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Identification of Somatic Structural Variants in Solid Tumors by Optical Genome Mapping.
Published in:
Journal of Personalized Medicine, 2021, v. 11, n. 2, p. 142, doi. 10.3390/jpm11020142
By:
- Goldrich, David Y.;
- LaBarge, Brandon;
- Chartrand, Scott;
- Zhang, Lijun;
- Sadowski, Henry B.;
- Zhang, Yang;
- Pham, Khoa;
- Way, Hannah;
- Lai, Chi-Yu Jill;
- Pang, Andy Wing Chun;
- Clifford, Benjamin;
- Hastie, Alex R.;
- Oldakowski, Mark;
- Goldenberg, David;
- Broach, James R.;
- Fantozzi, Silvia
Publication type:
Article
BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes.
Published in:
Plant Biotechnology Journal, 2016, v. 14, n. 7, p. 1523, doi. 10.1111/pbi.12513
By:
- Staňková, Helena;
- Hastie, Alex R.;
- Chan, Saki;
- Vrána, Jan;
- Tulpová, Zuzana;
- Kubaláková, Marie;
- Visendi, Paul;
- Hayashi, Satomi;
- Luo, Mingcheng;
- Batley, Jacqueline;
- Edwards, David;
- Doležel, Jaroslav;
- Šimková, Hana
Publication type:
Article
Yeast two-hybrid interaction partner screening through in vivo Cre-mediated Binary Interaction Tag generation.
Published in:
Nucleic Acids Research, 2007, v. 35, n. 21, p. e141, doi. 10.1093/nar/gkm894
By:
- Hastie, Alex R.;
- Pruitt, Steven C.
Publication type:
Article
Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly.
Published in:
Nature Biotechnology, 2012, v. 30, n. 8, p. 771, doi. 10.1038/nbt.2303
By:
- Lam, Ernest T;
- Hastie, Alex;
- Lin, Chin;
- Ehrlich, Dean;
- Das, Somes K;
- Austin, Michael D;
- Deshpande, Paru;
- Cao, Han;
- Nagarajan, Niranjan;
- Xiao, Ming;
- Kwok, Pui-Yan
Publication type:
Article
Structural forms of the human amylase locus and their relationships to SNPs, haplotypes and obesity.
Published in:
Nature Genetics, 2015, v. 47, n. 8, p. 921, doi. 10.1038/ng.3340
By:
- Usher, Christina L;
- Pato, Carlos N;
- Pato, Michele T;
- McCarthy, Mark I;
- Altshuler, David M;
- Handsaker, Robert E;
- McCarroll, Steven A;
- Esko, Tõnu;
- Tuke, Marcus A;
- Weedon, Michael N;
- Frayling, Timothy M;
- Hastie, Alex R;
- Cao, Han;
- Moon, Jennifer E;
- Hirschhorn, Joel N;
- Kashin, Seva;
- Fuchsberger, Christian;
- Boehnke, Michael;
- Metspalu, Andres
Publication type:
Article
Assembly and diploid architecture of an individual human genome via single-molecule technologies.
Published in:
Nature Methods, 2015, v. 12, n. 8, p. 780, doi. 10.1038/nmeth.3454
By:
- Pendleton, Matthew;
- Sebra, Robert;
- Pang, Andy Wing Chun;
- Ummat, Ajay;
- Franzen, Oscar;
- Rausch, Tobias;
- Stütz, Adrian M;
- Stedman, William;
- Anantharaman, Thomas;
- Hastie, Alex;
- Dai, Heng;
- Fritz, Markus Hsi-Yang;
- Cao, Han;
- Cohain, Ariella;
- Deikus, Gintaras;
- Durrett, Russell E;
- Blanchard, Scott C;
- Altman, Roger;
- Chin, Chen-Shan;
- Guo, Yan
Publication type:
Article
Chromosome-length genome assembly and karyotype of the endangered black-footed ferret (Mustela nigripes).
Published in:
Journal of Heredity, 2023, v. 114, n. 5, p. 539, doi. 10.1093/jhered/esad035
By:
- Kliver, Sergei;
- Houck, Marlys L;
- Perelman, Polina L;
- Totikov, Azamat;
- Tomarovsky, Andrey;
- Dudchenko, Olga;
- Omer, Arina D;
- Colaric, Zane;
- Weisz, David;
- Aiden, Erez Lieberman;
- Chan, Saki;
- Hastie, Alex;
- Komissarov, Aleksey;
- Ryder, Oliver A;
- Graphodatsky, Alexander;
- Johnson, Warren E;
- Maldonado, Jesús E;
- Pukazhenthi, Budhan S;
- Marinari, Paul E;
- Wildt, David E
Publication type:
Article
Construction and comparison of three reference‐quality genome assemblies for soybean.
