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  1. Biomedical research is becoming increasingly large-scale and international. Cloud computing enables the comprehensive integration of genomic and clinical data, and the global sharing and collaborative processi...

    Authors: Fruzsina Molnár-Gábor, Rupert Lueck, Sergei Yakneen and Jan O. Korbel
    Citation: Genome Medicine 2017 9:58
    Content type: Opinion Published on:

  2. Genome rearrangements are critical oncogenic driver events in many malignancies. However, the identification and resolution of the structure of cancer genomic rearrangements remain challenging even with whole ...

    Authors: Stephanie U. Greer, Lincoln D. Nadauld, Billy T. Lau, Jiamin Chen, Christina Wood-Bouwens, James M. Ford, Calvin J. Kuo and Hanlee P. Ji
    Citation: Genome Medicine 2017 9:57
    Content type: Research Published on:

  3. Recent advances in genome sequencing of single microbial cells enable the assignment of functional roles to members of the human microbiome that cannot currently be cultured. This approach can reveal the genom...

    Authors: Andrew C. Tolonen and Ramnik J. Xavier
    Citation: Genome Medicine 2017 9:56
    Content type: Comment Published on:

  4. The pathogenesis of neurological and mental health disorders often involves multiple genes, complex interactions, as well as brain- and development-specific biological mechanisms. These characteristics make id...

    Authors: Saskia Freytag, Rosemary Burgess, Karen L. Oliver and Melanie Bahlo
    Citation: Genome Medicine 2017 9:55
    Content type: Software Published on:

  5. Profiles of DNA methylation of many tissues relevant in human disease have been obtained from microarrays and are publicly available. These can be used to generate maps of chromatin compartmentalization, demar...

    Authors: Poppy Simmonds, Erick Loomis and Edward Curry
    Citation: Genome Medicine 2017 9:54
    Content type: Research Published on:

  6. It is frequently assumed that pre-invasive lesions are simpler precursors of cancer and will contain a limited subset of the genomic changes seen in their associated invasive disease. Driver mutations are thou...

    Authors: Henry M. Wood, Catherine Daly, Rebecca Chalkley, Burcu Senguven, Lisa Ross, Philip Egan, Preetha Chengot, Jennifer Graham, Neeraj Sethi, Thian K. Ong, Kenneth MacLennan, Pamela Rabbitts and Caroline Conway
    Citation: Genome Medicine 2017 9:53
    Content type: Research Published on:

  8. Genome-wide loss-of-function profiling is widely used for systematic identification of genetic dependencies in cancer cells; however, the poor reproducibility of RNA interference (RNAi) screens has been a majo...

    Authors: Alok Jaiswal, Gopal Peddinti, Yevhen Akimov, Krister Wennerberg, Sergey Kuznetsov, Jing Tang and Tero Aittokallio
    Citation: Genome Medicine 2017 9:51
    Content type: Research Published on:

  9. Copaxone is an efficacious and safe therapy that has demonstrated clinical benefit for over two decades in patients with relapsing forms of multiple sclerosis (MS). On an individual level, patients show variab...

    Authors: Colin J. Ross, Fadi Towfic, Jyoti Shankar, Daphna Laifenfeld, Mathis Thoma, Matthew Davis, Brian Weiner, Rebecca Kusko, Ben Zeskind, Volker Knappertz, Iris Grossman and Michael R. Hayden
    Citation: Genome Medicine 2017 9:50
    Content type: Research Published on:

  10. The Human Genome Project and advances in DNA sequencing technologies have revolutionized the identification of genetic disorders through the use of clinical exome sequencing. However, in a considerable number ...

    Authors: Charles A. Steward, Alasdair P. J. Parker, Berge A. Minassian, Sanjay M. Sisodiya, Adam Frankish and Jennifer Harrow
    Citation: Genome Medicine 2017 9:49
    Content type: Review Published on:

  11. Developmental disabilities have diverse genetic causes that must be identified to facilitate precise diagnoses. We describe genomic data from 371 affected individuals, 309 of which were sequenced as proband-pa...

