Fast and accurate short read alignment with Burrows-Wheeler transform

Cited by (1,699)

Items 201–300 of 1,699

1. Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics
   Nicolas C. Rochette, Angel G. Rivera‐Colón, Julian Catchen · 2019 · Molecular Ecology
2. Resistance Mechanisms for the Bruton's Tyrosine Kinase Inhibitor Ibrutinib
   Woyach, Jennifer A., Furman, Richard R., Liu, Ta-Ming, Ozer, Hatice Gulcin, Zapatka, Marc, Ruppert, Amy S., Xue, Ling, Li, Daniel Hsieh-Hsin, Steggerda, Susanne M., Versele, Matthias et al. · 2014 · New England Journal of Medicine
3. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
   Aird, Daniel, Ross, Michael G, Chen, Wei-Sheng, Danielsson, Maxwell, Fennell, Timothy, Russ, Carsten, Jaffe, David B, Nusbaum, Chad, Gnirke, Andreas · 2011 · Genome Biology
4. Impact of cytosine methylation on DNA binding specificities of human transcription factors
   Yin, Yimeng, Morgunova, Ekaterina, Jolma, Arttu, Kaasinen, Eevi, Sahu, Biswajyoti, Khund-Sayeed, Syed, Das, Pratyush K., Kivioja, Teemu, Dave, Kashyap, Zhong, Fan et al. · 2017 · Science
5. Spread of SARS-CoV-2 in the Icelandic population
   Gudbjartsson, Daniel F., Helgason, Agnar, Jonsson, Hakon, Magnusson, Olafur T., Melsted, Pall, Norddahl, Gudmundur L., Saemundsdottir, Jona, Sigurdsson, Asgeir, Sulem, Patrick, Agustsdottir, Arna B. et al. · 2020 · New England Journal of Medicine
6. CPGAVAS2, an integrated plastome sequence annotator and analyzer
   Linchun Shi, Haimei Chen, Mei Jiang, Liqiang Wang, Xi Wu, Linfang Huang, Chang Liu · 2019 · Nucleic Acids Research
7. ESR1 ligand-binding domain mutations in hormone-resistant breast cancer
   Weiyi Toy, Yang Shen, Helen H. Won, Bradley Green, Rita A. Sakr, Marie Will, Zhiqiang Li, Kinisha P. Gala, Sean William Fanning, Tari A. King et al. · 2013 · Nature Genetics
8. MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery
   Wang, Kai, Singh, Darshan, Zeng, Zheng, Coleman, Stephen J., Huang, Yan, Savich, Gleb L., He, Xiaping, Mieczkowski, Piotr, Grimm, Sara A., Perou, Charles M. et al. · 2010 · Nucleic Acids Research
9. Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma
   Itay Tirosh, Andrew Sean Venteicher, Christine M. Hebert, Leah E. Escalante, Anoop P. Patel, Keren Yizhak, Jonathan M. Fisher, Christopher Rodman, Christopher Mount, Mariella G. Filbin et al. · 2016 · Nature
10. Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems
    Sergey Shmakov, Omar O. Abudayyeh, Kira S. Makarova, Yuri I. Wolf, Jonathan S. Gootenberg, Ekaterina Semenova, Минахин Леонид Станиславович, Julia Joung, Silvana Konermann, Konstantin Severinov et al. · 2015 · Molecular Cell
11. Mutational signature in colorectal cancer caused by genotoxic pks+ E. coli
    Pleguezuelos-Manzano, Cayetano, Puschhof, Jens, Rosendahl Huber, Axel, van Hoeck, Arne, Wood, Henry M., Nomburg, Jason, Gurjao, Carino, Manders, Freek, Dalmasso, Guillaume, Stege, Paul B. et al. · 2020 · Nature
12. Single-cell messenger RNA sequencing reveals rare intestinal cell types
