The Sequence Alignment/Map format and SAMtools

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1. Development of a high density 600K SNP genotyping array for chicken
   Andreas Kranis, Almas Gheyas, Clarissa Boschiero, Frances S Turner, Le Yu, Sarah E. Smith, Richard Talbot, Ali Pirani, Fiona Brew, Pete Kaiser et al. · 2013 · BMC Genomics
2. The SMAD2/3 interactome reveals that TGFβ controls m6A mRNA methylation in pluripotency
   Alessandro Bertero, Stephanie Emma Brown, Pedro Madrigal, Anna Osnato, Daniel Ortmann, Loukia Yiangou, Juned Kadiwala, Nina C. Hubner, Igor Ruiz de los Mozos, Christoph Sadée et al. · 2018 · Nature
3. Arabidopsis Transcriptome Analysis Reveals Key Roles of Melatonin in Plant Defense Systems
   Sarah M. Weeda, Na Zhang, Xiaolei Zhao, Grace M. Ndip, Yang‐Dong Guo, Gregory A. Buck, Conggui Fu, Shuxin Ren · 2014 · PLoS ONE
4. The genomes of two key bumblebee species with primitive eusocial organization
   Ben M. Sadd, Seth Michael Barribeau, Guy Bloch, Dirk C. de Graaf, Peter K. Dearden, Christine G. Elsik, Jürgen R. Gadau, Cornelis J.P. Grimmelikhuijzen, Martin Hasselmann, Jeffrey D. Lozier et al. · 2015 · Genome biology
5. Identification of rare sequence variation underlying heritable pulmonary arterial hypertension
   Gräf, Stefan, Haimel, Matthias, Bleda, Marta, Hadinnapola, Charaka, Southgate, Laura, Li, Wei, Hodgson, Joshua, Liu, Bin, Salmon, Richard M., Southwood, Mark et al. · 2018 · Nature Communications
6. Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome
   Shoemaker, Robert, Deng, Jie, Wang, Wei, Zhang, Kun · 2010 · Genome Research
7. Ancient Wolf Genome Reveals an Early Divergence of Domestic Dog Ancestors and Admixture into High-Latitude Breeds
   Pontus Skoglund, Erik Ersmark, Eleftheria Palkopoulou, Love Dalén · 2015 · Current Biology
8. Unlocking the vault: next‐generation museum population genomics
   Ke Bi, Tyler P. Linderoth, Dan Vanderpool, Jeffrey Martin Good, Rasmus Nielsen, Craig C. Moritz · 2013 · Molecular Ecology
9. SVIM: structural variant identification using mapped long reads
   David Heller, Martin Vingron · 2019 · Bioinformatics
10. Non-viral, specifically targeted CAR-T cells achieve high safety and efficacy in B-NHL
    Jiqin Zhang, Yongxian Hu, Jiaxuan Yang, Wei Li, Mingming Zhang, Qingcan Wang, Linjie Zhang, Guoqing Wei, Yue Tian, Kui Zhao et al. · 2022 · Nature
11. An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations
    Julie Brind’Amour, Sheng Liu, Matthew B. Hudson, Carol C. L. Chen, Mohammad Mahdi Karimi, Matthew C. Lorincz · 2015 · Nature Communications
12. CottonFGD: an integrated functional genomics database for cotton
    Τao Zhu, Chengzhen Liang, Zhigang Meng, Guoqing Sun, Zhaoghong Meng, Sandui Guo, Rui Zhang · 2017 · BMC Plant Biology
13. A cis-regulatory atlas in maize at single-cell resolution
    Alexandre P. Marand, Zongliang Chen, Andrea Gallavotti, Robert J. Schmitz · 2021 · Cell
14. Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells
    Alexej S. Abyzov, Jessica Mariani, Dean Palejev, Ying Zhang, Michael Seamus Haney, Livia Tomasini, Anthony F. Ferrandino, Lior Rosenberg Belmaker, Anna M. Szekely, Michael Wilson et al. · 2012 · Nature
15. Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis
    Thomas Briese, Amit Kapoor, Nischay Mishra, Komal Jain, Arvind Kumar, Omar Jabado, Walter Ian Lipkin · 2015 · mBio
16. Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity
    Fei Duan, Jorge Duitama, Sahar Al Seesi, Cory M. Ayres, Steven A. Corcelli, Arpita Pawashe, Tatiana Blanchard, David McMahon, John Sidney, Alessandro Sette et al. · 2014 · The Journal of Experimental Medicine
17. Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription
    Rui Xiao, Jiayu Chen, Zhengyu Liang, Daji Luo, Geng Chen, Zhi John Lu, Yang Chen, Bing Zhou, Hairi Li, Xian Du et al. · 2019 · Cell
18. Alternative 3′ UTRs modify the localization, regulatory potential, stability, and plasticity of mRNAs in neuronal compartments
    Tushev, Georgi, Glock, Caspar, Heumüller, Maximilian, Biever, Anne, Jovanovic, Marko, Schuman, Erin M. · 2018 · Neuron
19. Bottlenecks and Selective Sweeps during Domestication Have Increased Deleterious Genetic Variation in Dogs
    Marsden, Clare D., Ortega-Del Vecchyo, Diego, O’Brien, Dennis P., Taylor, Jeremy F., Ramirez, Oscar, Vilà, Carles, Marques-Bonet, Tomas, Schnabel, Robert D., Wayne, Robert K., Lohmueller, Kirk E. · 2016 · Proceedings of the National Academy of Sciences
20. Pangenome Graphs
    Eizenga, Jordan M., Novak, Adam M., Sibbesen, Jonas A., Heumos, Simon, Ghaffaari, Ali, Hickey, Glenn, Chang, Xian, Seaman, Josiah D., Rounthwaite, Robin, Ebler, Jana et al. · 2020 · Annual Review of Genomics and Human Genetics
21. Community characteristics of the gut microbiomes of competitive cyclists
    Petersen, Lauren M., Bautista, Eddy J., Nguyen, Hoan, Hanson, Blake M., Chen, Lei, Lek, Sai H., Sodergren, Erica, Weinstock, George M. · 2017 · Microbiome
22. The landscape of somatic mutations in Down syndrome–related myeloid disorders
    Kenichi Yoshida, Tsutomu Toki, Yusuke Okuno, Rika Kanezaki, Yuichi Shiraishi, Aiko Sato‐Otsubo, Masashi Sanada, Myoung-ja Park, Kiminori Terui, Hiromichi Suzuki et al. · 2013 · Nature Genetics
23. Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity
    Renmao Tian, Daliang Ning, Zhili He, Ping Zhang, Sarah J. Spencer, Shu-Hong Gao, Weiling Shi, Linwei Wu, Ya Zhang, Yunfeng Yang et al. · 2020 · Microbiome
24. Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome
    Xiaomin Liu, Xin Tong, Yuanqiang Zou, Xiaoqian Lin, Hui Zhao, Liu Tian, Zhuye Jie, Qi Wang, Zhe Zhang, Haorong Lu et al. · 2022 · Nature Genetics
25. Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data
    Schirmer, Melanie, D’Amore, Rosalinda, Ijaz, Umer Z., Hall, Neil, Quince, Christopher · 2016 · BMC Bioinformatics
26. Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis
    Sahraeian, Sayed Mohammad Ebrahim, Mohiyuddin, Marghoob, Sebra, Robert, Tilgner, Hagen, Afshar, Pegah T., Au, Kin Fai, Bani Asadi, Narges, Gerstein, Mark B., Wong, Wing Hung, Snyder, Michael P. et al. · 2017 · Nature Communications
27. Poretools: a toolkit for analyzing nanopore sequence data
