The Sequence Alignment/Map format and SAMtools

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1. High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios
   Byrska-Bishop, Marta, Evani, Uday S., Zhao, Xuefang, Basile, Anna O., Abel, Haley J., Regier, Allison A., Corvelo, André, Clarke, Wayne E., Musunuri, Rajeeva, Nagulapalli, Kshithija et al. · 2022 · Cell
2. Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing
   Charissa R. Kim, Ruli Gao, Emi Sei, Rachel Brandt, Johan Hartman, Thomas Hatschek, Nicola Crosetto, Theodoros Foukakis, Nicholas E. Navin · 2018 · Cell
3. Developmental Relationships of Four Exhausted CD8+ T Cell Subsets Reveals Underlying Transcriptional and Epigenetic Landscape Control Mechanisms
   Jean‐Christophe Beltra, Sasikanth Manne, Mohamed S. Abdel-Hakeem, Makoto Kurachi, Josephine Ruth Giles, Zeyu Chen, Valentina Casella, Shin Foong Ngiow, Omar Khan, Yinghui Huang et al. · 2020 · Immunity
4. 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
5. 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
6. 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
7. 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
8. Codon Optimality Is a Major Determinant of mRNA Stability
   Presnyak, Vladimir, Alhusaini, Najwa, Chen, Ying-Hsin, Martin, Sophie, Morris, Nathan, Kline, Nicholas, Olson, Sara, Weinberg, David, Baker, Kristian E., Graveley, Brenton R. et al. · 2015 · Cell
9. Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis
   Iliev, Iliyan D., Funari, Vincent A., Taylor, Kent D., Nguyen, Quoclinh, Reyes, Christopher N., Strom, Samuel P., Brown, Jordan, Becker, Courtney A., Fleshner, Phillip R., Dubinsky, Marla et al. · 2012 · Science
10. 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
11. Stromal gene expression defines poor-prognosis subtypes in colorectal cancer
    Calon, Alexandre, Lonardo, Enza, Berenguer-Llergo, Antonio, Espinet, Elisa, Hernando-Momblona, Xavier, Iglesias, Mar, Sevillano, Marta, Palomo-Ponce, Sergio, Tauriello, Daniele V F, Byrom, Daniel et al. · 2015 · Nature Genetics
12. 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
13. Identification of mobile genetic elements with geNomad
    Antônio Pedro Camargo, Simon Roux, Frederik Schulz, Michal Babinski, Yan Xu, Bin Hu, Patrick Chain, Stephen Nayfach, Nikos C. Kyrpides · 2023 · Nature Biotechnology
14. vcfr : a package to manipulate and visualize variant call format data in R
    Brian J. Knaus, Niklaus J. Grünwald · 2016 · Molecular Ecology Resources
15. SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies
    Manish Goel, Hequan Sun, Wen‐Biao Jiao, Korbinian Schneeberger · 2019 · Genome biology
16. Distinct Immune Cell Populations Define Response to Anti-PD-1 Monotherapy and Anti-PD-1/Anti-CTLA-4 Combined Therapy
    Gide, Tuba N., Quek, Camelia, Menzies, Alexander M., Tasker, Annie T., Shang, Ping, Holst, Jeff, Madore, Jason, Lim, Su Yin, Velickovic, Rebecca, Wongchenko, Matthew et al. · 2019 · Cancer Cell
17. Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation
    Thomas, Andrew Maltez, Manghi, Paolo, Asnicar, Francesco, Pasolli, Edoardo, Armanini, Federica, Zolfo, Moreno, Beghini, Francesco, Manara, Serena, Karcher, Nicolai, Pozzi, Chiara et al. · 2019 · Nature Medicine