    Grün, Dominic, Lyubimova, Anna, Kester, Lennart, Wiebrands, Kay, Basak, Onur, Sasaki, Nobuo, Clevers, Hans, van Oudenaarden, Alexander · 2015 · Nature
13. Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations
    O'Roak, Brian J, Deriziotis, Pelagia, Lee, Choli, Vives, Laura, Schwartz, Jerrod J, Girirajan, Santhosh, Karakoc, Emre, MacKenzie, Alexandra P, Ng, Sarah B, Baker, Carl et al. · 2011 · Nature Genetics
14. Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell
    Zong, Chenghang, Lu, Sijia, Chapman, Alec R., Xie, X. Sunney · 2012 · Science
15. Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance
    Shaffer, Sydney M., Dunagin, Margaret C., Torborg, Stefan R., Torre, Eduardo A., Emert, Benjamin, Krepler, Clemens, Beqiri, Marilda, Sproesser, Katrin, Brafford, Patricia A., Xiao, Min et al. · 2017 · Nature
16. Pan-cancer whole-genome analyses of metastatic solid tumours
    Priestley, Peter, Baber, Jonathan, Lolkema, Martijn P., Steeghs, Neeltje, de Bruijn, Ewart, Shale, Charles, Duyvesteyn, Korneel, Haidari, Susan, van Hoeck, Arne, Onstenk, Wendy et al. · 2019 · Nature
17. Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa
    Sarah L. Lebeis, Sur Herrera Paredes, Derek S. Lundberg, Natalie W. Breakfield, Jase Gehring, Meredith McDonald, Stephanie Malfatti, Tijana Glavina del Rio, Corbin D. Jones, Susannah Green Tringe et al. · 2015 · Science
18. Improved maize reference genome with single-molecule technologies
    Yinping Jiao, Paul S. Peluso, Jinghua Shi, Tiffany Y Liang, Michelle C. Stitzer, Bo Wang, Michael S. Campbell, Joshua C. Stein, Xuehong Wei, Chen-Shan Chin et al. · 2017 · Nature
19. NextPolish: a fast and efficient genome polishing tool for long-read assembly
    Jiang Yong Hu, Junpeng Fan, Zongyi Sun, Shanlin Liu · 2019 · Bioinformatics
20. Integrated molecular analysis of clear-cell renal cell carcinoma
    Yusuke Sato, Tetsuichi Yoshizato, Yuichi Shiraishi, Shigekatsu Maekawa, Yusuke Okuno, Takumi Kamura, Teppei Shimamura, Aiko Sato‐Otsubo, Genta Nagae, Hiromichi Suzuki et al. · 2013 · Nature Genetics
21. In vivo genome editing via CRISPR/Cas9 mediated homology-independent targeted integration
    Suzuki, Keiichiro, Tsunekawa, Yuji, Hernandez-Benitez, Reyna, Wu, Jun, Zhu, Jie, Kim, Euiseok J., Hatanaka, Fumiyuki, Yamamoto, Mako, Araoka, Toshikazu, Li, Zhe et al. · 2016 · Nature
22. Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma
    Krauthammer, Michael, Kong, Yong, Ha, Byung Hak, Evans, Perry, Bacchiocchi, Antonella, McCusker, Jamie P, Cheng, Elaine, Davis, Matthew J, Goh, Gerald, Choi, Murim et al. · 2012 · Nature Genetics
23. Target-enrichment strategies for next-generation sequencing
    Lira Mamanova, Alison J. Coffey, Carol E Scott, Iwanka Kozarewa, Emily H. Turner, Akash Kumar, Eleanor K. Howard, Jay Shendure, Dann Turner · 2010 · Nature Methods
24. Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data
    Tim J. Carver, Simon R. Harris, Matthew Berriman, Julian Parkhill, Jacqueline A. Keane · 2011 · Bioinformatics