    Authors: Kevin M. Bowling, Michelle L. Thompson, Michelle D. Amaral, Candice R. Finnila, Susan M. Hiatt, Krysta L. Engel, J. Nicholas Cochran, Kyle B. Brothers, Kelly M. East, David E. Gray, Whitley V. Kelley, Neil E. Lamb, Edward J. Lose, Carla A. Rich, Shirley Simmons, Jana S. Whittle…
    Citation: Genome Medicine 2017 9:43
    Content type: Research Published on:

  12. Understanding the genetic basis of disease is an important challenge in biology and medicine. The observation that disease-related proteins often interact with one another has motivated numerous network-based ...

    Authors: Yael Silberberg, Martin Kupiec and Roded Sharan
    Citation: Genome Medicine 2017 9:48
    Content type: Research Published on:

  13. Skeletal muscle is one of the primary tissues involved in the development of type 2 diabetes (T2D). The close association between obesity and T2D makes it difficult to isolate specific effects attributed to th...

    Authors: Leif Väremo, Tora Ida Henriksen, Camilla Scheele, Christa Broholm, Maria Pedersen, Mathias Uhlén, Bente Klarlund Pedersen and Jens Nielsen
    Citation: Genome Medicine 2017 9:47
    Content type: Research Published on:

  14. Approximately 15% of primary colorectal cancers have DNA mismatch repair deficiency, causing a complex genome with thousands of small mutations—the microsatellite instability (MSI) phenotype. We investigated m...

    Authors: Anita Sveen, Bjarne Johannessen, Torstein Tengs, Stine A. Danielsen, Ina A. Eilertsen, Guro E. Lind, Kaja C. G. Berg, Edward Leithe, Leonardo A. Meza-Zepeda, Enric Domingo, Ola Myklebost, David Kerr, Ian Tomlinson, Arild Nesbakken, Rolf I. Skotheim and Ragnhild A. Lothe
    Citation: Genome Medicine 2017 9:46
    Content type: Research Published on:

  17. Recent advances in β-cell regeneration in vivo are providing insights into the mechanisms involved in the conversion of distinct pancreatic cell lineages into β cells. These mechanisms mostly involve reactivat...

    Authors: Solomon Afelik and Meritxell Rovira
    Citation: Genome Medicine 2017 9:42
    Content type: Comment Published on:

    The Erratum to this article has been published in Genome Medicine 2017 9:52

  18. The return of research results (RoR) remains a complex and well-debated issue. Despite the debate, actual data related to the experience of giving individual results back, and the impact these results may have...

    Authors: Amber L. Johns, Skye H. McKay, Jeremy L. Humphris, Mark Pinese, Lorraine A. Chantrill, R. Scott Mead, Katherine Tucker, Lesley Andrews, Annabel Goodwin, Conrad Leonard, Hilda A. High, Katia Nones, Ann-Marie Patch, Neil D. Merrett, Nick Pavlakis, Karin S. Kassahn…
    Citation: Genome Medicine 2017 9:41
    Content type: Research Published on:

  19. Parkinson’s disease (PD) presently is conceptualized as a protein aggregation disease in which pathology involves both the enteric and the central nervous system, possibly spreading from one to another via the...

    Authors: J. R. Bedarf, F. Hildebrand, L. P. Coelho, S. Sunagawa, M. Bahram, F. Goeser, P. Bork and U. Wüllner
    Citation: Genome Medicine 2017 9:39
    Content type: Research Published on:

    The Erratum to this article has been published in Genome Medicine 2017 9:61

  20. The growth factor receptor network (GFRN) plays a significant role in driving key oncogenic processes. However, assessment of global GFRN activity is challenging due to complex crosstalk among GFRN components,...

    Authors: Mumtahena Rahman, Shelley M. MacNeil, David F. Jenkins, Gajendra Shrestha, Sydney R. Wyatt, Jasmine A. McQuerry, Stephen R. Piccolo, Laura M. Heiser, Joe W. Gray, W. Evan Johnson and Andrea H. Bild
    Citation: Genome Medicine 2017 9:40
    Content type: Research Published on:

  21. The increasing affordability of DNA sequencing has allowed it to be widely deployed in pathology laboratories. However, this has exposed many issues with the analysis and reporting of variants for clinical dia...

