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  1. Corynebacterium diphtheriae, the agent of diphtheria, is a genetically diverse bacterial species. Although antimicrobial resistance has emerged against several drugs including first-line penicillin, the genomic d...

    Authors: Melanie Hennart, Leonardo G. Panunzi, Carla Rodrigues, Quentin Gaday, Sarah L. Baines, Marina Barros-Pinkelnig, Annick Carmi-Leroy, Melody Dazas, Anne Marie Wehenkel, Xavier Didelot, Julie Toubiana, Edgar Badell and Sylvain Brisse

    Citation: Genome Medicine 2020 12:107

    Content type: Research

    Published on:

  2. Genome-wide association studies (GWAS) have identified pervasive sharing of genetic architectures across multiple immune-mediated diseases (IMD). By learning the genetic basis of IMD risk from common diseases,...

    Authors: Oliver S. Burren, Guillermo Reales, Limy Wong, John Bowes, James C. Lee, Anne Barton, Paul A. Lyons, Kenneth G. C. Smith, Wendy Thomson, Paul D. W. Kirk and Chris Wallace

    Citation: Genome Medicine 2020 12:106

    Content type: Research

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  3. DNA methylation has been shown to be associated with adiposity in adulthood. However, whether similar DNA methylation patterns are associated with childhood and adolescent body mass index (BMI) is largely unkn...

    Authors: Florianne O. L. Vehmeijer, Leanne K. Küpers, Gemma C. Sharp, Lucas A. Salas, Samantha Lent, Dereje D. Jima, Gwen Tindula, Sarah Reese, Cancan Qi, Olena Gruzieva, Christian Page, Faisal I. Rezwan, Philip E. Melton, Ellen Nohr, Geòrgia Escaramís, Peter Rzehak…

    Citation: Genome Medicine 2020 12:105

    Content type: Research

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  4. Multidrug-resistant (MDR) Mycobacterium tuberculosis complex strains not detected by commercial molecular drug susceptibility testing (mDST) assays due to the RpoB I491F resistance mutation are threatening the co...

    Authors: Patrick Beckert, Elisabeth Sanchez-Padilla, Matthias Merker, Viola Dreyer, Thomas A. Kohl, Christian Utpatel, Claudio U. Köser, Ivan Barilar, Nazir Ismail, Shaheed Vally Omar, Marisa Klopper, Robin M. Warren, Harald Hoffmann, Gugu Maphalala, Elisa Ardizzoni, Bouke C. de Jong…

    Citation: Genome Medicine 2020 12:104

    Content type: Research

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  5. The gut-liver axis plays a pivotal role in the pathogenesis of hepatocellular carcinoma (HCC). However, the correlations between the gut microbiome and the liver tumor transcriptome in patients with HCC and th...

    Authors: Hechen Huang, Zhigang Ren, Xingxing Gao, Xiaoyi Hu, Yuan Zhou, Jianwen Jiang, Haifeng Lu, Shengyong Yin, Junfang Ji, Lin Zhou and Shusen Zheng

    Citation: Genome Medicine 2020 12:102

    Content type: Research

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  6. Heat shock proteins (HSPs), a representative family of chaperone genes, play crucial roles in malignant progression and are pursued as attractive anti-cancer therapeutic targets. Despite tremendous efforts to ...

    Authors: Zhao Zhang, Ji Jing, Youqiong Ye, Zhiao Chen, Ying Jing, Shengli Li, Wei Hong, Hang Ruan, Yaoming Liu, Qingsong Hu, Jun Wang, Wenbo Li, Chunru Lin, Lixia Diao, Yubin Zhou and Leng Han

    Citation: Genome Medicine 2020 12:101

    Content type: Research

    Published on:

  7. Polygenic risk scores (PRSs) are a summarization of an individual’s genetic risk for a disease or trait. These scores are being generated in research and commercial settings to study how they may be used to gu...