    Nicholas James Loman, Aaron R. Quinlan · 2014 · Bioinformatics
28. Posttranscriptional m6A Editing of HIV-1 mRNAs Enhances Viral Gene Expression
    Edward M. Kennedy, Hal P. Bogerd, Anand V. R. Kornepati, Dong Kang, Delta Ghoshal, Joy B. Marshall, Brigid Chiyoko Poling, Kevin Tsai, Nandan S. Gokhale, Stacy M. Horner et al. · 2016 · Cell Host & Microbe
29. Selective Loss of PARG Restores PARylation and Counteracts PARP Inhibitor-Mediated Synthetic Lethality
    Ewa Gogola, Alexandra A. Duarte, Julian R. de Ruiter, Wouter W. Wiegant, Jonas Andreas Schmid, Roebi de Bruijn, Dominic I. James, Sergi Guerrero Llobet, Daniël J. Vis, Stefano Annunziato et al. · 2018 · Cancer Cell
30. Increased MAPK reactivation in early resistance to dabrafenib/trametinib combination therapy of BRAF-mutant metastatic melanoma
    Long, Georgina V., Fung, Carina, Menzies, Alexander M., Pupo, Gulietta M., Carlino, Matteo S., Hyman, Jessica, Shahheydari, Hamideh, Tembe, Varsha, Thompson, John F., Saw, Robyn P. et al. · 2014 · Nature Communications
31. Reliable Identification of Genomic Variants from RNA-Seq Data
    Robert Piskol, Gokul Ramaswami, Jin Billy Li · 2013 · The American Journal of Human Genetics
32. Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden
    Quan Long, Fernando A. Rabanal, Dazhe Meng, Christian D. Huber, Ashley Farlow, Alexander Platzer, Qingrun Zhang, Bjarni Jóhann Vilhjálmsson, Arthur Korte, Viktoria Nizhynska et al. · 2013 · Nature Genetics
33. A human cell atlas of fetal chromatin accessibility
    Silvia Domcke, Andrew J. Hill, Riza M. Daza, Junyue Cao, Diana R. O’Day, Hannah A. Pliner, Kimberly A. Aldinger, Dmitry Pokholok, Fan Zhang, Jennifer H. Milbank et al. · 2020 · Science
34. A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package
    Meng, Jia, Lu, Zhiliang, Liu, Hui, Zhang, Lin, Zhang, Shaowu, Chen, Yidong, Rao, Manjeet K., Huang, Yufei · 2014 · Methods
35. Single-cell multi-omics sequencing of mouse early embryos and embryonic stem cells
    Guo, Fan, Li, Lin, Li, Jingyun, Wu, Xinglong, Hu, Boqiang, Zhu, Ping, Wen, Lu, Tang, Fuchou · 2017 · Cell Research
36. Using Exome Sequencing to Reveal Mutations in TREM2 Presenting as a Frontotemporal Dementia–like Syndrome Without Bone Involvement
    Guerreiro, Rita João, Lohmann, Ebba, Brás, José Miguel, Gibbs, Jesse Raphael, Rohrer, Jonathan D., Gurunlian, Nicole, Dursun, Burcu, Bilgic, Basar, Hanagasi, Hasmet, Gurvit, Hakan et al. · 2013 · JAMA Neurology
37. MutMap+: Genetic Mapping and Mutant Identification without Crossing in Rice
    Rym Fekih, Hiroki Takagi, Muluneh Tamiru, Akira Abe, Satoshi Natsume, Hiroki Yaegashi, Shailendra Sharma, Shiveta Sharma, Hiroyuki Kanzaki, Hideo Matsumura et al. · 2013 · PLoS ONE
38. Whole Exome Sequencing to Identify a Novel Gene (Caveolin-1) Associated With Human Pulmonary Arterial Hypertension
    Eric D. Austin, Lijiang Ma, Charles A. LeDuc, Erika B. Rosenzweig, Alain Borczuk, John A. Phillips, Teresa Palomero, Pavel Sumazin, Hyunjae Ryan Kim, Megha H. Talati et al. · 2012 · Circulation Cardiovascular Genetics
39. Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing
    Huashui Ai, Xiaodong Fang, Bin Juan Yang, Zhiyong Huang, Hao Chen, Likai Mao, Feng Zhang, Lu Zhang, Leilei Cui, Weiming He et al. · 2015 · Nature Genetics
40. Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV
    J. Fah Sathirapongsasuti, Hane Lee, Basil A. J. Horst, Georg Brunner, Alistair J. Cochran, Scott W. Binder, John F Quackenbush, Stanley F. Nelson · 2011 · Bioinformatics
41. Strain-level microbial epidemiology and population genomics from shotgun metagenomics
    Matthias Scholz, Doyle V. Ward, Edoardo Pasolli, T. Tolio, Moreno Zolfo, Francesco Asnicar, Duy Tin Truong, Adrian Tett, Ardythe Luxion Morrow, Nicola Segata · 2016 · Nature Methods
42. Aristolochic acids and their derivatives are widely implicated in liver cancers in Taiwan and throughout Asia
    Alvin Wei Tian Ng, Song Ling Poon, Mi Ni Huang, Jing Quan Lim, Arnoud Boot, Willie Yu, Yuka Suzuki, Saranya Thangaraju, Cedric Chuan Young Ng, Patrick B. O. Tan et al. · 2017 · Science Translational Medicine
43. Resistance gene cloning from a wild crop relative by sequence capture and association genetics
    Sanu Arora, Burkhard Steuernagel, Kumar Gaurav, Sutha Chandramohan, Yunming Long, Oadi Matny, Ryan Johnson, Jacob M. Enk, Sambasivam K. Periyannan, Narinder Singh et al. · 2019 · Nature Biotechnology
44. A Hypermorphic Missense Mutation in PLCG2 , Encoding Phospholipase Cγ2, Causes a Dominantly Inherited Autoinflammatory Disease with Immunodeficiency
    Zhou, Qing, Lee, Geun-Shik, Brady, Jillian, Datta, Shrimati, Katan, Matilda, Sheikh, Afzal, Martins, Marta S., Bunney, Tom D., Santich, Brian H., Moir, Susan et al. · 2012 · The American Journal of Human Genetics
45. Genome-wide copy number analysis of single cells
    Timour Baslan, Jude Kendall, Linda Rodgers, Hilary Cox, Mike Riggs, Asya Stepansky, Jennifer E. Troge, Kandasamy Ravi, Diane Esposito, B. Vasantha Lakshmi et al. · 2012 · Nature Protocols
46. The real cost of sequencing: higher than you think!
    Andrea Sboner, Xinmeng Jasmine Mu, Dov S. Greenbaum, Raymond K. Auerbach, Mark Gerstein · 2011 · Genome biology
47. R-ChIP Using Inactive RNase H Reveals Dynamic Coupling of R-loops with Transcriptional Pausing at Gene Promoters
    Liang Chen, Jiayu Chen, Xuan Zhang, Ying Gu, Rui Xiao, Changwei Shao, Peng Tang, Hao Qian, Daji Luo, Hairi Li et al. · 2017 · Molecular Cell
48. Effector T-cell trafficking between the leptomeninges and the cerebrospinal fluid
    Schläger, Christian, Körner, Henrike, Krueger, Martin, Vidoli, Stefano, Haberl, Michael, Mielke, Dorothee, Brylla, Elke, Issekutz, Thomas, Cabañas, Carlos, Nelson, Peter J. et al. · 2016 · Nature
49. Exome sequencing and the genetic basis of complex traits
    Kiezun, Adam, Garimella, Kiran, Do, Ron, Stitziel, Nathan O, Neale, Benjamin M, McLaren, Paul J, Gupta, Namrata, Sklar, Pamela, Sullivan, Patrick F, Moran, Jennifer L et al. · 2012 · Nature Genetics
50. Fine mapping of genome activation in bovine embryos by RNA sequencing
    Alexander Graf, Stefan Krebs, Valeri Zakhartchenko, Björn Schwalb, Helmut Blum, Eckhard Wolf · 2014 · Proceedings of the National Academy of Sciences