25. Patient HLA class I genotype influences cancer response to checkpoint blockade immunotherapy
    Chowell, Diego, Morris, Luc G. T., Grigg, Claud M., Weber, Jeffrey K., Samstein, Robert M., Makarov, Vladimir, Kuo, Fengshen, Kendall, Sviatoslav M., Requena, David, Riaz, Nadeem et al. · 2018 · Science
26. Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome
    John L. Bowman, Takayuki Kohchi, Katsuyuki T. Yamato, Jerry W. Jenkins, Shengqiang Shu, Kimitsune Ishizaki, Shohei Yamaoka, Ryuichi Nishihama, Yasukazu Nakamura, Frédéric Berger et al. · 2017 · Cell
27. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform
    Kircher, Martin, Sawyer, Susanna, Meyer, Matthias · 2012 · Nucleic Acids Research
28. BCG Educates Hematopoietic Stem Cells to Generate Protective Innate Immunity against Tuberculosis
    Kaufmann, Eva, Sanz, Joaquin, Dunn, Jonathan L., Khan, Nargis, Mendonça, Laura E., Pacis, Alain, Tzelepis, Fanny, Pernet, Erwan, Dumaine, Anne, Grenier, Jean-Christophe et al. · 2018 · Cell
29. Genome evolution across 1,011 Saccharomyces cerevisiae isolates
    Peter, Jackson, De Chiara, Matteo, Friedrich, Anne, Yue, Jia-Xing, Pflieger, David, Bergström, Anders, Sigwalt, Anastasie, Barre, Benjamin, Freel, Kelle, Llored, Agnès et al. · 2018 · Nature
30. Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory
    Mark Chaisson, Glenn Tesler · 2012 · BMC Bioinformatics
31. Genomic features of response to combination immunotherapy in patients with advanced non-small-cell lung cancer
    Hellmann, Matthew D., Nathanson, Tavi, Rizvi, Hira, Creelan, Benjamin C., Sanchez-Vega, Francisco, Ahuja, Arun, Ni, Ai, Novik, Jacki B., Mangarin, Levi M.B., Abu-Akeel, Mohsen et al. · 2018 · Cancer Cell
32. APOE4 Causes Widespread Molecular and Cellular Alterations Associated with Alzheimer’s Disease Phenotypes in Human iPSC-Derived Brain Cell Types
    Lin, Yuan-Ta, Seo, Jinsoo, Gao, Fan, Feldman, Heather M., Wen, Hsin-Lan, Penney, Jay, Cam, Hugh P., Gjoneska, Elizabeta, Raja, Waseem K., Cheng, Jemmie et al. · 2018 · Neuron
33. The genetic landscape of high-risk neuroblastoma
    Trevor J. Pugh, Olena Morozova, Edward F. Attiyeh, Shahab Asgharzadeh, Jun Stephen Wei, Daniel Auclair, Scott L. Carter, Kristian Cibulskis, Megan Hanna, Adam Kieżun et al. · 2013 · Nature Genetics
34. Integrated Proteogenomic Characterization of HBV-Related Hepatocellular Carcinoma
    Gao, Qiang, Zhu, Hongwen, Dong, Liangqing, Shi, Weiwei, Chen, Ran, Song, Zhijian, Huang, Chen, Li, Junqiang, Dong, Xiaowei, Zhou, Yanting et al. · 2019 · Cell
35. BCG Vaccination Protects against Experimental Viral Infection in Humans through the Induction of Cytokines Associated with Trained Immunity
    Rob J.W. Arts, Simone J.C.F.M. Moorlag, Boris Novakovic, Yang Li, Shuang-Yin Wang, Marije Oosting, Vinod Kumar, Ramnik J. Xavier, Cisca Wijmenga, Leo A. B. Joosten et al. · 2018 · Cell Host & Microbe
36. A Patient-Derived Glioblastoma Organoid Model and Biobank Recapitulates Inter- and Intra-tumoral Heterogeneity