    Authors: Shang-Fu Chen, Raquel Dias, Doug Evans, Elias L. Salfati, Shuchen Liu, Nathan E. Wineinger and Ali Torkamani

    Citation: Genome Medicine 2020 12:100

    Content type: Research

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  8. Tight regulatory loops orchestrate commitment to B cell fate within bone marrow. Genetic lesions in this gene regulatory network underlie the emergence of the most common childhood cancer, acute lymphoblastic ...

    Authors: Juha Mehtonen, Susanna Teppo, Mari Lahnalampi, Aleksi Kokko, Riina Kaukonen, Laura Oksa, Maria Bouvy-Liivrand, Alena Malyukova, Artturi Mäkinen, Saara Laukkanen, Petri I. Mäkinen, Samuli Rounioja, Pekka Ruusuvuori, Olle Sangfelt, Riikka Lund, Tapio Lönnberg…

    Citation: Genome Medicine 2020 12:99

    Content type: Research

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  9. One of the major challenges in obesity treatment is to explain the high variability in the individual’s response to specific dietary and physical activity interventions. With this study, we tested the hypothes...

    Authors: Maria Keller, Anat Yaskolka Meir, Stephan H. Bernhart, Yftach Gepner, Ilan Shelef, Dan Schwarzfuchs, Gal Tsaban, Hila Zelicha, Lydia Hopp, Luise Müller, Kerstin Rohde, Yvonne Böttcher, Peter F. Stadler, Michael Stumvoll, Matthias Blüher, Peter Kovacs…

    Citation: Genome Medicine 2020 12:97

    Content type: Research

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  10. Whole-genome sequencing (WGS) is increasingly used to map the spread of bacterial and viral pathogens in nosocomial settings. A limiting factor for more widespread adoption of WGS for hospital infection preven...

    Authors: Ana Berbel Caban, Theodore R. Pak, Ajay Obla, Amy C. Dupper, Kieran I. Chacko, Lindsey Fox, Alexandra Mills, Brianne Ciferri, Irina Oussenko, Colleen Beckford, Marilyn Chung, Robert Sebra, Melissa Smith, Sarah Conolly, Gopi Patel, Andrew Kasarskis…

    Citation: Genome Medicine 2020 12:96

    Content type: Research

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  11. Genomic studies of patients with COVID-19, or exposed to it, are underway to delineate host factors associated with variability in susceptibility, infectivity, and disease severity. Here, we highlight the ethi...

    Authors: Gail Geller, Priya Duggal, Chloe L. Thio, Debra Mathews, Jeffrey P. Kahn, Lisa L. Maragakis and Brian T. Garibaldi

    Citation: Genome Medicine 2020 12:95

    Content type: Comment

    Published on:

  12. High-grade serous ovarian cancer (HGSOC) is a major unmet need in oncology. The remaining uncertainty on its originating tissue has hampered the discovery of molecular oncogenic pathways and the development of...

    Authors: Pietro Lo Riso, Carlo Emanuele Villa, Gilles Gasparoni, Andrea Vingiani, Raffaele Luongo, Anna Manfredi, Annemarie Jungmann, Alessia Bertolotti, Francesca Borgo, Annalisa Garbi, Michela Lupia, Pasquale Laise, Vivek Das, Giancarlo Pruneri, Giuseppe Viale, Nicoletta Colombo…

    Citation: Genome Medicine 2020 12:94

    Content type: Research

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  13. Humans and viruses have co-evolved for millennia resulting in a complex host genetic architecture. Understanding the genetic mechanisms of immune response to viral infection provides insight into disease etiol...

    Authors: Linda Kachuri, Stephen S. Francis, Maike L. Morrison, George A. Wendt, Yohan Bossé, Taylor B. Cavazos, Sara R. Rashkin, Elad Ziv and John S. Witte

    Citation: Genome Medicine 2020 12:93

    Content type: Research

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  14. Multiple studies suggest a key role for gut microbiota in IgE-mediated food allergy (FA) development, but to date, none has studied it in the persistent state.