51. Characterization of a Novel Influenza Virus in Cattle and Swine: Proposal for a New Genus in the Orthomyxoviridae Family
    Ben M. Hause, Emily A. Collin, Runxia Liu, Bing Huang, Zizhang Sheng, Wuxun Lu, Dan Wang, Eric A. Nelson, Feng Li · 2014 · mBio
52. Cross-Comparison of Exome Analysis, Next-Generation Sequencing of Amplicons, and the iPLEX® ADME PGx Panel for Pharmacogenomic Profiling
    Eng Wee Chua, Simone L. Cree, Kim N. T. Ton, Klaus Lehnert, Phillip Shepherd, Nuala Ann Helsby, Martin Alexander Kennedy · 2016 · Frontiers in Pharmacology
53. The prevalence, evolution and chromatin signatures of plant regulatory elements
    Zefu Lu, Alexandre P. Marand, William A. Ricci, Christina L. Ethridge, Xiaoyu Zhang, Robert J. Schmitz · 2019 · Nature Plants
54. Locoregional delivery of IL-13Rα2-targeting CAR-T cells in recurrent high-grade glioma: a phase 1 trial
    Christine E. Brown, Jonathan C. Hibbard, Darya Alizadeh, M. Suzette Blanchard, Heini M. Natri, Dongrui Wang, Julie R. Ostberg, Brenda Aguilar, Jamie R. Wagner, Jinny A. Paul et al. · 2024 · Nature Medicine
55. Estimating genetic kin relationships in prehistoric populations
    Monroy Kuhn, Jose Manuel, Jakobsson, Mattias, Günther, Torsten · 2018 · PLOS ONE
56. UVB-Induced Tumor Heterogeneity Diminishes Immune Response in Melanoma
    Yochai Wolf, Osnat Bartok, Sushant Patkar, Gitit Bar Eli, Sapir Cohen, Kevin Litchfield, Ronen Levy, Alejandro Jiménez-Sánchez, Sophie Trabish, Joo Sang Lee et al. · 2019 · Cell
57. Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses
    Hong Zhou, Jingkai Ji, Xing Chen, Yuhai Bi, Juan Li, Qihui Wang, Tao Hu, Hao Song, Runchu Zhao, Yanhua Chen et al. · 2021 · Cell
58. Genomic Diversity and Admixture Differs for Stone-Age Scandinavian Foragers and Farmers
    Pontus Skoglund, Helena Malmström, Ayça Omrak, Maanasa Raghavan, Cristina E. Valdiosera, Torsten Günther, Per N Hall, Kristiina Tambets, Jüri Parik, Karl-Göran Sjögren et al. · 2014 · Science
59. The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems
    Krzysztof Chylinski, Anaïs Le Rhun, Emmanuelle Charpentier · 2013 · RNA Biology
60. Comparative sequencing analysis reveals high genomic concordance between matched primary and metastatic colorectal cancer lesions
    Angela Rose Brannon, Efsevia Vakiani, Brooke E. Sylvester, Sasinya N. Scott, Gregory C McDermott, Ronak H. Shah, Krishan Kania, Agnes J. Viale, Dayna M. Oschwald, Vladimir Vacic et al. · 2014 · Genome biology
61. Identifying Recent Adaptations in Large-Scale Genomic Data
    Grossman, Sharon R., Andersen, Kristian G., Shlyakhter, Ilya, Tabrizi, Shervin, Winnicki, Sarah, Yen, Angela, Park, Daniel J., Griesemer, Dustin, Karlsson, Elinor K., Wong, Sunny H. et al. · 2013 · Cell
62. The deubiquitinase OTULIN is an essential negative regulator of inflammation and autoimmunity
    Damgaard, Rune Busk, Walker, Jennifer A., Marco-Casanova, Paola, Morgan, Neil V., Titheradge, Hannah L., Elliott, Paul R., McHale, Duncan, Maher, Eamonn R., McKenzie, Andrew N.J., Komander, David · 2016 · Cell
63. ArrayExpress update—trends in database growth and links to data analysis tools