Published in:
Plant Journal, 2019, v. 100, n. 5, p. 1066, doi. 10.1111/tpj.14500
By:
- Valliyodan, Babu;
- Cannon, Steven B.;
- Bayer, Philipp E.;
- Shu, Shengqiang;
- Brown, Anne V.;
- Ren, Longhui;
- Jenkins, Jerry;
- Chung, Claire Y.‐L.;
- Chan, Ting‐Fung;
- Daum, Christopher G.;
- Plott, Christopher;
- Hastie, Alex;
- Baruch, Kobi;
- Barry, Kerrie W.;
- Huang, Wei;
- Patil, Gunvant;
- Varshney, Rajeev K.;
- Hu, Haifei;
- Batley, Jacqueline;
- Yuan, Yuxuan
Publication type:
Article
Discovery of multi‐megabase polymorphic inversions by chromosome conformation capture sequencing in large‐genome plant species.
Published in:
Plant Journal, 2018, v. 96, n. 6, p. 1309, doi. 10.1111/tpj.14109
By:
- Himmelbach, Axel;
- Ruban, Alevtina;
- Walde, Ines;
- Šimková, Hana;
- Doležel, Jaroslav;
- Hastie, Alex;
- Stein, Nils;
- Mascher, Martin
Publication type:
Article
Comprehensive definition of genome features in Spirodela polyrhiza by high-depth physical mapping and short-read DNA sequencing strategies.
Published in:
Plant Journal, 2017, v. 89, n. 3, p. 617, doi. 10.1111/tpj.13400
By:
- Michael, Todd P.;
- Bryant, Douglas;
- Gutierrez, Ryan;
- Borisjuk, Nikolai;
- Chu, Philomena;
- Zhang, Hanzhong;
- Xia, Jing;
- Zhou, Junfei;
- Peng, Hai;
- El Baidouri, Moaine;
- Hallers, Boudewijn;
- Hastie, Alex R.;
- Liang, Tiffany;
- Acosta, Kenneth;
- Gilbert, Sarah;
- McEntee, Connor;
- Jackson, Scott A.;
- Mockler, Todd C.;
- Zhang, Weixiong;
- Lam, Eric
Publication type:
Article
Rapid Genome Mapping in Nanochannel Arrays for Highly Complete and Accurate <i>De Novo</i> Sequence Assembly of the Complex <i>Aegilops tauschii</i> Genome.
Published in:
PLoS ONE, 2013, v. 8, n. 2, p. 1, doi. 10.1371/journal.pone.0055864
By:
- Hastie, Alex R.;
- Dong, Lingli;
- Smith, Alexis;
- Finklestein, Jeff;
- Lam, Ernest T.;
- Huo, Naxin;
- Cao, Han;
- Kwok, Pui-Yan;
- Deal, Karin R.;
- Dvorak, Jan;
- Luo, Ming-Cheng;
- Gu, Yong;
- Xiao, Ming
Publication type:
Article
Improvement of the banana "Musa acuminata" reference sequence using NGS data and semi-automated bioinformatics methods.
Published in:
BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2579-4
By:
- Martin, Guillaume;
- Baurens, Franc-Christophe;
- Droc, Gaëtan;
- Rouard, Mathieu;
- Cenci, Alberto;
- Kilian, Andrzej;
- Hastie, Alex;
- Doležel, Jaroslav;
- Aury, Jean-Marc;
- Alberti, Adriana;
- Carreel, Françoise;
- D'Hont, Angélique
Publication type:
Article
Genetic Predisposition to Neurological Complications in Patients with COVID-19.
Published in:
2023
By:
- Sahajpal, Nikhil Shri;
- Hastie, Alex R.;
- Schieck, Maximilian;
- Mondal, Ashis K.;
- Felde, Marc;
- van der Made, Caspar I.;
- Chou, Janet S.;
- Randolph, Adrienne G.;
- Illig, Thomas;
- Zody, Michael C.;
- Brownstein, Catherine A.;
- Beggs, Alan H.;
- Hoischen, Alexander;
- Chaubey, Alka;
- Kolhe, Ravindra
Publication type:
Case Study
Multi-platform discovery of haplotype-resolved structural variation in human genomes.