    Authors: Michael R. Goldberg, Hadar Mor, Dafna Magid Neriya, Faiga Magzal, Efrat Muller, Michael Y. Appel, Liat Nachshon, Elhanan Borenstein, Snait Tamir, Yoram Louzoun, Ilan Youngster, Arnon Elizur and Omry Koren

    Citation: Genome Medicine 2020 12:92

    Content type: Research

    Published on:

  15. Wnt signaling is an evolutionarily conserved developmental pathway that is frequently hyperactivated in cancer. While multiple protein-coding genes regulated by Wnt signaling are known, the functional lncRNAs ...

    Authors: Shiyang Liu, Nathan Harmston, Trudy Lee Glaser, Yunka Wong, Zheng Zhong, Babita Madan, David M. Virshup and Enrico Petretto

    Citation: Genome Medicine 2020 12:89

    Content type: Research

    Published on:

  16. Autism spectrum disorder (ASD) is a neurodevelopmental disorder with complex heritability and higher prevalence in males. The neonatal epigenome has the potential to reflect past interactions between genetic a...

    Authors: Charles E. Mordaunt, Julia M. Jianu, Benjamin I. Laufer, Yihui Zhu, Hyeyeon Hwang, Keith W. Dunaway, Kelly M. Bakulski, Jason I. Feinberg, Heather E. Volk, Kristen Lyall, Lisa A. Croen, Craig J. Newschaffer, Sally Ozonoff, Irva Hertz-Picciotto, M. Daniele Fallin, Rebecca J. Schmidt…

    Citation: Genome Medicine 2020 12:88

    Content type: Research

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  17. During aging, there is a physiological decline, an increase of morbidity and mortality, and a natural change in the gut microbiome. In this study, we investigated the influence of the gut microbiome on differe...

    Authors: Dana Binyamin, Nir Werbner, Meital Nuriel-Ohayon, Atara Uzan, Hadar Mor, Atallah Abbas, Oren Ziv, Raffaele Teperino, Roee Gutman and Omry Koren

    Citation: Genome Medicine 2020 12:87

    Content type: Research

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  18. Quantifying tissue-infiltrating immune and stromal cells provides clinically relevant information for various diseases. While numerous methods can quantify immune or stromal cells in human tissue samples from ...

    Authors: Florent Petitprez, Sacha Levy, Cheng-Ming Sun, Maxime Meylan, Christophe Linhard, Etienne Becht, Nabila Elarouci, David Tavel, Lubka T. Roumenina, Mira Ayadi, Catherine Sautès-Fridman, Wolf H. Fridman and Aurélien de Reyniès

    Citation: Genome Medicine 2020 12:86

    Content type: Method

    Published on:

  19. Solid tumors such as pancreatic ductal adenocarcinoma (PDAC) comprise not just tumor cells but also a microenvironment with which the tumor cells constantly interact. Detailed characterization of the cellular ...

    Authors: Wei Lin, Pawan Noel, Erkut H. Borazanci, Jeeyun Lee, Albert Amini, In Woong Han, Jin Seok Heo, Gayle S. Jameson, Cory Fraser, Margaux Steinbach, Yanghee Woo, Yuman Fong, Derek Cridebring, Daniel D. Von Hoff, Joon Oh Park and Haiyong Han

    Citation: Genome Medicine 2020 12:80

    Content type: Research

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  20. APOBEC-driven mutagenesis and functional positive selection of mutated genes may synergistically drive the higher frequency of some hotspot driver mutations compared to other mutations within the same gene, as...

    Authors: Ming-Jun Shi, Xiang-Yu Meng, Jacqueline Fontugne, Chun-Long Chen, François Radvanyi and Isabelle Bernard-Pierrot

    Citation: Genome Medicine 2020 12:85

    Content type: Research

    Published on:

  21. Mitochondrial DNA copy number (mtDNA-CN) has been associated with a variety of aging-related diseases, including all-cause mortality. However, the mechanism by which mtDNA-CN influences disease is not currentl...

