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  1. Deep learning is a subdiscipline of artificial intelligence that uses a machine learning technique called artificial neural networks to extract patterns and make predictions from large data sets. The increasin...

    Authors: Khoa A. Tran, Olga Kondrashova, Andrew Bradley, Elizabeth D. Williams, John V. Pearson and Nicola Waddell
    Citation: Genome Medicine 2021 13:152
  2. Rapid advances in the past decade have shown that dysbiosis of the gut microbiome is a key hallmark of rheumatoid arthritis (RA). Yet, the relationship between the gut microbiome and clinical improvement in RA...

    Authors: Vinod K. Gupta, Kevin Y. Cunningham, Benjamin Hur, Utpal Bakshi, Harvey Huang, Kenneth J. Warrington, Veena Taneja, Elena Myasoedova, John M. Davis III and Jaeyun Sung
    Citation: Genome Medicine 2021 13:149
  3. Klebsiella spp. are opportunistic pathogens which can cause severe infections, are often multi-drug resistant and are a common cause of hospital-acquired infections. Multiple new Klebsiella species have recently ...

    Authors: Aline Cuénod, Daniel Wüthrich, Helena M. B. Seth-Smith, Chantal Ott, Christian Gehringer, Frédéric Foucault, Roxanne Mouchet, Ali Kassim, Gunturu Revathi, Deborah R. Vogt, Stefanie von Felten, Stefano Bassetti, Sarah Tschudin-Sutter, Timm Hettich, Götz Schlotterbeck, Christina Homberger…
    Citation: Genome Medicine 2021 13:150
  4. DNA sequencing is increasingly incorporated into the routine care of cancer patients, many of whom also carry inherited, moderate/high-penetrance variants associated with other diseases. Yet, the prevalence an...

    Authors: Zishan Wang, Xiao Fan, Yufeng Shen, Meghana S Pagadala, Rebecca Signer, Kamil J. Cygan, William G. Fairbrother, Hannah Carter, Wendy K. Chung and Kuan-lin Huang
    Citation: Genome Medicine 2021 13:147
  5. Epstein-Barr virus (EBV)-associated gastric carcinomas (EBVaGCs) present unique molecular signatures, but the tumorigenesis of EBVaGCs and the role EBV plays during this process remain poorly understood.

    Authors: Zhang-Hua Chen, Shu-Mei Yan, Xi-Xi Chen, Qi Zhang, Shang-Xin Liu, Yang Liu, Yi-Ling Luo, Chao Zhang, Miao Xu, Yi-Fan Zhao, Li-Yun Huang, Bin-Liu Liu, Tian-Liang Xia, Da-Zhi Xu, Yao Liang, Yong-Ming Chen…
    Citation: Genome Medicine 2021 13:146
  6. We developed a sensitive sequencing approach that simultaneously profiles microsatellite instability, chromosomal instability, and subclonal structure in cancer. We assessed diverse repeat motifs across 225 mi...

    Authors: GiWon Shin, Stephanie U. Greer, Erik Hopmans, Susan M. Grimes, HoJoon Lee, Lan Zhao, Laura Miotke, Carlos Suarez, Alison F. Almeda, Sigurdis Haraldsdottir and Hanlee P. Ji
    Citation: Genome Medicine 2021 13:145
  7. The incidence of Gram-negative bloodstream infections (BSIs), predominantly caused by Escherichia coli and Klebsiella species, continues to increase; however, the causes of this are unclear and effective interven...

    Authors: Samuel Lipworth, Karina-Doris Vihta, Kevin Chau, Leanne Barker, Sophie George, James Kavanagh, Timothy Davies, Alison Vaughan, Monique Andersson, Katie Jeffery, Sarah Oakley, Marcus Morgan, Susan Hopkins, Timothy E. A. Peto, Derrick W. Crook, Ann Sarah Walker…
    Citation: Genome Medicine 2021 13:144
  8. Gene expression-based subtyping has the potential to form a new paradigm for stratified treatment of colorectal cancer. However, current frameworks are based on the transcriptomic profiles of primary tumors, a...