    Jacob, Fadi, Salinas, Ryan D., Zhang, Daniel Y., Nguyen, Phuong T.T., Schnoll, Jordan G., Wong, Samuel Zheng Hao, Thokala, Radhika, Sheikh, Saad, Saxena, Deeksha, Prokop, Stefan et al. · 2020 · Cell
37. Uncovering the roles of rare variants in common disease through whole-genome sequencing
    Cirulli, Elizabeth T., Goldstein, David B. · 2010 · Nature Reviews Genetics
38. Whole-exome sequencing of pancreatic cancer defines genetic diversity and therapeutic targets
    Witkiewicz, Agnieszka K., McMillan, Elizabeth A., Balaji, Uthra, Baek, GuemHee, Lin, Wan-Chi, Mansour, John, Mollaee, Mehri, Wagner, Kay-Uwe, Koduru, Prasad, Yopp, Adam et al. · 2015 · Nature Communications
39. TOX is a critical regulator of tumour-specific T cell differentiation
    Scott, Andrew C., Dündar, Friederike, Zumbo, Paul, Chandran, Smita S., Klebanoff, Christopher A., Shakiba, Mojdeh, Trivedi, Prerak, Menocal, Laura, Appleby, Heather, Camara, Steven et al. · 2019 · Nature
40. Chemically modified guide RNAs enhance CRISPR-Cas genome editing in human primary cells
    Hendel, Ayal, Bak, Rasmus O, Clark, Joseph T, Kennedy, Andrew B, Ryan, Daniel E, Roy, Subhadeep, Steinfeld, Israel, Lunstad, Benjamin D, Kaiser, Robert J, Wilkens, Alec B et al. · 2015 · Nature Biotechnology
41. HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures
    Davies, Helen, Glodzik, Dominik, Morganella, Sandro, Yates, Lucy R, Staaf, Johan, Zou, Xueqing, Ramakrishna, Manasa, Martin, Sancha, Boyault, Sandrine, Sieuwerts, Anieta M et al. · 2017 · Nature Medicine
42. MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization
    Guanliang Meng, YY Li, Chentao Yang, Shanlin Liu · 2019 · Nucleic Acids Research
43. Engineering Quantitative Trait Variation for Crop Improvement by Genome Editing
    Daniel Rodríguez-Leal, Zachary H. Lemmon, Jarrett Man, Madelaine Elisabeth Bartlett, Zachary B. Lippman · 2017 · Cell
44. Genetic and functional drivers of diffuse large B cell lymphoma
    Reddy, Anupama, Zhang, Jenny, Davis, Nicholas S., Moffitt, Andrea B., Love, Cassandra L., Waldrop, Alexander, Leppa, Sirpa, Pasanen, Annika, Meriranta, Leo, Karjalainen-Lindsberg, Marja-Liisa et al. · 2017 · Cell
45. The Ensembl gene annotation system
    Bronwen L. Aken, Sarah Ayling, Daniel G. Barrell, Laura Clarke, V. Curwen, Susan Fairley, Julio Fernandez-Banet, Konstantinos Billis, Carlos García Girón, Thibaut Hourlier et al. · 2016 · Database
46. Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture
    Nadin Rohland, David Reich · 2012 · Genome Research
47. Neural circular RNAs are derived from synaptic genes and regulated by development and plasticity
    You, Xintian, Vlatkovic, Irena, Babic, Ana, Will, Tristan, Epstein, Irina, Tushev, Georgi, Akbalik, Güney, Wang, Mantian, Glock, Caspar, Quedenau, Claudia et al. · 2015 · Nature Neuroscience
48. A human liver cell atlas reveals heterogeneity and epithelial progenitors
    Aizarani, Nadim, Saviano, Antonio, Sagar, Mailly, Laurent, Durand, Sarah, Herman, Josip S., Pessaux, Patrick, Baumert, Thomas F., Grün, Dominic · 2019 · Nature