18. 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
19. 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
20. 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
21. Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species
    Seungill Kim, Minkyu Park, Seon‐In Yeom, Yong-Min Kim, Je Min Lee, Hyun Ah Lee, Eun–Young Seo, Jaeyoung Choi, Kyeongchae Cheong, Ki Tae Kim et al. · 2014 · Nature Genetics
22. The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA
    Dan Dominissini, Sigrid Nachtergaele, Sharon Moshitch-Moshkovitz, Eyal Peer, Nitzan Kol, Moshe Shay Ben-Haim, Qing Dai, Ayelet Di Segni, Mali Salmon‐Divon, Wesley C. Clark et al. · 2016 · Nature
23. Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant
    Yurkovetskiy, Leonid, Wang, Xue, Pascal, Kristen E., Tomkins-Tinch, Christopher, Nyalile, Thomas P., Wang, Yetao, Baum, Alina, Diehl, William E., Dauphin, Ann, Carbone, Claudia et al. · 2020 · Cell
24. Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome
    Miao Yu, Gary C. Hon, Keith E. Szulwach, Chun‐Xiao Song, Liang Zhang, Audrey Kim, Xuekun Li, Qing Dai, Yin Shen, Beomseok Park et al. · 2012 · Cell
25. Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads
    Kajitani, Rei, Toshimoto, Kouta, Noguchi, Hideki, Toyoda, Atsushi, Ogura, Yoshitoshi, Okuno, Miki, Yabana, Mitsuru, Harada, Masayuki, Nagayasu, Eiji, Maruyama, Haruhiko et al. · 2014 · Genome Research
26. Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements
    Thakore, Pratiksha I, D'Ippolito, Anthony M, Song, Lingyun, Safi, Alexias, Shivakumar, Nishkala K, Kabadi, Ami M, Reddy, Timothy E, Crawford, Gregory E, Gersbach, Charles A · 2015 · Nature Methods
27. 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
28. The draft genome of sweet orange (Citrus sinensis)
    Qiang Xu, Ling-Ling Chen, Xiaoan Ruan, Dijun Chen, Andan Zhu, Chunli Chen, Denis Bertrand, Wen‐Biao Jiao, Baohai Hao, Matthew T. Lyon et al. · 2012 · Nature Genetics
29. Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells
    Thomas M. Carlile, María F. Rojas-Durán, Boris Zinshteyn, Hakyung Shin, Kristen M. Bartoli, Wendy V. Gilbert · 2014 · Nature
30. BamTools: a C++ API and toolkit for analyzing and managing BAM files
    Derek W. Barnett, Erik K. Garrison, Aaron R. Quinlan, Michael P. Strömberg, Gábor Marth · 2011 · Bioinformatics
31. YY1 Is a Structural Regulator of Enhancer-Promoter Loops
    Weintraub, Abraham S., Li, Charles H., Zamudio, Alicia V., Sigova, Alla A., Hannett, Nancy M., Day, Daniel S., Abraham, Brian J., Cohen, Malkiel A., Nabet, Behnam, Buckley, Dennis L. et al. · 2017 · Cell
32. Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia
    Vı́ctor Quesada, Laura Conde, Neus Villamor, Gonzalo R. Ordóñez, Pedro Jares, Laia Bassaganyas, Andrew J. Ramsay, Sı́lvia Beà, Magda Pinyol, Alejandra Martínez‐Trillos et al. · 2011 · Nature Genetics
33. Sensitive tumour detection and classification using plasma cell-free DNA methylomes
    Shen, Shu Yi, Singhania, Rajat, Fehringer, Gordon, Chakravarthy, Ankur, Roehrl, Michael H. A., Chadwick, Dianne, Zuzarte, Philip C., Borgida, Ayelet, Wang, Ting Ting, Li, Tiantian et al. · 2018 · Nature