    Authors: Seyed H. Moosavi, Peter W. Eide, Ina A. Eilertsen, Tuva H. Brunsell, Kaja C. G. Berg, Bård I. Røsok, Kristoffer W. Brudvik, Bjørn A. Bjørnbeth, Marianne G. Guren, Arild Nesbakken, Ragnhild A. Lothe and Anita Sveen
    Citation: Genome Medicine 2021 13:143
  9. Colorectal cancer is the 2nd leading cause of cancer-related deaths with few patients benefiting from biomarker-guided therapy. Mutation expression is essential for accurate interpretation of mutations as biom...

    Authors: Anita Sveen, Bjarne Johannessen, Ina A. Eilertsen, Bård I. Røsok, Marie Gulla, Peter W. Eide, Jarle Bruun, Kushtrim Kryeziu, Leonardo A. Meza-Zepeda, Ola Myklebost, Bjørn A. Bjørnbeth, Rolf I. Skotheim, Arild Nesbakken and Ragnhild A. Lothe
    Citation: Genome Medicine 2021 13:142
  10. Genome-wide association studies (GWAS) have identified over 56 susceptibility loci associated with Alzheimer’s disease (AD), but the genes responsible for these associations remain largely unknown.

    Authors: Yanfa Sun, Jingjing Zhu, Dan Zhou, Saranya Canchi, Chong Wu, Nancy J. Cox, Robert A. Rissman, Eric R. Gamazon and Lang Wu
    Citation: Genome Medicine 2021 13:141
  11. Epithelial ovarian cancer (OC) is a heterogenous disease consisting of five major histologically distinct subtypes: high-grade serous (HGSOC), low-grade serous (LGSOC), endometrioid (ENOC), clear cell (CCOC) a...

    Authors: Bethany M. Barnes, Louisa Nelson, Anthony Tighe, George J. Burghel, I-Hsuan Lin, Sudha Desai, Joanne C. McGrail, Robert D. Morgan and Stephen S. Taylor
    Citation: Genome Medicine 2021 13:140
  12. Authors: David Z. Pan, Zong Miao, Caroline Comenho, Sandhya Rajkumar, Amogha Koka, Seung Hyuk T. Lee, Marcus Alvarez, Dorota Kaminska, Arthur Ko, Janet S. Sinsheimer, Karen L. Mohlke, Nicholas Mancuso, Linda Liliana Muñoz-Hernandez, Miguel Herrera-Hernandez, Maria Teresa Tusié-Luna, Carlos Aguilar-Salinas…
    Citation: Genome Medicine 2021 13:139

    The original article was published in Genome Medicine 2021 13:123

  13. Multidrug-resistant Mycobacterium tuberculosis (Mtb) is a significant global public health threat. Genotypic resistance prediction from Mtb DNA sequences offers an alternative to laboratory-based drug-susceptibil...

    Authors: Matthias I. Gröschel, Martin Owens, Luca Freschi, Roger Vargas Jr, Maximilian G. Marin, Jody Phelan, Zamin Iqbal, Avika Dixit and Maha R. Farhat
    Citation: Genome Medicine 2021 13:138
  14. Exercise training is well established as the most effective way to enhance muscle performance and muscle building. The composition of skeletal muscle fiber type affects systemic energy expenditures, and pertur...

    Authors: Yajuan Li, Yaohua Zhang, Qingsong Hu, Sergey D. Egranov, Zhen Xing, Zhao Zhang, Ke Liang, Youqiong Ye, Yinghong Pan, Sujash S. Chatterjee, Brandon Mistretta, Tina K. Nguyen, David H. Hawke, Preethi H. Gunaratne, Mien-Chie Hung, Leng Han…
    Citation: Genome Medicine 2021 13:137
  15. Metagenome sampling bias for geographical location and lifestyle is partially responsible for the incomplete catalog of reference genomes of gut microbial species. Thus, genome assembly from currently under-re...

    Authors: Chan Yeong Kim, Muyoung Lee, Sunmo Yang, Kyungnam Kim, Dongeun Yong, Hye Ryun Kim and Insuk Lee
    Citation: Genome Medicine 2021 13:134
  16. Sleep-disordered breathing is a common disorder associated with significant morbidity. The genetic architecture of sleep-disordered breathing remains poorly understood. Through the NHLBI Trans-Omics for Precis...