49. CRISPR/Cas9-mediated gene editing in human tripronuclear zygotes
    Liang, Puping, Xu, Yanwen, Zhang, Xiya, Ding, Chenhui, Huang, Rui, Zhang, Zhen, Lv, Jie, Xie, Xiaowei, Chen, Yuxi, Li, Yujing et al. · 2015 · Protein & Cell
50. Counting absolute numbers of molecules using unique molecular identifiers
    Kivioja, Teemu, Vähärautio, Anna, Karlsson, Kasper, Bonke, Martin, Enge, Martin, Linnarsson, Sten, Taipale, Jussi · 2012 · Nature Methods
51. Toward almost closed genomes with GapFiller
    Marten Boetzer, Walter Pirovano · 2012 · Genome biology
52. The genetic architecture of type 2 diabetes
    Fuchsberger, Christian, Flannick, Jason, Teslovich, Tanya M., Mahajan, Anubha, Agarwala, Vineeta, Gaulton, Kyle J., Ma, Clement, Fontanillas, Pierre, Moutsianas, Loukas, McCarthy, Davis J. et al. · 2016 · Nature
53. Clonal evolution in breast cancer revealed by single nucleus genome sequencing
    Wang, Yong, Waters, Jill, Leung, Marco L., Unruh, Anna, Roh, Whijae, Shi, Xiuqing, Chen, Ken, Scheet, Paul, Vattathil, Selina, Liang, Han et al. · 2014 · Nature
54. Somatic mutant clones colonize the human esophagus with age
    Martincorena, Iñigo, Fowler, Joanna C., Wabik, Agnieszka, Lawson, Andrew R. J., Abascal, Federico, Hall, Michael W. J., Cagan, Alex, Murai, Kasumi, Mahbubani, Krishnaa, Stratton, Michael R. et al. · 2018 · Science
55. Spatial and temporal diversity in genomic instability processes defines lung cancer evolution
    de Bruin, Elza C., McGranahan, Nicholas, Mitter, Richard, Salm, Max, Wedge, David C., Yates, Lucy, Jamal-Hanjani, Mariam, Shafi, Seema, Murugaesu, Nirupa, Rowan, Andrew J. et al. · 2014 · Science
56. Advances in understanding cancer genomes through second-generation sequencing
    Matthew M. Meyerson, Stacey Gabriel, Gad A. Getz · 2010 · Nature Reviews Genetics
57. Genome sequence of a 45,000-year-old modern human from western Siberia
    Fu, Qiaomei, Li, Heng, Moorjani, Priya, Jay, Flora, Slepchenko, Sergey M., Bondarev, Aleksei A., Johnson, Philip L. F., Aximu-Petri, Ayinuer, Prüfer, Kay, de Filippo, Cesare et al. · 2014 · Nature
58. Chinese Glioma Genome Atlas (CGGA): A Comprehensive Resource with Functional Genomic Data from Chinese Glioma Patients
    Zheng Zhao, Kenan Zhang, Qiangwei Wang, Guanzhang Li, Fan Zeng, Ying Zhang, Fan Wu, Ruichao Chai, Zheng Wang, Chuanbao Zhang et al. · 2021 · Genomics Proteomics & Bioinformatics
59. Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean
    Zhengkui Zhou, Yu Jiang, Zheng Wang, Zhiheng Gou, Jun Lyu, Weiyu Li, Yanjun Yu, Liping Shu, Yingjun Zhao, Yanming Ma et al. · 2015 · Nature Biotechnology
60. Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas
    Abeshouse, Adam, Adebamowo, Clement, Adebamowo, Sally N., Akbani, Rehan, Akeredolu, Teniola, Ally, Adrian, Anderson, Matthew L., Anur, Pavana, Appelbaum, Elizabeth L., Armenia, Joshua et al. · 2017 · Cell
61. The genomic landscape of diffuse intrinsic pontine glioma and pediatric non-brainstem high-grade glioma