    Authors: Kenneth D. Doig, Andrew Fellowes, Anthony H. Bell, Andrei Seleznev, David Ma, Jason Ellul, Jason Li, Maria A. Doyle, Ella R. Thompson, Amit Kumar, Luis Lara, Ravikiran Vedururu, Gareth Reid, Thomas Conway, Anthony T. Papenfuss and Stephen B. Fox
    Citation: Genome Medicine 2017 9:38
    Content type: Software Published on:

  23. High tumor mutational burden (TMB) is an emerging biomarker of sensitivity to immune checkpoint inhibitors and has been shown to be more significantly associated with response to PD-1 and PD-L1 blockade immuno...

    Authors: Zachary R. Chalmers, Caitlin F. Connelly, David Fabrizio, Laurie Gay, Siraj M. Ali, Riley Ennis, Alexa Schrock, Brittany Campbell, Adam Shlien, Juliann Chmielecki, Franklin Huang, Yuting He, James Sun, Uri Tabori, Mark Kennedy, Daniel S. Lieber…
    Citation: Genome Medicine 2017 9:34
    Content type: Research Published on:

  25. Bioinformatic analysis of genomic sequencing data to identify somatic mutations in cancer samples is far from achieving the required robustness and standardisation. In this study we generated a whole exome seq...

    Authors: Maurizio Callari, Stephen-John Sammut, Leticia De Mattos-Arruda, Alejandra Bruna, Oscar M. Rueda, Suet-Feung Chin and Carlos Caldas
    Citation: Genome Medicine 2017 9:35
    Content type: Method Published on:

  26. Head and neck squamous cell carcinomas (HNSCCs) represent a heterogeneous group of cancers for which human papilloma virus (HPV) infection is an emerging risk factor. Previous studies showed promoter hypermeth...

    Authors: Davide Degli Esposti, Athena Sklias, Sheila C. Lima, Stéphanie Beghelli-de la Forest Divonne, Vincent Cahais, Nora Fernandez-Jimenez, Marie-Pierre Cros, Szilvia Ecsedi, Cyrille Cuenin, Liacine Bouaoun, Graham Byrnes, Rosita Accardi, Anne Sudaka, Valérie Giordanengo, Hector Hernandez-Vargas, Luis Felipe Ribeiro Pinto…
    Citation: Genome Medicine 2017 9:33
    Content type: Research Published on:

  27. The infant gut is rapidly colonized by microorganisms soon after birth, and the composition of the microbiota is dynamic in the first year of life. Although a stable microbiome may not be established until 1 t...

    Authors: Jennifer C. Stearns, Michael A. Zulyniak, Russell J. de Souza, Natalie C. Campbell, Michelle Fontes, Mateen Shaikh, Malcolm R. Sears, Allan B. Becker, Piushkumar J. Mandhane, Padmaja Subbarao, Stuart E. Turvey, Milan Gupta, Joseph Beyene, Michael G. Surette and Sonia S. Anand
    Citation: Genome Medicine 2017 9:32
    Content type: Research Published on:

  28. Colorectal adenocarcinomas are characterized by abnormal mitochondrial DNA (mtDNA) copy number and genomic instability, but a molecular interaction between mitochondrial and nuclear genome remains unknown. Her...

    Authors: Vinodh Srinivasainagendra, Michael W. Sandel, Bhupendra Singh, Aishwarya Sundaresan, Ved P. Mooga, Prachi Bajpai, Hemant K. Tiwari and Keshav K. Singh
    Citation: Genome Medicine 2017 9:31
    Content type: Research Published on:

  29. Encoded by the var gene family, highly variable Plasmodium falciparum erythrocyte membrane protein-1 (PfEMP1) proteins mediate tissue-specific cytoadherence of infected erythrocytes, resulting in immune evasion a...

    Authors: Antoine Dara, Elliott F. Drábek, Mark A. Travassos, Kara A. Moser, Arthur L. Delcher, Qi Su, Timothy Hostelley, Drissa Coulibaly, Modibo Daou, Ahmadou Dembele, Issa Diarra, Abdoulaye K. Kone, Bourema Kouriba, Matthew B. Laurens, Amadou Niangaly, Karim Traore…
    Citation: Genome Medicine 2017 9:30
    Content type: Research Published on:

  30. Age-related macular degeneration (AMD) is a common condition of vision loss with disease development strongly influenced by environmental and genetic factors. Recently, 34 loci were associated with AMD at geno...