    Authors: Christina A. Castellani, Ryan J. Longchamps, Jason A. Sumpter, Charles E. Newcomb, John A. Lane, Megan L. Grove, Jan Bressler, Jennifer A. Brody, James S. Floyd, Traci M. Bartz, Kent D. Taylor, Penglong Wang, Adrienne Tin, Josef Coresh, James S. Pankow, Myriam Fornage…

    Citation: Genome Medicine 2020 12:84

    Content type: Research

    Published on:

  22. Immune checkpoint blockade (ICB) therapy has demonstrated considerable clinical benefit in several malignancies, but has shown favorable response in only a small proportion of cancer patients. Recent studies h...

    Authors: Youqiong Ye, Xinwei Kuang, Zuozhong Xie, Long Liang, Zhao Zhang, Yongchang Zhang, Fangyu Ma, Qian Gao, Ruimin Chang, Heng-Huan Lee, Shuang Zhao, Juan Su, Hui Li, Jingbo Peng, Huifang Chen, Minzhu Yin…

    Citation: Genome Medicine 2020 12:83

    Content type: Research

    Published on:

  23. Systemic sclerosis (SSc) is a genetically complex autoimmune disease mediated by the interplay between genetic and epigenetic factors in a multitude of immune cells, with CD4+ T lymphocytes as one of the princ...

    Authors: Tianlu Li, Lourdes Ortiz-Fernández, Eduardo Andrés-León, Laura Ciudad, Biola M. Javierre, Elena López-Isac, Alfredo Guillén-Del-Castillo, Carmen Pilar Simeón-Aznar, Esteban Ballestar and Javier Martin

    Citation: Genome Medicine 2020 12:81

    Content type: Research

    Published on:

  24. Identification of actionable genomic vulnerabilities is key to precision oncology. Utilizing a large-scale drug screening in patient-derived xenografts, we uncover driver gene alteration connections, derive dr...

    Authors: Lidia Mateo, Miquel Duran-Frigola, Albert Gris-Oliver, Marta Palafox, Maurizio Scaltriti, Pedram Razavi, Sarat Chandarlapaty, Joaquin Arribas, Meritxell Bellet, Violeta Serra and Patrick Aloy

    Citation: Genome Medicine 2020 12:78

    Content type: Method

    Published on:

  25. Long non-coding RNAs (lncRNAs) are extensively intricate in the tumorigenesis and metastasis of various cancer types. Nevertheless, the detailed molecular mechanisms of lncRNA in non-small cell lung cancer (NS...

    Authors: Cheng-Cao Sun, Wei Zhu, Shu-Jun Li, Wei Hu, Jian Zhang, Yue Zhuo, Han Zhang, Juan Wang, Yu Zhang, Shao-Xin Huang, Qi-Qiang He and De-Jia Li

    Citation: Genome Medicine 2020 12:77

    Content type: Research

    Published on:

  26. Congenital heart disease (CHD) occurs in almost 1% of newborn children and is considered a multifactorial disorder. CHD may segregate in families due to significant contribution of genetic factors in the disea...

    Authors: Jose M. G. Izarzugaza, Sabrina G. Ellesøe, Canan Doganli, Natasja Spring Ehlers, Marlene D. Dalgaard, Enrique Audain, Gregor Dombrowsky, Karina Banasik, Alejandro Sifrim, Anna Wilsdon, Bernard Thienpont, Jeroen Breckpot, Marc Gewillig, J. David Brook, Marc-Phillip Hitz, Lars A. Larsen…

    Citation: Genome Medicine 2020 12:76

    Content type: Research

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  27. Exome sequencing is now mainstream in clinical practice. However, identification of pathogenic Mendelian variants remains time-consuming, in part, because the limited accuracy of current computational predicti...