    Gang Wu, Yongjin Li, Chunxu Qu, Xiang 'Anthony' Chen, Michael N. Edmonson, Xiaotu Ma, Panduka Nagahawatte, Erin Hedlund, Michael Rusch, Robert Huether et al. · 2014 · Nature Genetics
62. Towards precision medicine
    Ashley, Euan A. · 2016 · Nature Reviews Genetics
63. The U6 snRNA m 6 A Methyltransferase METTL16 Regulates SAM Synthetase Intron Retention
    Kathryn E. Pendleton, Beibei Chen, Kuanqing Liu, Olga V. Hunter, Yang Xie, Benjamin P. Tu, Nicholas K. Conrad · 2017 · Cell
64. DNA sequencing at 40: past, present and future
    Jay Shendure, Shankar Balasubramanian, George McDonald Church, Walter Gilbert, Jane Rogers, Jeffery A. Schloss, R Waterston · 2017 · Nature
65. Promoter-bound METTL3 maintains myeloid leukaemia by m6A-dependent translation control
    Isaia Barbieri, Konstantinos Tzelepis, Luca Pandolfini, Junwei Shi, Gonzalo Millán-Zambrano, Samuel C. Robson, Demetrios Aspris, Valentina Migliori, Andrew J. Bannister, Namshik Han et al. · 2017 · Nature
66. Organoid Profiling Identifies Common Responders to Chemotherapy in Pancreatic Cancer
    Tiriac, Hervé, Belleau, Pascal, Engle, Dannielle D., Plenker, Dennis, Deschênes, Astrid, Somerville, Tim D. D., Froeling, Fieke E. M., Burkhart, Richard A., Denroche, Robert E., Jang, Gun-Ho et al. · 2018 · Cancer Discovery
67. Sequential cancer mutations in cultured human intestinal stem cells
    Drost, Jarno, van Jaarsveld, Richard H., Ponsioen, Bas, Zimberlin, Cheryl, van Boxtel, Ruben, Buijs, Arjan, Sachs, Norman, Overmeer, René M., Offerhaus, G. Johan, Begthel, Harry et al. · 2015 · Nature
68. Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine
    Chun‐Xiao Song, Keith E. Szulwach, Ye Fu, Qing Dai, Chengqi Yi, Xuekun Li, Yujing Li, Chih-Hsin Chen, Wen Zhang, Xing Jian et al. · 2010 · Nature Biotechnology
69. Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer
    Chung, Woosung, Eum, Hye Hyeon, Lee, Hae-Ock, Lee, Kyung-Min, Lee, Han-Byoel, Kim, Kyu-Tae, Ryu, Han Suk, Kim, Sangmin, Lee, Jeong Eon, Park, Yeon Hee et al. · 2017 · Nature Communications
70. Gene co-expression analysis for functional classification and gene–disease predictions
    van Dam, Sipko, Võsa, Urmo, van der Graaf, Adriaan, Franke, Lude, de Magalhães, João Pedro · 2017 · Briefings in Bioinformatics
71. Loss-of-Function Mutations in <i>APOC3,</i> Triglycerides, and Coronary Disease
    The TG and HDL Working Group of the Exome Sequencing Project, National Heart, Lung, and Blood Institute · 2014 · New England Journal of Medicine
72. Identification of genomic alterations in oesophageal squamous cell cancer
    Yongmei Song, Lin Li, Yunwei Ou, Zhibo Gao, En‐Min Li, Xiangchun Li, Weimin Zhang, Jiaqian Wang, Li‐Yan Xu, Yong Zhou et al. · 2014 · Nature
73. Long‐term expanding human airway organoids for disease modeling
    Sachs, Norman, Papaspyropoulos, Angelos, Zomer‐van Ommen, Domenique D, Heo, Inha, Böttinger, Lena, Klay, Dymph, Weeber, Fleur, Huelsz‐Prince, Guizela, Iakobachvili, Nino, Amatngalim, Gimano D et al. · 2019 · The EMBO Journal