    Authors: Brian E. Cade, Jiwon Lee, Tamar Sofer, Heming Wang, Man Zhang, Han Chen, Sina A. Gharib, Daniel J. Gottlieb, Xiuqing Guo, Jacqueline M. Lane, Jingjing Liang, Xihong Lin, Hao Mei, Sanjay R. Patel, Shaun M. Purcell, Richa Saxena…
    Citation: Genome Medicine 2021 13:136
  17. Genetic variants in the voltage-gated sodium channels SCN1A, SCN2A, SCN3A, and SCN8A are leading causes of epilepsy, developmental delay, and autism spectrum disorder. The mRNA splicing patterns of all four genes...

    Authors: Lindsay Liang, Siavash Fazel Darbandi, Sirisha Pochareddy, Forrest O. Gulden, Michael C. Gilson, Brooke K. Sheppard, Atehsa Sahagun, Joon-Yong An, Donna M. Werling, John L. R. Rubenstein, Nenad Sestan, Kevin J. Bender and Stephan J. Sanders
    Citation: Genome Medicine 2021 13:135
  18. The enrichment of Gram-negative bacteria of oral origin in the esophageal microbiome has been associated with the development of metaplasia. However, to date, no study has comprehensively assessed the relation...

    Authors: Nandan P. Deshpande, Stephen M. Riordan, Claire J. Gorman, Shaun Nielsen, Tonia L. Russell, Carolina Correa-Ospina, Bentotage S. M. Fernando, Shafagh A. Waters, Natalia Castaño-Rodríguez, Si Ming Man, Nicodemus Tedla, Marc R. Wilkins and Nadeem O. Kaakoush
    Citation: Genome Medicine 2021 13:133
  19. Gene copy number variations (CNVs) contribute to genetic diversity and disease prevalence across populations. Substantial efforts have been made to decipher the relationship between CNVs and pathogenesis but w...

    Authors: Li Zhang, Jingru Shi, Jian Ouyang, Riquan Zhang, Yiran Tao, Dongsheng Yuan, Chengkai Lv, Ruiyuan Wang, Baitang Ning, Ruth Roberts, Weida Tong, Zhichao Liu and Tieliu Shi
    Citation: Genome Medicine 2021 13:132
  20. The plasticity of monocytes enables them to exert multiple roles during an immune response, including promoting immune tolerance. How monocytes alter their functions to convey immune tolerance in the context o...

    Authors: Xanthe Brands, Bastiaan W. Haak, Augustijn M. Klarenbeek, Joe Butler, Fabrice Uhel, Wanhai Qin, Natasja A. Otto, Marja E. Jakobs, Daniël R. Faber, René Lutter, W. Joost Wiersinga, Tom van der Poll and Brendon P. Scicluna
    Citation: Genome Medicine 2021 13:131
  21. Merkel cell carcinoma (MCC) is a rare but aggressive skin cancer with limited treatment possibilities. Merkel cell tumors display with neuroendocrine features and Merkel cell polyomavirus (MCPyV) infection in ...

    Authors: Hemant Gujar, Arjun Mehta, Hong-Tao Li, Yvonne C. Tsai, Xiangning Qiu, Daniel J. Weisenberger, Miriam Galvonas Jasiulionis, Gino K. In and Gangning Liang
    Citation: Genome Medicine 2021 13:130
  22. Tumor response to therapy is affected by both the cell types and the cell states present in the tumor microenvironment. This is true for many cancer treatments, including immune checkpoint inhibitors (ICIs). W...

    Authors: Emily F. Davis-Marcisak, Allison A. Fitzgerald, Michael D. Kessler, Ludmila Danilova, Elizabeth M. Jaffee, Neeha Zaidi, Louis M. Weiner and Elana J. Fertig
    Citation: Genome Medicine 2021 13:129
  23. Human pancreatic islets are a central focus of research in metabolic studies. Transcriptomics is frequently used to interrogate alterations in cultured human islet cells using single-cell RNA-sequencing (scRNA...

    Authors: Giorgio Basile, Sevim Kahraman, Ercument Dirice, Hui Pan, Jonathan M. Dreyfuss and Rohit N. Kulkarni
    Citation: Genome Medicine 2021 13:128
  24. Cancer evolution depends on epigenetic and genetic diversity. Historically, in multiple myeloma (MM), subclonal diversity and tumor evolution have been investigated mostly from a genetic perspective.