Published in:
Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-018-08148-z
By:
- Chaisson, Mark J. P.;
- Sanders, Ashley D.;
- Zhao, Xuefang;
- Malhotra, Ankit;
- Porubsky, David;
- Rausch, Tobias;
- Gardner, Eugene J.;
- Rodriguez, Oscar L.;
- Guo, Li;
- Collins, Ryan L.;
- Fan, Xian;
- Wen, Jia;
- Handsaker, Robert E.;
- Fairley, Susan;
- Kronenberg, Zev N.;
- Kong, Xiangmeng;
- Hormozdiari, Fereydoun;
- Lee, Dillon;
- Wenger, Aaron M.;
- Hastie, Alex R.
Publication type:
Article
Genome maps across 26 human populations reveal population-specific patterns of structural variation.
Published in:
Nature Communications, 2019, v. 10, n. 1, p. 1, doi. 10.1038/s41467-019-08992-7
By:
- Levy-Sakin, Michal;
- Pastor, Steven;
- Mostovoy, Yulia;
- Li, Le;
- Leung, Alden K. Y.;
- McCaffrey, Jennifer;
- Young, Eleanor;
- Lam, Ernest T.;
- Hastie, Alex R.;
- Wong, Karen H. Y.;
- Chung, Claire Y. L.;
- Ma, Walfred;
- Sibert, Justin;
- Rajagopalan, Ramakrishnan;
- Jin, Nana;
- Chow, Eugene Y. C.;
- Chu, Catherine;
- Poon, Annie;
- Lin, Chin;
- Naguib, Ahmed
Publication type:
Article
Detection of Genomic Structural Variations Associated with Drug Sensitivity and Resistance in Acute Leukemia.
Published in:
Cancers, 2024, v. 16, n. 2, p. 418, doi. 10.3390/cancers16020418
By:
- Finlay, Darren;
- Murad, Rabi;
- Hong, Karl;
- Lee, Joyce;
- Pang, Andy Wing Chun;
- Lai, Chi-Yu;
- Clifford, Benjamin;
- Burian, Carol;
- Mason, James;
- Hastie, Alex R.;
- Yin, Jun;
- Vuori, Kristiina
Publication type:
Article
Clinical Utility of Optical Genome Mapping and 523-Gene Next Generation Sequencing Panel for Comprehensive Evaluation of Myeloid Cancers.
Published in:
Cancers, 2023, v. 15, n. 12, p. 3214, doi. 10.3390/cancers15123214
By:
- Sahajpal, Nikhil Shri;
- Mondal, Ashis K.;
- Singh, Harmanpreet;
- Vashisht, Ashutosh;
- Ananth, Sudha;
- Saul, Daniel;
- Hastie, Alex R.;
- Hilton, Benjamin;
- DuPont, Barbara R.;
- Savage, Natasha M.;
- Kota, Vamsi;
- Chaubey, Alka;
- Cortes, Jorge E.;
- Kolhe, Ravindra
Publication type:
Article
Encountering Other Men at the Movies: Racialised Masculinities on the Internet Movie Database (IMDb).
Published in:
Participations: Journal of Audience & Reception Studies, 2024, v. 20, n. 1, p. 49
By:
- Hastie, Alex
Publication type:
Article
Fully phased sequence of a diploid human genome determined de novo from the DNA of a single individual.
Published in:
G3: Genes | Genomes | Genetics, 2020, v. 10, n. 9, p. 1, doi. 10.1534/g3.119.400995
By:
- Soifer, Ilya;
- Fong, Nicole L.;
- Yi, Nelda;
- Ireland, Andrea T.;
- Lam, Irene;
- Sooknah, Matthew;
- Paw, Jonathan S.;
- Peluso, Paul;
- Concepcion, Gregory T.;
- Rank, David;
- Hastie, Alex R.;
- Jojic, Vladimir;
- Graham Ruby, J.;
- Botstein, David;
- Roy, Margaret A.
Publication type:
Article
Public access, private land, and spatial politics: The geographical importance of the right of way in Coventry, England.
Published in:
Transactions of the Institute of British Geographers, 2022, v. 47, n. 2, p. 484, doi. 10.1111/tran.12514
By:
- Thorogood, Joe;
- Hastie, Alex;
- Hill‐Butler, Charley
Publication type:
Article
Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius.
Published in:
Nature Communications, 2016, v. 7, n. 2, p. 10164, doi. 10.1038/ncomms10164
By:
- Rosenfeld, Jeffrey A.;
- Reeves, Darryl;
- Brugler, Mercer R.;
- Narechania, Apurva;
- Simon, Sabrina;
- Durrett, Russell;
- Foox, Jonathan;
- Shianna, Kevin;
- Schatz, Michael C.;
- Gandara, Jorge;
- Afshinnekoo, Ebrahim;
- Lam, Ernest T.;
- Hastie, Alex R.;
- Chan, Saki;
- Cao, Han;
- Saghbini, Michael;
- Kentsis, Alex;
- Planet, Paul J.;
- Kholodovych, Vladyslav;
- Tessler, Michael
Publication type:
Article
Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum.