74. Clonal evolution and resistance to EGFR blockade in the blood of colorectal cancer patients
    Giulia Siravegna, Benedetta Mussolin, Michela Buscarino, Giorgio Corti, Andrea Cassingena, Giovanni Crisafulli, Agostino Ponzetti, Chiara Cremolini, Alessio Amatu, Calogero Lauricella et al. · 2015 · Nature Medicine
75. vcfr : a package to manipulate and visualize variant call format data in R
    Brian J. Knaus, Niklaus J. Grünwald · 2016 · Molecular Ecology Resources
76. Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer
    Charles M. Rudin, Steffen Durinck, Eric W. Stawiski, John Thomas Poirier, Zora D. Modrusan, David S. Shames, Emily Anne Smith Bergbower, Yinghui Guan, James Shin, Joseph Guillory et al. · 2012 · Nature Genetics
77. Enhanced detection of circulating tumor DNA by fragment size analysis
    Florent C. Mouliere, Dineika Chandrananda, Anna Piskorz, Elizabeth K. Moore, James Morris, Lise Barlebo Ahlborn, Richard James Mair, Teodora Goranova, Francesco Marass, Katrin Heider et al. · 2018 · Science Translational Medicine
78. Computational methods for transcriptome annotation and quantification using RNA-seq
    Garber, Manuel, Grabherr, Manfred G, Guttman, Mitchell, Trapnell, Cole · 2011 · Nature Methods
79. Using Drosophila melanogaster as a Model for Genotoxic Chemical Mutational Studies with a New Program, SnpSift
    Pablo Cingolani, Viral M. Patel, Melissa Coon, Tung Thanh Nguyen, Susan J. Land, Douglas Mark Ruden, Xiangyi Lu · 2012 · Frontiers in Genetics
80. A natural killer–dendritic cell axis defines checkpoint therapy–responsive tumor microenvironments
    Barry, Kevin C., Hsu, Joy, Broz, Miranda L., Cueto, Francisco J., Binnewies, Mikhail, Combes, Alexis J., Nelson, Amanda E., Loo, Kimberly, Kumar, Raj, Rosenblum, Michael D. et al. · 2018 · Nature Medicine
81. Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library
    Koike-Yusa, Hiroko, Li, Yilong, Tan, E-Pien, Velasco-Herrera, Martin Del Castillo, Yusa, Kosuke · 2014 · Nature Biotechnology
82. RETRACTED ARTICLE: Microbiome analyses of blood and tissues suggest cancer diagnostic approach
    Poore, Gregory D., Kopylova, Evguenia, Zhu, Qiyun, Carpenter, Carolina, Fraraccio, Serena, Wandro, Stephen, Kosciolek, Tomasz, Janssen, Stefan, Metcalf, Jessica, Song, Se Jin et al. · 2020 · Nature · Retracted
83. SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies
    Manish Goel, Hequan Sun, Wen‐Biao Jiao, Korbinian Schneeberger · 2019 · Genome biology
84. Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome
    Sahar Abubucker, Nicola Segata, Johannes B. Goll, Alyxandria M. Schubert, Jacques Izard, Brandi L. Cantarel, Beltran Rodriguez-Mueller, Jeremy Zucker, Mathangi Thiagarajan, Bernard Henrissat et al. · 2012 · PLoS Computational Biology
85. Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications
    Andy Rimmer, Hang T. T. Phan, Iain Mathieson, Zamin Iqbal, Stephen R.F. Twigg, Andrew O.M. Wilkie, Gil McVean, Gerton A. Lunter · 2014 · Nature Genetics