    Authors: Jennifer Derrien, Catherine Guérin-Charbonnel, Victor Gaborit, Loïc Campion, Magali Devic, Elise Douillard, Nathalie Roi, Hervé Avet-Loiseau, Olivier Decaux, Thierry Facon, Jan-Philipp Mallm, Roland Eils, Nikhil C. Munshi, Philippe Moreau, Carl Herrmann, Florence Magrangeas…
    Citation: Genome Medicine 2021 13:127
  25. Screening for short tandem repeat (STR) expansions in next-generation sequencing data can enable diagnosis, optimal clinical management/treatment, and accurate genetic counseling of patients with repeat expans...

    Authors: Indhu-Shree Rajan-Babu, Junran J. Peng, Readman Chiu, Chenkai Li, Arezoo Mohajeri, Egor Dolzhenko, Michael A. Eberle, Inanc Birol and Jan M. Friedman
    Citation: Genome Medicine 2021 13:126

    The Publisher Correction to this article has been published in Genome Medicine 2021 13:151

  26. Berberine and Bifidobacterium have been reported to improve glucose tolerance in people with hyperglycemia or other metabolic disorders. This study aimed to assess the hypoglycemic effect and the regulation of th...

    Authors: Jie Ming, Xinwen Yu, Xiaoqiang Xu, Li Wang, Chao Ding, Zhifeng Wang, Xuan Xie, Sheli Li, Wenjuan Yang, Shu Luo, Qingzhen He, Yafang Du, Zhufang Tian, Xiling Gao, Kaiyan Ma, Yujie Fang…
    Citation: Genome Medicine 2021 13:125
  27. The emergence of SARS-CoV-2 underscores the need to better understand the evolutionary processes that drive the emergence and adaptation of zoonotic viruses in humans. In the betacoronavirus genus, which also ...

    Authors: Juan Ángel Patiño-Galindo, Ioan Filip, Ratul Chowdhury, Costas D. Maranas, Peter K. Sorger, Mohammed AlQuraishi and Raul Rabadan
    Citation: Genome Medicine 2021 13:124
  28. Obesity predisposes individuals to multiple cardiometabolic disorders, including type 2 diabetes (T2D). As body mass index (BMI) cannot reliably differentiate fat from lean mass, the metabolically detrimental ...

    Authors: David Z. Pan, Zong Miao, Caroline Comenho, Sandhya Rajkumar, Amogha Koka, Seung Hyuk T. Lee, Marcus Alvarez, Dorota Kaminska, Arthur Ko, Janet S. Sinsheimer, Karen L. Mohlke, Nicholas Mancuso, Linda Liliana Muñoz-Hernandez, Miguel Herrera-Hernandez, Maria Teresa Tusié-Luna, Carlos Aguilar-Salinas…
    Citation: Genome Medicine 2021 13:123

    The Author Correction to this article has been published in Genome Medicine 2021 13:139

  29. Gene expression is highly variable across tissues of multi-cellular organisms, influencing the codon usage of the tissue-specific transcriptome. Cancer disrupts the gene expression pattern of healthy tissue re...

    Authors: Douglas Meyer, Jacob Kames, Haim Bar, Anton A. Komar, Aikaterini Alexaki, Juan Ibla, Ryan C. Hunt, Luis V. Santana-Quintero, Anton Golikov, Michael DiCuccio and Chava Kimchi-Sarfaty
    Citation: Genome Medicine 2021 13:122
  30. Pathogen whole genome sequencing (WGS) is being incorporated into public health surveillance and disease control systems worldwide and has the potential to make significant contributions to infectious disease ...

    Authors: Angeline S. Ferdinand, Margaret Kelaher, Courtney R. Lane, Anders Gonçalves da Silva, Norelle L. Sherry, Susan A. Ballard, Patiyan Andersson, Tuyet Hoang, Justin T. Denholm, Marion Easton, Benjamin P. Howden and Deborah A. Williamson
    Citation: Genome Medicine 2021 13:121
  31. If each cancer cell produces on average more than one cancer cell, we see a net growth of the tumors and metastases and vice versa. We review recent clinical results for microsatellite stable metastatic colore...