Published in:
Nature, 2015, v. 527, n. 7579, p. 508, doi. 10.1038/nature15714
By:
- VanBuren, Robert;
- Bryant, Doug;
- Edger, Patrick P.;
- Tang, Haibao;
- Burgess, Diane;
- Challabathula, Dinakar;
- Spittle, Kristi;
- Hall, Richard;
- Gu, Jenny;
- Lyons, Eric;
- Freeling, Michael;
- Bartels, Dorothea;
- Ten Hallers, Boudewijn;
- Hastie, Alex;
- Michael, Todd P.;
- Mockler, Todd C.
Publication type:
Article
Analytic Validation of Optical Genome Mapping in Hematological Malignancies.
Published in:
Biomedicines, 2023, v. 11, n. 12, p. 3263, doi. 10.3390/biomedicines11123263
By:
- Pang, Andy W. C.;
- Kosco, Karena;
- Sahajpal, Nikhil S.;
- Sridhar, Arthi;
- Hauenstein, Jen;
- Clifford, Benjamin;
- Estabrook, Joey;
- Chitsazan, Alex D.;
- Sahoo, Trilochan;
- Iqbal, Anwar;
- Kolhe, Ravindra;
- Raca, Gordana;
- Hastie, Alex R.;
- Chaubey, Alka
Publication type:
Article
Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays.
Published in:
Genetics, 2016, v. 202, n. 1, p. 351, doi. 10.1534/genetics.115.183483
By:
- Mak, Angel C. Y.;
- Lai, Yvonne Y. Y.;
- Lam, Ernest T.;
- Tsz-Piu Kwok;
- Leung, Alden K. Y.;
- Poon, Annie;
- Mostovoy, Yulia;
- Hastie, Alex R.;
- Stedman, William;
- Anantharaman, Thomas;
- Andrews, Warren;
- Xiang Zhou;
- Pang, Andy W. C.;
- Heng Dai;
- Chu, Catherine;
- Chin Lin;
- Wu, Jacob J. K.;
- L. Li, Catherine M.;
- Jing-Woei Li;
- Yim, Aldrin K. Y.
Publication type:
Article
Optical Genome Mapping for Applications in Repeat Expansion Disorders.
Published in:
Current Protocols, 2024, v. 4, n. 7, p. 1, doi. 10.1002/cpz1.1094
By:
- van der Sanden, Bart;
- Neveling, Kornelia;
- Pang, Andy Wing Chun;
- Shukor, Syukri;
- Gallagher, Michael D.;
- Burke, Stephanie L.;
- Kamsteeg, Erik‐Jan;
- Hastie, Alex;
- Hoischen, Alexander
Publication type:
Article
Correction: Optical Genome Mapping for Oncology Applications.
Published in:
Current Protocols, 2023, v. 3, n. 11, p. 1, doi. 10.1002/cpz1.946
By:
- Sahajpal, Nikhil Shri;
- Mondal, Ashis K.;
- Hastie, Alex;
- Chaubey, Alka;
- Kolhe, Ravindra
Publication type:
Article
Optical Genome Mapping for Oncology Applications.
Published in:
Current Protocols, 2023, v. 3, n. 10, p. 1, doi. 10.1002/cpz1.910
By:
- Sahajpal, Nikhil Shri;
- Mondal, Ashis K.;
- Hastie, Alex;
- Chaubey, Alka;
- Kolhe, Ravindra
Publication type:
Article
Comparative Benchmarking of Optical Genome Mapping and Chromosomal Microarray Reveals High Technological Concordance in CNV Identification and Additional Structural Variant Refinement.
Published in:
Genes, 2023, v. 14, n. 10, p. 1868, doi. 10.3390/genes14101868
By:
- Barseghyan, Hayk;
- Pang, Andy Wing Chun;
- Clifford, Benjamin;
- Serrano, Moises A.;
- Chaubey, Alka;
- Hastie, Alex R.
Publication type:
Article
Optical Genome Mapping: Integrating Structural Variations for Precise Homologous Recombination Deficiency Score Calculation.
Published in:
Genes, 2023, v. 14, n. 9, p. 1683, doi. 10.3390/genes14091683
By:
- Sahajpal, Nikhil Shri;
- Mondal, Ashis K.;
- Vashisht, Ashutosh;
- Singh, Harmanpreet;
- Pang, Andy Wing Chun;
- Saul, Daniel;
- Nivin, Omar;
- Hilton, Benjamin;
- DuPont, Barbara R.;
- Kota, Vamsi;
- Savage, Natasha M.;
- Hastie, Alex R.;
- Chaubey, Alka;
- Kolhe, Ravindra
Publication type:
Article
Optical Genome Mapping and Single Nucleotide Polymorphism Microarray: An Integrated Approach for Investigating Products of Conception.