    Gabriella Rustici, Nikolay N. Kolesnikov, Marco Brandizi, Tony Burdett, Miroslaw Dylag, Ibrahim Emam, Anna Farne, Emma Hastings, Jon Ison, Maria Keays et al. · 2012 · Nucleic Acids Research
64. METTL3 regulates heterochromatin in mouse embryonic stem cells
    Wenqi Xu, Jiahui Li, Chenxi He, Jing Wen, Honghui Ma, Bowen Rong, 刁建波, Liyong Wang, Jiahua Wang, Feizhen Wu et al. · 2021 · Nature
65. Exome sequencing identifies somatic mutations of DDX3X in natural killer/T-cell lymphoma
    Lu Jiang, Zhaohui Gu, Zi‐Xun Yan, Xia Zhao, Yinyin Xie, Ziguan Zhang, Chun‐Ming Pan, Yuan Hu, Changping Cai, Ying Dong et al. · 2015 · Nature Genetics
66. Web Apollo: a web-based genomic annotation editing platform
    Eduardo Lee, Gregg A. Helt, Justin Reese, Monica C. Muñoz-Torres, Christopher P. Childers, Robert Buels, Lincoln David Stein, Ian H Holmes, Christine G. Elsik, Suzanna Lewis · 2013 · Genome biology
67. The Chinese pine genome and methylome unveil key features of conifer evolution
    Shihui Niu, Jiang Li, Wenhao Bo, Weifei Yang, Andrea Zuccolo, Stefania Giacomello, Xi Chen, Fang-Xu Han, Junhe Yang, Yi-tong Song et al. · 2021 · Cell
68. Genome evolution and diversity of wild and cultivated potatoes
    Dié Tang, Yuxin Jia, Jinzhe Zhang, Hongbo Li, Lin Zhang Cheng, Pei Wang, Zhigui Bao, Zhihong Liu, Shuangshuang Feng, Xijian Zhu et al. · 2022 · Nature
69. Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits
    Corradin, Olivia, Saiakhova, Alina, Akhtar-Zaidi, Batool, Myeroff, Lois, Willis, Joseph, Cowper-Sal·lari, Richard, Lupien, Mathieu, Markowitz, Sanford, Scacheri, Peter C. · 2014 · Genome Research
70. LTR-Retrotransposon Control by tRNA-Derived Small RNAs
    Schorn, Andrea J., Gutbrod, Michael J., LeBlanc, Chantal, Martienssen, Rob · 2017 · Cell
71. Million-year-old DNA sheds light on the genomic history of mammoths
    van der Valk, Tom, Pečnerová, Patrícia, Díez-del-Molino, David, Bergström, Anders, Oppenheimer, Jonas, Hartmann, Stefanie, Xenikoudakis, Georgios, Thomas, Jessica A., Dehasque, Marianne, Sağlıcan, Ekin et al. · 2021 · Nature
72. Virological characteristics of the SARS-CoV-2 Omicron BA.2 spike
    Daichi Yamasoba, Izumi Kimura, Hesham Nasser, Yuhei Morioka, Naganori Nao, Jumpei Ito, Keiya Uriu, Masumi Tsuda, Jiří Zahradník, Kotaro Shirakawa et al. · 2022 · Cell
73. Dynamic Transcription of Distinct Classes of Endogenous Retroviral Elements Marks Specific Populations of Early Human Embryonic Cells
    Jonathan Göke, Xinyi Lu, Yun-Shen Chan, Huck‐Hui Ng, Lam-Ha Ly, Friedrich Sachs, Iwona Szczerbinska · 2015 · Cell stem cell
74. Tomato facultative parthenocarpy results from Sl AGAMOUS ‐ LIKE 6 loss of function
    Chen Klap, Ester Yeshayahou, Anthony Bolger, Tzahi Arazi, Suresh K. Gupta, Sara Shabtai, Björn Usadel, Yehiam Salts, Rivka Barg · 2016 · Plant Biotechnology Journal
75. A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research
    Mathilde Poyet, Mathieu Groussin, Sean M. Gibbons, Julián Ávila-Pacheco, Xiaofang Jiang, Sean Michael Kearney, Allison R. Perrotta, Brittany M. Berdy, Shijie Zhao, Tami D. Lieberman et al. · 2019 · Nature Medicine
76. Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis
    Francesc Coll, Jody Emile Phelan, Grant A. Hill-Cawthorne, Mridul B. Nair, Kim Mallard, Shahjahan Ali, Abdallah M. Abdallah, Saad Ali Alghamdi, Mona Alsomali, Abdallah O. Ahmed et al. · 2018 · Nature Genetics
77. Early human dispersals within the Americas
    J. Víctor Moreno-Mayar, Lasse Vinner, Peter de Barros Damgaard, Constanza de la Fuente Castro, Jeffrey Chan, Jeffrey P. Spence, Morten E. Allentoft, Tharsika Vimala, Fernando Racimo, Thomaz Pinotti et al. · 2018 · Science
78. Transcriptional regulation of strigolactone signalling in Arabidopsis
    Lei Wang, Bing Wang, Hong Jun Yu, Hongyan Guo, Tao Lin, Liquan Kou, Anqi Wang, Ning Shao, Haiyan Ma, Guosheng Xiong et al. · 2020 · Nature
79. mapDamage: testing for damage patterns in ancient DNA sequences
    Ginolhac, Aurelien, Rasmussen, Morten, Gilbert, M. Thomas P., Willerslev, Eske, Orlando, Ludovic · 2011 · Bioinformatics
80. MutMap accelerates breeding of a salt-tolerant rice cultivar
    Hiroki Takagi, Muluneh Tamiru, Akira Abe, Kentaro Yoshida, Aiko Uemura, Hiroki Yaegashi, Tsutomu Obara, Kaori Oikawa, Hiroe Utsushi, Eiko Kanzaki et al. · 2015 · Nature Biotechnology
81. Trisomy 21 consistently activates the interferon response
    Sullivan, Kelly D, Lewis, Hannah C, Hill, Amanda A, Pandey, Ahwan, Jackson, Leisa P, Cabral, Joseph M, Smith, Keith P, Liggett, L Alexander, Gomez, Eliana B, Galbraith, Matthew D et al. · 2016 · eLife
82. High-throughput, pooled sequencing identifies mutations in NUBPL and FOXRED1 in human complex I deficiency
    Sarah E. Calvo, Elena J. Tucker, Alison G. Compton, Denise M. Kirby, Gabriel Crawford, Noël P. Burtt, Manuel A. Rivas, Candace Guiducci, Damien L. Bruno, Olga Goldberger et al. · 2010 · Nature Genetics
83. Multi-cancer analysis of clonality and the timing of systemic spread in paired primary tumors and metastases
    Zheng Hu, Zan Li, Zhicheng Ma, Christina N. Curtis · 2020 · Nature Genetics
84. Epigenetic Priming of Memory Updating during Reconsolidation to Attenuate Remote Fear Memories
    Gräff, Johannes, Joseph, Nadine F., Horn, Meryl E., Samiei, Alireza, Meng, Jia, Seo, Jinsoo, Rei, Damien, Bero, Adam W., Phan, Trongha X., Wagner, Florence et al. · 2014 · Cell
85. Transcriptomics in the RNA-seq era
    Paul McGettigan · 2013 · Current Opinion in Chemical Biology
86. The genetic basis and cell of origin of mixed phenotype acute leukaemia
    Thomas Alexander, Zhaohui Gu, Ilaria Iacobucci, Kirsten M. Dickerson, John Kim Choi, Beisi Xu, Debbie Payne-Turner, Hiroki Yoshihara, Mignon L. Loh, John Horan et al. · 2018 · Nature
87. Evolutionary dynamics of bacteria in a human host environment
    Lei Yang, Lars Jelsbak, Rasmus L. Marvig, Søren Damkiær, Christopher Thomas Workman, Martin Holm Rau, Susse Kirkelund Hansen, Anders Folkesson, Helle Krogh Johansen, Oana Ciofu et al. · 2011 · Proceedings of the National Academy of Sciences
88. REDItools: high-throughput RNA editing detection made easy
    Ernesto Picardi, Graziano Pesole · 2013 · Bioinformatics