    Authors: Shuang Li, K. Joeri van der Velde, Dick de Ridder, Aalt D. J. van Dijk, Dimitrios Soudis, Leslie R. Zwerwer, Patrick Deelen, Dennis Hendriksen, Bart Charbon, Marielle E. van Gijn, Kristin Abbott, Birgit Sikkema-Raddatz, Cleo C. van Diemen, Wilhelmina S. Kerstjens-Frederikse, Richard J. Sinke and Morris A. Swertz

    Citation: Genome Medicine 2020 12:75

    Content type: Method

    Published on:

  28. The concentrations of the highly atherogenic lipoprotein(a) [Lp(a)] are mainly genetically determined by the LPA gene locus. However, up to 70% of the coding sequence is located in the complex so-called kringle I...

    Authors: Silvia Di Maio, Rebecca Grüneis, Gertraud Streiter, Claudia Lamina, Manuel Maglione, Sebastian Schoenherr, Dietmar Öfner, Barbara Thorand, Annette Peters, Kai-Uwe Eckardt, Anna Köttgen, Florian Kronenberg and Stefan Coassin

    Citation: Genome Medicine 2020 12:74

    Content type: Research

    Published on:

  29. For circadian medicine to influence health, such as when to take a drug or undergo a procedure, a biomarker of molecular clock phase is required––one that is easily measured and generalizable across a broad po...

    Authors: Gang Wu, Marc D. Ruben, Lauren J. Francey, David F. Smith, Joseph D. Sherrill, John E. Oblong, Kevin J. Mills and John B. Hogenesch

    Citation: Genome Medicine 2020 12:73

    Content type: Research

    Published on:

  30. DNA originating from degenerate tumour cells can be detected in the circulation in many tumour types, where it can be used as a marker of disease burden as well as to monitor treatment response. Although circu...

    Authors: Edmund Lau, Patrick McCoy, Fairleigh Reeves, Ken Chow, Michael Clarkson, Edmond M. Kwan, Kate Packwood, Helen Northen, Miao He, Zoya Kingsbury, Stefano Mangiola, Michael Kerger, Marc A. Furrer, Helen Crowe, Anthony J. Costello, David J. McBride…

    Citation: Genome Medicine 2020 12:72

    Content type: Research

    Published on:

  31. The ongoing COVID-19 pandemic has created an urgency to identify novel vaccine targets for protective immunity against SARS-CoV-2. Early reports identify protective roles for both humoral and cell-mediated imm...

    Authors: Asaf Poran, Dewi Harjanto, Matthew Malloy, Christina M. Arieta, Daniel A. Rothenberg, Divya Lenkala, Marit M. van Buuren, Terri A. Addona, Michael S. Rooney, Lakshmi Srinivasan and Richard B. Gaynor

    Citation: Genome Medicine 2020 12:70

    Content type: Research

    Published on:

  32. Current computational methods on Hi-C analysis focused on identifying Mb-size domains often failed to unveil the underlying functional and mechanistic relationship of chromatin structure and gene regulation. W...

    Authors: Yufan Zhou, Xiaolong Cheng, Yini Yang, Tian Li, Jingwei Li, Tim H.-M. Huang, Junbai Wang, Shili Lin and Victor X. Jin

    Citation: Genome Medicine 2020 12:69

    Content type: Method

    Published on:

  33. Many genetic/genomic disorders are caused by genomic rearrangements. Standard methods can often characterize these variations only partly, e.g., copy number changes or breakpoints. It is important to fully und...

    Authors: Satomi Mitsuhashi, Sachiko Ohori, Kazutaka Katoh, Martin C. Frith and Naomichi Matsumoto

    Citation: Genome Medicine 2020 12:67

    Content type: Research

    Published on:

  34. Although the microbiome is established as an important regulator of health and disease, the role of viruses that inhabit asymptomatic humans (collectively, the virome) is less defined. While we are still chara...

    Authors: Fatemeh Adiliaghdam and Kate L. Jeffrey

    Citation: Genome Medicine 2020 12:66

    Content type: Comment

    Published on:

  35. SARS-CoV-2 is a recently emerged respiratory pathogen that has significantly impacted global human health. We wanted to rapidly characterise the transcriptomic, proteomic and phosphoproteomic landscape of this...