34. Pan-Genome of Wild and Cultivated Soybeans
    Yucheng Liu, Huilong Du, Pengcheng Li, Yanting Shen, Hua Peng, Shulin Liu, Guoan Zhou, Haikuan Zhang, Zhi Liu, Miao Shi et al. · 2020 · Cell
35. Assessment of global health risk of antibiotic resistance genes
    Zhenyan Zhang, Qi Zhang, Tingzhang Wang, Nuohan Xu, Tao Lu, Wenjie Hong, Josep Peñuelas, Michael Richard Gillings, Meixia Wang, Wenwen Gao et al. · 2022 · Nature Communications
36. SRST2: Rapid genomic surveillance for public health and hospital microbiology labs
    Michael Inouye, Harriet Dashnow, Lesley Raven, Mark B. Schultz, Bernard J. Pope, Takehiro Tomita, Justin Zobel, Kathryn E. Holt · 2014 · Genome Medicine
37. Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing
    Michael Alonge, Ludivine Lebeigle, Melanie Kirsche, Katie Jenike, Shujun Ou, Sergey S. Aganezov, Xingang Wang, Zachary B. Lippman, Michael C. Schatz, Sebastian Soyk · 2022 · Genome biology
38. 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
39. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing
    Shukla, Sanjeev, Kavak, Ersen, Gregory, Melissa, Imashimizu, Masahiko, Shutinoski, Bojan, Kashlev, Mikhail, Oberdoerffer, Philipp, Sandberg, Rickard, Oberdoerffer, Shalini · 2011 · Nature
40. Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma
    Apinya Jusakul, Ioana Cutcutache, Chern Han Yong, Jing Quan Lim, Mi Ni Huang, Nisha Padmanabhan, Vishwa Nellore, Sarinya Kongpetch, Alvin Wei Tian Ng, Ley Moy Ng et al. · 2017 · Cancer Discovery
41. BEDOPS: high-performance genomic feature operations
    Shane J. Neph, Michael S. Kuehn, Alex P. Reynolds, Eric Haugen, Robert E. Thurman, Audra Johnson, Eric Rynes, Matthew T. Maurano, Jeff D. Vierstra, Sean Thomas et al. · 2012 · Bioinformatics
42. The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut
    David J. Bertioli, Steven B. Cannon, Lutz Froenicke, Guodong Huang, Andrew D Farmer, Ethalinda K. S. Cannon, Xin Liu, Dongying Gao, Josh Paul Clevenger, Sudhansu Dash et al. · 2016 · Nature Genetics
43. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans
    Raghavan, Maanasa, Skoglund, Pontus, Graf, Kelly E., Metspalu, Mait, Albrechtsen, Anders, Moltke, Ida, Rasmussen, Simon, Stafford Jr, Thomas W., Orlando, Ludovic, Metspalu, Ene et al. · 2014 · Nature
44. Heightened Innate Immune Responses in the Respiratory Tract of COVID-19 Patients
    Zhuo Long Zhou, Lili Ren, Li Zhang, Jiaxin Zhong, Yan Xiao, Zhilong Jia, Li Guo, Jing Yang, Chun Wang, Shuai Jiang et al. · 2020 · Cell Host & Microbe
45. The genomic signature of dog domestication reveals adaptation to a starch-rich diet
    Axelsson, Erik, Ratnakumar, Abhirami, Arendt, Maja-Louise, Maqbool, Khurram, Webster, Matthew T., Perloski, Michele, Liberg, Olof, Arnemo, Jon M., Hedhammar, Åke, Lindblad-Toh, Kerstin · 2013 · Nature
46. Completing bacterial genome assemblies with multiplex MinION sequencing
    Ryan R. Wick, Louise M. Judd, Claire L. Gorrie, Kathryn E. Holt · 2017 · Microbial Genomics
47. Anti-tumour immunity controlled through mRNA m6A methylation and YTHDF1 in dendritic cells
    Han, Dali, Liu, Jun, Chen, Chuanyuan, Dong, Lihui, Liu, Yi, Chang, Renbao, Huang, Xiaona, Liu, Yuanyuan, Wang, Jianying, Dougherty, Urszula et al. · 2019 · Nature