Published in:
Genes, 2022, v. 13, n. 4, p. 643, doi. 10.3390/genes13040643
By:
- Sahajpal, Nikhil Shri;
- Mondal, Ashis K.;
- Ananth, Sudha;
- Pundkar, Chetan;
- Jones, Kimya;
- Williams, Colin;
- Fee, Timothy;
- Weissman, Amanda;
- Tripodi, Giuseppe;
- Oza, Eesha;
- Gavrilova-Jordan, Larisa;
- Omar, Nivin;
- Hastie, Alex R.;
- DuPont, Barbara R.;
- Layman, Lawrence;
- Chaubey, Alka;
- Kolhe, Ravindra
Publication type:
Article
Optical Genome Mapping as a Next-Generation Cytogenomic Tool for Detection of Structural and Copy Number Variations for Prenatal Genomic Analyses.
Published in:
Genes, 2021, v. 12, n. 3, p. 398, doi. 10.3390/genes12030398
By:
- Sahajpal, Nikhil Shri;
- Barseghyan, Hayk;
- Kolhe, Ravindra;
- Hastie, Alex;
- Chaubey, Alka;
- Choy, Richard
Publication type:
Article
Assessing structural variation in a personal genome--towards a human reference diploid genome.
Published in:
BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1479-3
By:
- English, Adam C.;
- Salerno, William J.;
- Hampton, Oliver A.;
- Gonzaga-Jauregui, Claudia;
- Ambreth, Shruthi;
- Ritter, Deborah I.;
- Beck, Christine R.;
- Davis, Caleb F.;
- Dahdouli, Mahmoud;
- Ma, Singer;
- Carroll, Andrew;
- Veeraraghavan, Narayanan;
- Bruestle, Jeremy;
- Drees, Becky;
- Hastie, Alex;
- Lam, Ernest T.;
- White, Simon;
- Mishra, Pamela;
- Min Wang;
- Yi Han
Publication type:
Article
Assessing structural variation in a personal genome—towards a human reference diploid genome.
Published in:
BMC Genomics, 2015, v. 16, n. 1, p. 286, doi. 10.1186/s12864-015-1479-3
By:
- English, Adam C;
- Salerno, William J;
- Hampton, Oliver A;
- Gonzaga-Jauregui, Claudia;
- Ambreth, Shruthi;
- Ritter, Deborah I;
- Beck, Christine R;
- Davis, Caleb F;
- Dahdouli, Mahmoud;
- Ma, Singer;
- Carroll, Andrew;
- Veeraraghavan, Narayanan;
- Bruestle, Jeremy;
- Drees, Becky;
- Hastie, Alex;
- Lam, Ernest T;
- White, Simon;
- Mishra, Pamela;
- Min Wang;
- Yi Han
Publication type:
Article
Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle.
Published in:
Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-15848-y
By:
- Low, Wai Yee;
- Tearle, Rick;
- Liu, Ruijie;
- Koren, Sergey;
- Rhie, Arang;
- Bickhart, Derek M.;
- Rosen, Benjamin D.;
- Kronenberg, Zev N.;
- Kingan, Sarah B.;
- Tseng, Elizabeth;
- Thibaud-Nissen, Françoise;
- Martin, Fergal J.;
- Billis, Konstantinos;
- Ghurye, Jay;
- Hastie, Alex R.;
- Lee, Joyce;
- Pang, Andy W. C.;
- Heaton, Michael P.;
- Phillippy, Adam M.;
- Hiendleder, Stefan
Publication type:
Article
A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.).
Published in:
DNA Research, 2023, v. 30, n. 1, p. 1, doi. 10.1093/dnares/dsac033
By:
- McGrath, J Mitchell;
- Funk, Andrew;
- Galewski, Paul;
- Ou, Shujun;
- Townsend, Belinda;
- Davenport, Karen;
- Daligault, Hajnalka;
- Johnson, Shannon;
- Lee, Joyce;
- Hastie, Alex;
- Darracq, Aude;
- Willems, Glenda;
- Barnes, Steve;
- Liachko, Ivan;
- Sullivan, Shawn;
- Koren, Sergey;
- Phillippy, Adam;
- Wang, Jie;
- Liu, Tiffany;
- Pulman, Jane
Publication type:
Article

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