;
- Linton, Mark;
- Stratakos, Alexandros Ch.;
- Lavery, Ursula;
- Elmi, Abdi;
- Wren, Brendan W.;
- Dorrell, Nick;
- Corcionivoschi, Nicolae;
- Gundogdu, Ozan
Publication type:
Article
A Review of the Effect of Management Practices on Campylobacter Prevalence in Poultry Farms.
Published in:
Frontiers in Microbiology, 2018, p. N.PAG, doi. 10.3389/fmicb.2018.02002
By:
- Sibanda, Nompilo;
- McKenna, Aaron;
- Richmond, Anne;
- Ricke, Steven C.;
- Callaway, Todd;
- Stratakos, Alexandros Ch.;
- Gundogdu, Ozan;
- Corcionivoschi, Nicolae
Publication type:
Article
Mutational heterogeneity in cancer and the search for new cancer-associated genes.
Published in:
Nature, 2013, v. 499, n. 7457, p. 214, doi. 10.1038/nature12213
By:
- Lawrence, Michael S.;
- Stojanov, Petar;
- Polak, Paz;
- Kryukov, Gregory V.;
- Cibulskis, Kristian;
- Sivachenko, Andrey;
- Carter, Scott L.;
- Stewart, Chip;
- Mermel, Craig H.;
- Roberts, Steven A.;
- Kiezun, Adam;
- Hammerman, Peter S.;
- McKenna, Aaron;
- Drier, Yotam;
- Zou, Lihua;
- Ramos, Alex H.;
- Pugh, Trevor J.;
- Stransky, Nicolas;
- Helman, Elena;
- Kim, Jaegil
Publication type:
Article
Comprehensive genomic characterization of squamous cell lung cancers.
Published in:
Nature, 2012, v. 489, n. 7417, p. 519, doi. 10.1038/nature11404
By:
- Hammerman, Peter S.;
- Lawrence, Michael S.;
- Voet, Douglas;
- Jing, Rui;
- Cibulskis, Kristian;
- Sivachenko, Andrey;
- Stojanov, Petar;
- McKenna, Aaron;
- Lander, Eric S.;
- Gabriel, Stacey;
- Getz, Gad;
- Sougnez, Carrie;
- Imielinski, Marcin;
- Helman, Elena;
- Hernandez, Bryan;
- Pho, Nam H.;
- Meyerson, Matthew;
- Chu, Andy;
- Chun, Hye-Jung E.;
- Mungall, Andrew J.
Publication type:
Article
Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations.
Published in:
Nature, 2012, v. 488, n. 7409, p. 106, doi. 10.1038/nature11329
By:
- Pugh, Trevor J.;
- Weeraratne, Shyamal Dilhan;
- Archer, Tenley C.;
- Pomeranz Krummel, Daniel A.;
- Auclair, Daniel;
- Bochicchio, James;
- Carneiro, Mauricio O.;
- Carter, Scott L.;
- Cibulskis, Kristian;
- Erlich, Rachel L.;
- Greulich, Heidi;
- Lawrence, Michael S.;
- Lennon, Niall J.;
- McKenna, Aaron;
- Meldrim, James;
- Ramos, Alex H.;
- Ross, Michael G.;
- Russ, Carsten;
- Shefler, Erica;
- Sivachenko, Andrey
Publication type:
Article
Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair.
Published in:
Nucleic Acids Research, 2019, v. 47, n. 15, p. 7989, doi. 10.1093/nar/gkz487
By:
- Chen, Wei;
- McKenna, Aaron;
- Schreiber, Jacob;
- Haeussler, Maximilian;
- Yin, Yi;
- Agarwal, Vikram;
- Shendure, Jay
Publication type:
Article
ContEst: estimating cross-contamination of human samples in next-generation sequencing data.
Published in:
Bioinformatics, 2011, v. 27, n. 18, p. 2601, doi. 10.1093/bioinformatics/btr446
By:
- Cibulskis, Kristian;
- McKenna, Aaron;
- Fennell, Tim;
- Banks, Eric;
- DePristo, Mark;
- Getz, Gad
Publication type:
Article
Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter.
Published in:
Microbiome, 2020, v. 8, n. 1, p. N.PAG, doi. 10.1186/s40168-020-00908-8
By:
- McKenna, Aaron;
- Ijaz, Umer Zeeshan;
- Kelly, Carmel;
- Linton, Mark;
- Sloan, William T.;
- Green, Brian D.;
- Lavery, Ursula;
- Dorrell, Nick;
- Wren, Brendan W.;
- Richmond, Anne;
- Corcionivoschi, Nicolae;
- Gundogdu, Ozan
Publication type:
Article
Systematic genomic and translational efficiency studies of uveal melanoma.
Published in:
PLoS ONE, 2017, v. 12, n. 6, p. 1, doi. 10.1371/journal.pone.0178189
By:
- Johnson, Chelsea Place;
- Kim, Ivana K.;
- Esmaeli, Bita;
- Amin-Mansour, Ali;
- Treacy, Daniel J.;
- Carter, Scott L.;
- Hodis, Eran;
- Wagle, Nikhil;
- Seepo, Sara;
- Yu, Xiaoxing;
- Lane, Anne Marie;
- Gragoudas, Evangelos S.;
- Vazquez, Francisca;
- Nickerson, Elizabeth;
- Cibulskis, Kristian;
- McKenna, Aaron;
- Gabriel, Stacey B.;
- Getz, Gad;
- Van Allen, Eliezer M.;
- ‘t Hoen, Peter A. C.
Publication type:
Article

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