48. The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates
    Camille Berthelot, Frédéric Brunet, Domitille Chalopin, Amélie Juanchich, Maria Bernard, Benjamin Noël, Pascal Bento, Corinne Da Silva, Karine Labadie, Adriana Alberti et al. · 2014 · Nature Communications
49. Rewiring of the Fruit Metabolome in Tomato Breeding
    Guangtao Zhu, Shouchuang Wang, Zejun Huang, Shuaibin Zhang, Qinggang Liao, Chunzhi Zhang, Tao Lin, Qin Mao, Peng Meng, Chenkun Yang et al. · 2018 · Cell
50. Genomic analyses provide insights into the history of tomato breeding
    Tao Lin, Guangtao Zhu, Junhong Zhang, Xiangyang Xu, Qinghui Yu, Zheng Zheng, Zhonghua Zhang, Yaoyao Lun, Shuai Li, Xiaoxuan Wang et al. · 2014 · Nature Genetics
51. Using Tablet for visual exploration of second-generation sequencing data
    Iain Milne, Gordon Stephen, Micha Bayer, Peter Cock, Leighton Pritchard, Linda Cardle, Paul D. Shaw, David Marshall · 2012 · Briefings in Bioinformatics
52. Zc3h13 Regulates Nuclear RNA m6A Methylation and Mouse Embryonic Stem Cell Self-Renewal
    Jing Wen, Ruitu Lyu, Honghui Ma, Hongjie Shen, Chenxi He, Jiahua Wang, Fangfang Jiao, Hang Liu, Pengyuan Yang, Li Tan et al. · 2018 · Molecular Cell
53. Comparative population genomics of maize domestication and improvement
    Matthew B. Hufford, Xun Xu, Joost van Heerwaarden, Tanja Pyhäjärvi, Jer-Ming Chia, Reed A. Cartwright, Robert J. Elshire, Jeffrey C. Glaubitz, Kate E Guill, Shawn M. Kaeppler et al. · 2012 · Nature Genetics
54. Joint profiling of chromatin accessibility and gene expression in thousands of single cells
    Cao, Junyue, Cusanovich, Darren A., Ramani, Vijay, Aghamirzaie, Delasa, Pliner, Hannah A., Hill, Andrew J., Daza, Riza M., McFaline-Figueroa, Jose L., Packer, Jonathan S., Christiansen, Lena et al. · 2018 · Science
55. 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
56. Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms
    Rolf Sommer Kaas, Pimlapas Leekitcharoenphon, Frank M. Aarestrup, Ole Lund · 2014 · PLoS ONE
57. Therapeutic targeting of BET bromodomain proteins in castration-resistant prostate cancer
    Irfan Ahmed Asangani, Vijaya L. Dommeti, Xiaoju Wang, Rohit Malik, Marcin P. Cieslik, Rendong Yang, June F Escara-Wilke, Kari Wilder-Romans, Sudheer Dhanireddy, Carl G. Engelke et al. · 2014 · Nature
58. Scaling read aligners to hundreds of threads on general-purpose processors
    Ben Langmead, Christopher Wilks, Valentin Antonescu, Rone Charles · 2018 · Bioinformatics
59. Genomic Analysis of Non- NF2 Meningiomas Reveals Mutations in TRAF7 , KLF4 , AKT1 , and SMO
    Victoria Elizabeth Clark, Zeynep Erson-Omay, Akdes Serin Harmancı, Jun Yin, Justin L. Cotney, Koray Özduman, Timuçin Avşar, Jie Li, Phillip B. Murray, Octavian Henegariu et al. · 2013 · Science
60. Characterizing and measuring bias in sequence data
    Ross, Michael G, Russ, Carsten, Costello, Maura, Hollinger, Andrew, Lennon, Niall J, Hegarty, Ryan, Nusbaum, Chad, Jaffe, David B · 2013 · Genome Biology
61. Insertion-and-deletion-derived tumour-specific neoantigens and the immunogenic phenotype: a pan-cancer analysis