    Authors: Devabhaktuni Srikrishna and Kris Sachsenmeier
    Citation: Genome Medicine 2021 13:120
  32. Klebsiella pneumoniae, as a global priority pathogen, is well known for its capability of acquiring mobile genetic elements that carry resistance and/or virulence genes. Its virulence plasmid, previously deemed n...

    Authors: Yanping Xu, Jianfeng Zhang, Meng Wang, Meng Liu, Guitian Liu, Hongping Qu, Jialin Liu, Zixin Deng, Jingyong Sun, Hong-Yu Ou and Jieming Qu
    Citation: Genome Medicine 2021 13:119
  33. Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, has been associated with neurological and neuropsychiatric illness in many individuals. We...

    Authors: John F. Fullard, Hao-Chih Lee, Georgios Voloudakis, Shengbao Suo, Behnam Javidfar, Zhiping Shao, Cyril Peter, Wen Zhang, Shan Jiang, André Corvelo, Heather Wargnier, Emma Woodoff-Leith, Dushyant P. Purohit, Sadhna Ahuja, Nadejda M. Tsankova, Nathalie Jette…
    Citation: Genome Medicine 2021 13:118
  34. Multiple sclerosis (MS) is a major health problem, leading to a significant disability and patient suffering. Although chronic activation of the immune system is a hallmark of the disease, its pathogenesis is ...

    Authors: Marti Bernardo-Faura, Melanie Rinas, Jakob Wirbel, Inna Pertsovskaya, Vicky Pliaka, Dimitris E. Messinis, Gemma Vila, Theodore Sakellaropoulos, Wolfgang Faigle, Pernilla Stridh, Janina R. Behrens, Tomas Olsson, Roland Martin, Friedemann Paul, Leonidas G. Alexopoulos, Pablo Villoslada…
    Citation: Genome Medicine 2021 13:117
  35. The development of secondary resistance (SR) in metastatic colorectal cancer (mCRC) treated with anti-epidermal growth factor receptor (anti-EGFR) antibodies is not fully understood at the molecular level. Her...

    Authors: Deepak Vangala, Swetlana Ladigan, Sven T. Liffers, Soha Noseir, Abdelouahid Maghnouj, Tina-Maria Götze, Berlinda Verdoodt, Susanne Klein-Scory, Laura Godfrey, Martina K. Zowada, Mario Huerta, Daniel L. Edelstein, Jaime Martinez de Villarreal, Miriam Marqués, Jörg Kumbrink, Andreas Jung…
    Citation: Genome Medicine 2021 13:116
  36. The Global Alliance for Genomics and Health has approved a policy for the return of clinically actionable genomic research results, the first such policy approved by an international body. The policy acknowled...

    Authors: Anna C. F. Lewis, Bartha Maria Knoppers and Robert C. Green
    Citation: Genome Medicine 2021 13:115
  37. Renal medullary carcinomas (RMCs) are rare kidney cancers that occur in adolescents and young adults of African ancestry. Although RMC is associated with the sickle cell trait and somatic loss of the tumor sup...

    Authors: Kar-Tong Tan, Hyunji Kim, Jian Carrot-Zhang, Yuxiang Zhang, Won Jun Kim, Guillaume Kugener, Jeremiah A. Wala, Thomas P. Howard, Yueh-Yun Chi, Rameen Beroukhim, Heng Li, Gavin Ha, Seth L. Alper, Elizabeth J. Perlman, Elizabeth A. Mullen, William C. Hahn…
    Citation: Genome Medicine 2021 13:114
  38. Malignant pleural mesothelioma (MPM) is a heterogeneous cancer. Better knowledge of molecular and cellular intra-tumor heterogeneity throughout the thoracic cavity is required to develop efficient therapies. T...

    Authors: Clément Meiller, François Montagne, Theo Z. Hirsch, Stefano Caruso, Julien de Wolf, Quentin Bayard, Jean-Baptiste Assié, Léa Meunier, Yuna Blum, Lisa Quetel, Laure Gibault, Ecaterina Pintilie, Cécile Badoual, Sarah Humez, Françoise Galateau-Sallé, Marie-Christine Copin…
    Citation: Genome Medicine 2021 13:113
  39. Multi-omics data are good resources for prognosis and survival prediction; however, these are difficult to integrate computationally. We introduce DeepProg, a novel ensemble framework of deep-learning and mach...