    Authors: Felix Grassmann, Christina Kiel, Martina E. Zimmermann, Mathias Gorski, Veronika Grassmann, Klaus Stark, Iris M. Heid and Bernhard H. F. Weber
    Citation: Genome Medicine 2017 9:29
    Content type: Research Published on:

  31. The association of in vitro fertilisation (IVF) and DNA methylation has been studied predominantly at regulatory regions of imprinted genes and at just thousands of the ~28 million CpG sites in the human genome.

    Authors: Juan E. Castillo-Fernandez, Yuk Jing Loke, Sebastian Bass-Stringer, Fei Gao, Yudong Xia, Honglong Wu, Hanlin Lu, Yuan Liu, Jun Wang, Tim D. Spector, Richard Saffery, Jeffrey M. Craig and Jordana T. Bell
    Citation: Genome Medicine 2017 9:28
    Content type: Research Published on:

  32. Systemic sclerosis (SSc) is a multi-organ autoimmune disease characterized by skin fibrosis. Internal organ involvement is heterogeneous. It is unknown whether disease mechanisms are common across all involved...

    Authors: Jaclyn N. Taroni, Casey S. Greene, Viktor Martyanov, Tammara A. Wood, Romy B. Christmann, Harrison W. Farber, Robert A. Lafyatis, Christopher P. Denton, Monique E. Hinchcliff, Patricia A. Pioli, J. Matthew Mahoney and Michael L. Whitfield
    Citation: Genome Medicine 2017 9:27
    Content type: Research Published on:

  33. Given the rarity of most single-gene Mendelian disorders, concerted efforts of data exchange between clinical and scientific communities are critical to optimize molecular diagnosis and novel disease gene disc...

    Authors: Mohammad K. Eldomery, Zeynep Coban-Akdemir, Tamar Harel, Jill A. Rosenfeld, Tomasz Gambin, Asbjørg Stray-Pedersen, Sébastien Küry, Sandra Mercier, Davor Lessel, Jonas Denecke, Wojciech Wiszniewski, Samantha Penney, Pengfei Liu, Weimin Bi, Seema R. Lalani, Christian P. Schaaf…
    Citation: Genome Medicine 2017 9:26
    Content type: Research Published on:

  35. Imiquimod (IMQ) produces a cutaneous phenotype in mice frequently studied as an acute model of human psoriasis. Whether this phenotype depends on strain or sex has never been systematically investigated on a l...

    Authors: William R. Swindell, Kellie A. Michaels, Andrew J. Sutter, Doina Diaconu, Yi Fritz, Xianying Xing, Mrinal K. Sarkar, Yun Liang, Alex Tsoi, Johann E. Gudjonsson and Nicole L. Ward
    Citation: Genome Medicine 2017 9:24
    Content type: Research Published on:

  36. The Generation Scotland: Scottish Family Health Study (GS:SFHS) is a family-based population cohort with DNA, biological samples, socio-demographic, psychological and clinical data from approximately 24,000 ad...

    Authors: Reka Nagy, Thibaud S. Boutin, Jonathan Marten, Jennifer E. Huffman, Shona M. Kerr, Archie Campbell, Louise Evenden, Jude Gibson, Carmen Amador, David M. Howard, Pau Navarro, Andrew Morris, Ian J. Deary, Lynne J. Hocking, Sandosh Padmanabhan, Blair H. Smith…
    Citation: Genome Medicine 2017 9:23
    Content type: Research Published on:

  38. Understanding longitudinal variability of the microbiome in ill patients is critical to moving microbiome-based measurements and therapeutics into clinical practice. However, the vast majority of data regardin...

    Authors: Jessica R. Galloway-Peña, Daniel P. Smith, Pranoti Sahasrabhojane, W. Duncan Wadsworth, Bryan M. Fellman, Nadim J. Ajami, Elizabeth J. Shpall, Naval Daver, Michele Guindani, Joseph F. Petrosino, Dimitrios P. Kontoyiannis and Samuel A. Shelburne
    Citation: Genome Medicine 2017 9:21
    Content type: Research Published on:

  40. The integration of genomics with immunotherapy has potential value for cancer vaccine development. Given the clinical successes of immune checkpoint modulators, interest in cancer vaccines as therapeutic optio...