    Samra Turajlic, Kevin Litchfield, Hang Xu, Rachel Rosenthal, Nicholas McGranahan, James L. Reading, Yien Ning Sophia Wong, Andrew Rowan, Nnennaya Kanu, Maise Al Bakir et al. · 2017 · The Lancet Oncology
62. Anchored multiplex PCR for targeted next-generation sequencing
    Zongli Zheng, Matthew R. Liebers, Boryana H. Zhelyazkova, Yi Cao, Divya Panditi, Kerry D. Lynch, Juxiang Chen, Hayley E. Robinson, Hyo Sup Shim, Juliann Chmielecki et al. · 2014 · Nature Medicine
63. The UCSC genome browser and associated tools
    Kuhn, R. M., Haussler, D., Kent, W. J. · 2013 · Briefings in Bioinformatics
64. Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study
    Timothy M Walker, Camilla L. C. Ip, Ruth Harrell, Jason T. Evans, Georgia Kapatai, Martin J Dedicoat, David W. Eyre, Daniel J. Wilson, Peter Michael Hawkey, Derrick W. Crook et al. · 2012 · The Lancet Infectious Diseases
65. RNA-SeQC: RNA-seq metrics for quality control and process optimization
    DeLuca, David S., Levin, Joshua Z., Sivachenko, Andrey, Fennell, Timothy, Nazaire, Marc-Danie, Williams, Chris, Reich, Michael, Winckler, Wendy, Getz, Gad · 2012 · Bioinformatics
66. Expression of Linear and Novel Circular Forms of an INK4/ARF-Associated Non-Coding RNA Correlates with Atherosclerosis Risk
    Christin Elizabeth Burd, William R. Jeck, Yan Liu, Hanna Kelly Sanoff, Zefeng Wang, Norman E. Sharpless · 2010 · PLoS Genetics
67. Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma
    A. Gordon Robertson, Juliann Shih, Christina S. F. Yau, Ewan A. Gibb, Junna Oba, Karen L. Mungall, Julian M. Hess, Vladislav Uzunangelov, Vonn Walter, Ludmila Danilova et al. · 2017 · Cancer Cell
68. Lactic acid promotes PD-1 expression in regulatory T cells in highly glycolytic tumor microenvironments
    Kumagai, Shogo, Koyama, Shohei, Itahashi, Kota, Tanegashima, Tokiyoshi, Lin, Yi-tzu, Togashi, Yosuke, Kamada, Takahiro, Irie, Takuma, Okumura, Genki, Kono, Hidetoshi et al. · 2022 · Cancer Cell
69. Meta-omics analysis of elite athletes identifies a performance-enhancing microbe that functions via lactate metabolism
    Scheiman, Jonathan, Luber, Jacob M., Chavkin, Theodore A., MacDonald, Tara, Tung, Angela, Pham, Loc-Duyen, Wibowo, Marsha C., Wurth, Renee C., Punthambaker, Sukanya, Tierney, Braden T. et al. · 2019 · Nature Medicine
70. Role of TP53 mutations in the origin and evolution of therapy-related acute myeloid leukaemia
    Wong, Terrence N., Ramsingh, Giridharan, Young, Andrew L., Miller, Christopher A., Touma, Waseem, Welch, John S., Lamprecht, Tamara L., Shen, Dong, Hundal, Jasreet, Fulton, Robert S. et al. · 2015 · Nature
71. Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients
    André Kahles, Kjong-Van Lehmann, Nora C. Toussaint, Matthias Hüser, Stefan G. Stark, Timo T. Sachsenberg, Oliver Stegle, Oliver Kohlbacher, Chris Sander, Rory Johnson et al. · 2018 · Cancer Cell
72. Rapid and precise alignment of raw reads against redundant databases with KMA
    Philip T. L. C. Clausen, Frank M. Aarestrup, Ole Lund · 2018 · BMC Bioinformatics
73. ipyrad: Interactive assembly and analysis of RADseq datasets
    Deren A. R. Eaton, Isaac Overcast · 2019 · Bioinformatics