    Authors: Olivier B. Poirion, Zheng Jing, Kumardeep Chaudhary, Sijia Huang and Lana X. Garmire
    Citation: Genome Medicine 2021 13:112
  40. High-grade serous tubo-ovarian cancer (HGSTOC) is characterised by extensive inter- and intratumour heterogeneity, resulting in persistent therapeutic resistance and poor disease outcome. Molecular subtype cla...

    Authors: Siel Olbrecht, Pieter Busschaert, Junbin Qian, Adriaan Vanderstichele, Liselore Loverix, Toon Van Gorp, Els Van Nieuwenhuysen, Sileny Han, Annick Van den Broeck, An Coosemans, Anne-Sophie Van Rompuy, Diether Lambrechts and Ignace Vergote
    Citation: Genome Medicine 2021 13:111
  41. Authors: Yasmin Bylstra, Weng Khong Lim, Sylvia Kam, Koei Wan Tham, R. Ryanne Wu, Jing Xian Teo, Sonia Davila, Jyn Ling Kuan, Sock Hoai Chan, Nicolas Bertin, Cheng Xi Yang, Steve Rozen, Bin Tean Teh, Khung Keong Yeo, Stuart Alexander Cook, Saumya Shekhar Jamuar…
    Citation: Genome Medicine 2021 13:109

    The original article was published in Genome Medicine 2021 13:3

  42. Candidemia is one of the most common nosocomial bloodstream infections in the United States, causing significant morbidity and mortality in hospitalized patients, but the breadth of the host response to Candida i...

    Authors: Julie M. Steinbrink, Rachel A. Myers, Kaiyuan Hua, Melissa D. Johnson, Jessica L. Seidelman, Ephraim L. Tsalik, Ricardo Henao, Geoffrey S. Ginsburg, Christopher W. Woods, Barbara D. Alexander and Micah T. McClain
    Citation: Genome Medicine 2021 13:108
  43. Authors: Na Zhu, Emilia M. Swietlik, Carrie L. Welch, Michael W. Pauciulo, Jacob J. Hagen, Xueya Zhou, Yicheng Guo, Johannes Karten, Divya Pandya, Tobias Tilly, Katie A. Lutz, Jennifer M. Martin, Carmen M. Treacy, Erika B. Rosenzweig, Usha Krishnan, Anna W. Coleman…
    Citation: Genome Medicine 2021 13:106

    The original article was published in Genome Medicine 2021 13:80

  44. The microbiome has emerged as an environmental factor contributing to obesity and type 2 diabetes (T2D). Increasing evidence suggests links between circulating bacterial components (i.e., bacterial DNA), cardi...

    Authors: Rima M. Chakaroun, Lucas Massier, Anna Heintz-Buschart, Nedal Said, Joerg Fallmann, Alyce Crane, Tatjana Schütz, Arne Dietrich, Matthias Blüher, Michael Stumvoll, Niculina Musat and Peter Kovacs
    Citation: Genome Medicine 2021 13:105
  45. Associations of low lung function with features of poor cardio-metabolic health have been reported. It is, however, unclear whether these co-morbidities reflect causal associations, shared genetic heritability...

    Authors: Matthias Wielscher, Andre F. S. Amaral, Diana van der Plaat, Louise V. Wain, Sylvain Sebert, David Mosen-Ansorena, Juha Auvinen, Karl-Heinz Herzig, Abbas Dehghan, Debbie L. Jarvis and Marjo-Riitta Jarvelin
    Citation: Genome Medicine 2021 13:104
  46. Medulloblastoma (MB) is the most common malignant paediatric brain tumour and a leading cause of cancer-related mortality and morbidity. Existing treatment protocols are aggressive in nature resulting in signi...

    Authors: Laura A. Genovesi, Amanda Millar, Elissa Tolson, Matthew Singleton, Emily Hassall, Marija Kojic, Caterina Brighi, Emily Girard, Clara Andradas, Mani Kuchibhotla, Dharmesh D. Bhuva, Raelene Endersby, Nicholas G. Gottardo, Anne Bernard, Christelle Adolphe, James M. Olson…
    Citation: Genome Medicine 2021 13:103
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