86. The genome of the pear ( Pyrus bretschneideri Rehd.)
    Jun Wu, Zhiwen Wang, Zebin Shi, Shu Zhang, Ray Ming, Shilin Zhu, Muhammad Awais Khan, Shutian Tao, Schuyler Safi Korban, Hao Wang et al. · 2012 · Genome Research
87. An RNA vaccine drives immunity in checkpoint-inhibitor-treated melanoma
    Sahin, Ugur, Oehm, Petra, Derhovanessian, Evelyna, Jabulowsky, Robert A., Vormehr, Mathias, Gold, Maike, Maurus, Daniel, Schwarck-Kokarakis, Doreen, Kuhn, Andreas N., Omokoko, Tana et al. · 2020 · Nature
88. Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads
    Lunter, Gerton, Goodson, Martin · 2011 · Genome Research
89. High tumor mutation burden fails to predict immune checkpoint blockade response across all cancer types
    Daniel James McGrail, P.G. Pilié, N.U. Rashid, Leonie Voorwerk, Maarten Slagter, Marleen Kok, Eric W. Jonasch, Mustafa Khasraw, A.B. Heimberger, Bora Lim et al. · 2021 · Annals of Oncology
90. Clinical application of whole-exome sequencing across clinical indications
    Kyle Retterer, Jane Juusola, Megan T. Cho, Patrik Vitazka, Francisca Millan, Federica Gibellini, Annette Vertino-Bell, Nizar Smaoui, Julie Neidich, Kristin G. Monaghan et al. · 2015 · Genetics in Medicine
91. Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton
    Yan Hu, Jiedan Chen, Lei Fang, Zhiyuan Zhang, Wei Ma, Yongchao Niu, Longzhen Ju, Jieqiong Deng, Ting Zhao, Jinmin Lian et al. · 2019 · Nature Genetics
92. Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing
    Xue, Zhigang, Huang, Kevin, Cai, Chaochao, Cai, Lingbo, Jiang, Chun-yan, Feng, Yun, Liu, Zhenshan, Zeng, Qiao, Cheng, Liming, Sun, Yi E. et al. · 2013 · Nature
93. Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans
    Iñaki Comas, Mireia Coscollá, Tāo Luò, Sònia Borrell, Kathryn E. Holt, Midori Kato‐Maeda, Julian Parkhill, Bijaya Malla, Stefan Berg, Guy Edward Thwaites et al. · 2013 · Nature Genetics
94. Summarizing and correcting the GC content bias in high-throughput sequencing
    Benjamini, Yuval, Speed, Terence P. · 2012 · Nucleic Acids Research
95. Insights into human genetic variation and population history from 929 diverse genomes
    Bergström, Anders, McCarthy, Shane A., Hui, Ruoyun, Almarri, Mohamed A., Ayub, Qasim, Danecek, Petr, Chen, Yuan, Felkel, Sabine, Hallast, Pille, Kamm, Jack et al. · 2020 · Science
96. Regulatory evolution of innate immunity through co-option of endogenous retroviruses
    Chuong, Edward B., Elde, Nels C., Feschotte, Cédric · 2016 · Science
97. An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar
    Nathan D. Grubaugh, Karthik Gangavarapu, Joshua Quick, Nathaniel L. Matteson, Jaqueline Góes de Jesus, Bradley J. Main, Amanda L. Tan, Lauren M. Paul, Doug E. Brackney, Saran Grewal et al. · 2019 · Genome biology
98. Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies
    Chen, Rita E., Zhang, Xianwen, Case, James Brett, Winkler, Emma S., Liu, Yang, VanBlargan, Laura A., Liu, Jianying, Errico, John M., Xie, Xuping, Suryadevara, Naveenchandra et al. · 2021 · Nature Medicine
99. Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism
    Willsey, A. Jeremy, Sanders, Stephan J., Li, Mingfeng, Dong, Shan, Tebbenkamp, Andrew T., Muhle, Rebecca A., Reilly, Steven K., Lin, Leon, Fertuzinhos, Sofia, Miller, Jeremy A. et al. · 2013 · Cell
100. Exome sequencing in amyotrophic lateral sclerosis identifies risk genes and pathways
     Cirulli, Elizabeth T., Lasseigne, Brittany N., Petrovski, Slavé, Sapp, Peter C., Dion, Patrick A., Leblond, Claire S., Couthouis, Julien, Lu, Yi-Fan, Wang, Quanli, Krueger, Brian J. et al. · 2015 · Science