74. SAMBLASTER : fast duplicate marking and structural variant read extraction
    Gregory G. Faust, Ira M. Hall · 2014 · Bioinformatics
75. The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities
    James J. Davis, Alice Rebecca Wattam, Ramy Karam Aziz, Thomas Scott Brettin, Ralph M. Butler, Rory Butler, Philippe Chlenski, Neal R. Conrad, Allan W. Dickerman, Emily M. Dietrich et al. · 2019 · Nucleic Acids Research
76. Individual intestinal symbionts induce a distinct population of RORγ ⁺ regulatory T cells
    Sefik, Esen, Geva-Zatorsky, Naama, Oh, Sungwhan, Konnikova, Liza, Zemmour, David, McGuire, Abigail Manson, Burzyn, Dalia, Ortiz-Lopez, Adriana, Lobera, Mercedes, Yang, Jianfei et al. · 2015 · Science
77. Finding the genomic basis of local adaptation: pitfalls, practical solutions, and future directions
    Hoban, Sean, Kelley, Joanna L., Lotterhos, Katie E., Antolin, Michael F., Bradburd, Gideon, Lowry, David B., Poss, Mary L., Reed, Laura K., Storfer, Andrew, Whitlock, Michael C. · 2016 · The American Naturalist
78. A survey of sequence alignment algorithms for next-generation sequencing
    Li, H., Homer, N. · 2010 · Briefings in Bioinformatics
79. BlobTools: Interrogation of genome assemblies
    Dominik R. Laetsch, Mark Blaxter · 2017 · F1000Research
80. Great ape genetic diversity and population history
    Javier Prado-Martinez, Peter H. Sudmant, Jeffrey M. Kidd, Heng Li, Joanna L. Kelley, Belén Lorente-Galdós, Krishna R. Veeramah, August E. Woerner, Timothy D. O’Connor, Gabriel Santpere et al. · 2013 · Nature
81. The sequence read archive: explosive growth of sequencing data
    Kodama, Y., Shumway, M., Leinonen, R., on behalf of the International Nucleotide Sequence Database Collaboration · 2012 · Nucleic Acids Research
82. Gateways to the FANTOM5 promoter level mammalian expression atlas
    Lizio, Marina, Harshbarger, Jayson, Shimoji, Hisashi, Severin, Jessica, Kasukawa, Takeya, Sahin, Serkan, Abugessaisa, Imad, Fukuda, Shiro, Hori, Fumi, Ishikawa-Kato, Sachi et al. · 2015 · Genome Biology
83. A chemical genetic roadmap to improved tomato flavor
    Denise M. Tieman, Guangtao Zhu, Márcio F. R. Resende, Tao Lin, Cuong Nguyen, Dawn H. Bies, José Luís Rambla, Kristty Stephanie Ortiz Beltran, Mark G. Taylor, Bo Zhang et al. · 2017 · Science
84. Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators
    Akihiro Fujimoto, Yasushi Totoki, Tetsuo Abe, Keith A. Boroevich, Fumie Hosoda, Nguyễn Hải Hà, Masayuki Aoki, Naoya Hosono, Michiaki Kubo, Fuyuki Miya et al. · 2012 · Nature Genetics
85. Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells
    Blaschke, Kathryn, Ebata, Kevin T., Karimi, Mohammad M., Zepeda-Martínez, Jorge A., Goyal, Preeti, Mahapatra, Sahasransu, Tam, Angela, Laird, Diana J., Hirst, Martin, Rao, Anjana et al. · 2013 · Nature
86. Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations
    Rausch, Tobias, Jones, David T.W., Zapatka, Marc, Stütz, Adrian M., Zichner, Thomas, Weischenfeldt, Joachim, Jäger, Natalie, Remke, Marc, Shih, David, Northcott, Paul A. et al. · 2012 · Cell
87. Sparse whole-genome sequencing identifies two loci for major depressive disorder