    Authors: Ryan J. Hartmaier, Jehad Charo, David Fabrizio, Michael E. Goldberg, Lee A. Albacker, William Pao and Juliann Chmielecki
    Citation: Genome Medicine 2017 9:16
    Content type: Research Published on:

  42. Expression quantitative trait loci (eQTL) databases represent a valuable resource to link disease-associated SNPs to specific candidate genes whose gene expression is significantly modulated by the SNP under i...

    Authors: Dilip Kumar, Kia Joo Puan, Anand Kumar Andiappan, Bernett Lee, Geertje H. A. Westerlaken, Doreen Haase, Rossella Melchiotti, Zhuang Li, Nurhashikin Yusof, Josephine Lum, Geraldine Koh, Shihui Foo, Joe Yeong, Alexessander Couto Alves, Juha Pekkanen, Liang Dan Sun…
    Citation: Genome Medicine 2017 9:18
    Content type: Research Published on:

  44. Retinoid therapy is widely employed in clinical oncology to differentiate malignant cells into their more benign counterparts. However, certain high-risk cohorts, such as patients with MYCN-amplified neuroblas...

    Authors: David J. Duffy, Aleksandar Krstic, Melinda Halasz, Thomas Schwarzl, Anja Konietzny, Kristiina Iljin, Desmond G. Higgins and Walter Kolch
    Citation: Genome Medicine 2017 9:15
    Content type: Research Published on:

  45. While the role of the gut microbiome in inflammation and colorectal cancers has received much recent attention, there are few data to support an association between the oral microbiome and head and neck squamo...

    Authors: Hannah Wang, Pauline Funchain, Gurkan Bebek, Jessica Altemus, Huan Zhang, Farshad Niazi, Charissa Peterson, Walter T. Lee, Brian B. Burkey and Charis Eng
    Citation: Genome Medicine 2017 9:14
    Content type: Research Published on:

  46. The frequency of a variant in the general population is a key criterion used in the clinical interpretation of sequence variants. With certain exceptions, such as founder mutations, the rarity of a variant is ...

    Authors: Yuya Kobayashi, Shan Yang, Keith Nykamp, John Garcia, Stephen E. Lincoln and Scott E. Topper
    Citation: Genome Medicine 2017 9:13
    Content type: Research Published on:

  47. Glioblastoma multiforme (GBM) constitutes nearly half of all malignant brain tumors and has a median survival of 15 months. The standard treatment for these lesions includes maximal resection, radiotherapy, an...

    Authors: E. Zeynep Erson-Omay, Octavian Henegariu, S. Bülent Omay, Akdes Serin Harmancı, Mark W. Youngblood, Ketu Mishra-Gorur, Jie Li, Koray Özduman, Geneive Carrión-Grant, Victoria E. Clark, Caner ÇaÄŸlar, Mehmet BakırcıoÄŸlu, M. Necmettin Pamir, Viviane Tabar, Alexander O. Vortmeyer, Kaya Bilguvar…
    Citation: Genome Medicine 2017 9:12
    Content type: Research Published on:

  48. Neisseria meningitidis is a globally important cause of meningitis and septicaemia. Twelve capsular groups of meningococci are known, and quadrivalent vaccines against four of these (A...

    Authors: Daniel O’Connor, Elizabeth A. Clutterbuck, Amber J. Thompson, Matthew D. Snape, Maheshi N. Ramasamy, Dominic F. Kelly and Andrew J. Pollard
    Citation: Genome Medicine 2017 9:11
    Content type: Research Published on:

  50. Germline chromothripsis causes complex genomic rearrangements that are likely to affect multiple genes and their regulatory contexts. The contribution of individual rearrangements and affected genes to the phe...

    Authors: Sjors Middelkamp, Sebastiaan van Heesch, A. Koen Braat, Joep de Ligt, Maarten van Iterson, Marieke Simonis, Markus J. van Roosmalen, Martijn J. E. Kelder, Evelien Kruisselbrink, Ron Hochstenbach, Nienke E. Verbeek, Elly F. Ippel, Youri Adolfs, R. Jeroen Pasterkamp, Wigard P. Kloosterman, Ewart W. Kuijk…
    Citation: Genome Medicine 2017 9:9
    Content type: Research Published on:
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Genome Medicine

ISSN: 1756-994X

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