89. Divergence and Functional Degradation of a Sex Chromosome-like Supergene
    Elaina M. Tuttle, Alan O. Bergland, Marisa L. Korody, Michael S. Brewer, Daniel Newhouse, Patrick J. Minx, Maria Stager, Adam M. Betuel, Zachary A. Cheviron, Wesley C. Warren et al. · 2016 · Current Biology
90. Assembly of a pan-genome from deep sequencing of 910 humans of African descent
    Rachel M. Sherman, Juliet Forman, Valentin Antonescu, Daniela Puiu, Michelle Daya, Nicholas M. Rafaels, Meher Preethi Boorgula, Sameer Chavan, Candelaria Vergara, Victor E. Ortega et al. · 2018 · Nature Genetics
91. ERF115 Controls Root Quiescent Center Cell Division and Stem Cell Replenishment
    Jefri Heyman, Toon Cools, Filip Vandenbussche, Ken S. Heyndrickx, Jelle Van Leene, Ilse Vercauteren, Sandy Vanderauwera, Klaas Vandepoele, Geert De Jaeger, Dominique Van Der Straeten et al. · 2013 · Science
92. Meningeal lymphatic dysfunction exacerbates traumatic brain injury pathogenesis.
    Bolte, Ashley C., Dutta, Arun B., Hurt, Mariah E., Smirnov, Igor, Kovacs, Michael A., McKee, Celia A., Ennerfelt, Hannah E., Shapiro, Daniel, Nguyen, Bao H., Frost, Elizabeth L. et al. · 2020 · Nature Communications
93. Sense from sequence reads: methods for alignment and assembly
    Paul Flicek, Ewan Birney · 2009 · Nature Methods
94. A Comparative Study of Techniques for Differential Expression Analysis on RNA-Seq Data
    Zong Hong Zhang, Dhanisha J. Jhaveri, Vikki M. Marshall, Denis C. Bauer, Janette Edson, Ramesh K. Narayanan, Gregory J. Robinson, Andreas E. Lundberg, Perry Francis Bartlett, Naomi R. Wray et al. · 2014 · PLoS ONE
95. genomation: a toolkit to summarize, annotate and visualize genomic intervals
    Altuna Akalin, Vedran Franke, Kristian Vlahoviček, Christopher E. Mason, Dirk Schübeler · 2014 · Bioinformatics
96. Next-generation sequencing for cancer diagnostics: a practical perspective.
    Cliff J. Meldrum, Maria Doyle, Richard W. Tothill · 2011 · Europe PMC (PubMed Central)
97. Mutational landscape of gingivo-buccal oral squamous cell carcinoma reveals new recurrently-mutated genes and molecular subgroups
    Arindam Maitra, Nidhan K. Biswas, Kishore M. Amin, Pradnya Kowtal, Shantanu Kumar, Subrata Kumar Das, Rajiv Sarin, Partha Pratim Majumder, I Bagchi, Bijan B. Bairagya et al. · 2013 · Nature Communications
98. Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis
    Nádia Conceição‐Neto, Mark Zeller, Hanne Lefrère, Pieter De Bruyn, Leen Beller, Ward Deboutte, Claude Kwe Yinda, Rob Lavigne, Piet Maes, Marc A. Van Ranst et al. · 2015 · Scientific Reports
99. Bypassing Negative Epistasis on Yield in Tomato Imposed by a Domestication Gene
    Sebastian Soyk, Zachary H. Lemmon, Matan Oved, Josef Fisher, Katie L. Liberatore, Soon Ju Park, Anna Goren, Ke Jiang, Alexis Ramos, Esther van der Knaap et al. · 2017 · Cell
100. Marker-free carotenoid-enriched rice generated through targeted gene insertion using CRISPR-Cas9
     Oliver Xiaoou Dong, Shu Yu, Rashmi Jain, Nan Zhang, Phat Q. Duong, Corinne Butler, Yan Li, Anna Lipzen, Joel Martin, Kerrie Barry et al. · 2020 · Nature Communications