    CONVERGE consortium, Cai, Na, Bigdeli, Tim B., Kretzschmar, Warren, Li, Yihan, Liang, Jieqin, Song, Li, Hu, Jingchu, Li, Qibin, Jin, Wei et al. · 2015 · Nature
88. Landscape of genomic alterations in cervical carcinomas
    Akinyemi I. Ojesina, Lee Lichtenstein, Samuel S. Freeman, Chandra Sekhar Pedamallu, Iván Imaz-Rosshandler, Trevor J. Pugh, Andrew D. Cherniack, Lauren Ambrogio, Kristian Cibulskis, Bjørn Inge Bertelsen et al. · 2013 · Nature
89. Viral and host factors related to the clinical outcome of COVID-19
    Xiaonan Zhang, Yun Tan, Yun Ling, Gang Lü, Feng Liu, Zhigang Yi, Xiaofang Jia, Min Wu, Bisheng Shi, Shuibao Xu et al. · 2020 · Nature
90. Genomically Recoded Organisms Expand Biological Functions
    Marc J. Lajoie, Alexis J. Rovner, Daniel Bryan Goodman, Hans R. Aerni, Adrian D. Haimovich, Gleb Kuznetsov, Jaron A. M. Mercer, Harris H. Wang, Peter A. Carr, Joshua A. Mosberg et al. · 2013 · Science
91. Population genomic and genome-wide association studies of agroclimatic traits in sorghum
    Geoffrey P. Morris, Punna Ramu, Santosh Deshpande, C T Hash, Trushar M. Shah, Hari Deo Upadhyaya, Oscar Riera‐Lizarazu, Patrick J. Brown, Charlotte B. Acharya, Sharon E. Mitchell et al. · 2012 · Proceedings of the National Academy of Sciences
92. Ballgown bridges the gap between transcriptome assembly and expression analysis
    Alyssa C. Frazee, Geo M. Pertea, Andrew E. Jaffe, Ben Langmead, Steven L. Salzberg, Jeffrey T. Leek · 2015 · Nature Biotechnology
93. ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases
    Li Shen, Ning‐Yi Shao, Xiaochuan Liu, Eric J. Nestler · 2014 · BMC Genomics
94. A genomic catalog of Earth’s microbiomes
    Stephen Nayfach, Simon Roux, R. Seshadri, Daniel Udwary, Neha Jacob Varghese, Frederik Schulz, Dongying Wu, David Páez-Espino, I-Min A. Chen, Marcel Huntemann et al. · 2020 · Nature Biotechnology
95. Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR
    Hui Yang, Kai Wang · 2015 · Nature Protocols
96. The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions
    Hamid Bolouri, Jason E. Farrar, Timothy J. Triche, Rhonda E. Ries, Emilia L. Lim, Todd A. Alonzo, Yussanne P. Ma, Richard A. Moore, Andrew J. J. Mungall, Marco A. Marra et al. · 2017 · Nature Medicine
97. Recalibrating equus evolution using the genome sequence of an early middle pleistocene horse
    Orlando, Ludovic, Ginolhac, Aurélien, Zhang, Guojie, Froese, Duane, Albrechtsen, Anders, Stiller, Mathias, Schubert, Mikkel, Cappellini, Enrico, Petersen, Bent, Moltke, Ida et al. · 2013 · Nature
98. A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain
    Davie, Kristofer, Janssens, Jasper, Koldere, Duygu, De Waegeneer, Maxime, Pech, Uli, Kreft, Łukasz, Aibar, Sara, Makhzami, Samira, Christiaens, Valerie, Bravo González-Blas, Carmen et al. · 2018 · Cell
99. Microbial strain-level population structure and genetic diversity from metagenomes
    Truong, Duy Tin, Tett, Adrian, Pasolli, Edoardo, Huttenhower, Curtis, Segata, Nicola · 2017 · Genome Research
100. Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle
     Hans D. Daetwyler, Aurélien Capitan, Hubert Pausch, Paul Stothard, R. van Binsbergen, Rasmus Froberg Brøndum, Xiaoping Liao, Anis Djari, Sabrina C. Rodriguez, Cécile Grohs et al. · 2014 · Nature Genetics