    Authors: Andrew D. Davidson, Maia Kavanagh Williamson, Sebastian Lewis, Deborah Shoemark, Miles W. Carroll, Kate J. Heesom, Maria Zambon, Joanna Ellis, Philip A. Lewis, Julian A. Hiscox and David A. Matthews

    Citation: Genome Medicine 2020 12:68

    Content type: Research

    Published on:

  36. There is increasing evidence that the intestinal microbiota plays a crucial role in the maturation of the immune system and the prevention of diseases during childhood. Early-life short-course antibiotic use m...

    Authors: Ceren Ozkul, Victoria E. Ruiz, Thomas Battaglia, Joseph Xu, Claire Roubaud-Baudron, Ken Cadwell, Guillermo I. Perez-Perez and Martin J. Blaser

    Citation: Genome Medicine 2020 12:65

    Content type: Research

    Published on:

  37. A challenge in the post-GWAS era is to assign function to disease-associated variants. However, available resources do not include all tissues or environmental exposures that are relevant to all diseases. For ...

    Authors: Emma E. Thompson, Quynh Dang, Blair Mitchell-Handley, Kavitha Rajendran, Sumati Ram-Mohan, Julian Solway, Carole Ober and Ramaswamy Krishnan

    Citation: Genome Medicine 2020 12:64

    Content type: Research

    Published on:

  38. Small cell lung cancer (SCLC) is a more aggressive subtype of lung cancer that often results in rapid tumor growth, early metastasis, and acquired therapeutic resistance. Consequently, such phenotypical charac...

    Authors: Aileen Patricia Szczepanski, Zibo Zhao, Tori Sosnowski, Young Ah Goo, Elizabeth Thomas Bartom and Lu Wang

    Citation: Genome Medicine 2020 12:63

    Content type: Research

    Published on:

  39. When interpreting sequencing data from multiple spatial or longitudinal biopsies, detecting sample mix-ups is essential, yet more difficult than in studies of germline variation. In most genomic studies of tum...

    Authors: Brent S. Pedersen, Preetida J. Bhetariya, Joe Brown, Stephanie N. Kravitz, Gabor Marth, Randy L. Jensen, Mary P. Bronner, Hunter R. Underhill and Aaron R. Quinlan

    Citation: Genome Medicine 2020 12:62

    Content type: Software

    Published on:

  40. The molecular factors which control circulating levels of inflammatory proteins are not well understood. Furthermore, association studies between molecular probes and human traits are often performed by linear...

    Authors: Robert F. Hillary, Daniel Trejo-Banos, Athanasios Kousathanas, Daniel L. McCartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, Sven Erik Ojavee, Qian Zhang, David C. Liewald, Craig W. Ritchie, Kathryn L. Evans, Elliot M. Tucker-Drob, Naomi R. Wray, Allan F. McRae, Peter M. Visscher…

    Citation: Genome Medicine 2020 12:60

    Content type: Research

    Published on:

  41. Dietary glycans, widely used as food ingredients and not directly digested by humans, are of intense interest for their beneficial roles in human health through shaping the microbiome. Characterizing the consi...

    Authors: Richard Creswell, Jie Tan, Jonathan W. Leff, Brandon Brooks, Michael A. Mahowald, Ruth Thieroff-Ekerdt and Georg K. Gerber

    Citation: Genome Medicine 2020 12:59

    Content type: Research

    Published on:

  42. COVID-19 (coronavirus disease 2019) has caused a major epidemic worldwide; however, much is yet to be known about the epidemiology and evolution of the virus partly due to the scarcity of full-length SARS-CoV-...

    Authors: Minfeng Xiao, Xiaoqing Liu, Jingkai Ji, Min Li, Jiandong Li, Lin Yang, Wanying Sun, Peidi Ren, Guifang Yang, Jincun Zhao, Tianzhu Liang, Huahui Ren, Tian Chen, Huanzi Zhong, Wenchen Song, Yanqun Wang…

    Citation: Genome Medicine 2020 12:57

    Content type: Research

    Published on:

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