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  1. Content type: Research

    Organophosphates are the most frequently and largely applied insecticide in the world due to their biodegradable nature. Gut microbes were shown to degrade organophosphates and cause intestinal dysfunction. Th...

    Authors: Ganesan Velmurugan, Tharmarajan Ramprasath, Krishnan Swaminathan, Gilles Mithieux, Jeyaprakash Rajendhran, Mani Dhivakar, Ayothi Parthasarathy, D.D. Venkatesh Babu, Leishman John Thumburaj, Allen J. Freddy, Vasudevan Dinakaran, Shanavas Syed Mohamed Puhari, Balakrishnan Rekha, Yacob Jenifer Christy, Sivakumar Anusha, Ganesan Divya…

    Citation: Genome Biology 2017 18:8

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  2. Content type: Research

    Respiratory illness caused by viral infection is associated with the development and exacerbation of childhood asthma. Little is known about the effects of respiratory viral infections in the absence of illnes...

    Authors: Agata Wesolowska-Andersen, Jamie L. Everman, Rebecca Davidson, Cydney Rios, Rachelle Herrin, Celeste Eng, William J. Janssen, Andrew H. Liu, Sam S. Oh, Rajesh Kumar, Tasha E. Fingerlin, Jose Rodriguez-Santana, Esteban G. Burchard and Max A. Seibold

    Citation: Genome Biology 2017 18:12

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    The Correction to this article has been published in Genome Biology 2018 19:49

  3. Content type: Research

    In 2014, Western Africa experienced an unanticipated explosion of Ebola virus infections. What distinguishes fatal from non-fatal outcomes remains largely unknown, yet is key to optimising personalised treatme...

    Authors: Xuan Liu, Emily Speranza, César Muñoz-Fontela, Sam Haldenby, Natasha Y. Rickett, Isabel Garcia-Dorival, Yongxiang Fang, Yper Hall, Elsa-Gayle Zekeng, Anja Lüdtke, Dong Xia, Romy Kerber, Ralf Krumkamp, Sophie Duraffour, Daouda Sissoko, John Kenny…

    Citation: Genome Biology 2017 18:4

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  4. Content type: Method

    The mechanistic details of most disease-causing mutations remain poorly explored within the context of regulatory networks. We present a high-resolution three-dimensional integrated regulatory network (iRegNet...

    Authors: Siqi Liang, Nathaniel D. Tippens, Yaoda Zhou, Matthew Mort, Peter D. Stenson, David N. Cooper and Haiyuan Yu

    Citation: Genome Biology 2017 18:10

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  5. Content type: Erratum

    Authors: Alexie Papanicolaou, Marc F. Schetelig, Peter Arensburger, Peter W. Atkinson, Joshua B. Benoit, Kostas Bourtzis, Pedro Castañera, John P. Cavanaugh, Hsu Chao, Christopher Childers, Ingrid Curril, Huyen Dinh, HarshaVardhan Doddapaneni, Amanda Dolan, Shannon Dugan, Markus Friedrich…

    Citation: Genome Biology 2017 18:11

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    The original article was published in Genome Biology 2016 17:192

  6. Content type: Research

    Ultraviolet (UV) crosslinking and immunoprecipitation (CLIP) identifies the sites on RNAs that are in direct contact with RNA-binding proteins (RBPs). Several variants of CLIP exist, which require different co...

    Authors: Nejc Haberman, Ina Huppertz, Jan Attig, Julian König, Zhen Wang, Christian Hauer, Matthias W. Hentze, Andreas E. Kulozik, Hervé Le Hir, Tomaž Curk, Christopher R. Sibley, Kathi Zarnack and Jernej Ule

    Citation: Genome Biology 2017 18:7

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    The Erratum to this article has been published in Genome Biology 2017 18:154

  7. Content type: Method

    We present Gene-Aware Variant INterpretation (GAVIN), a new method that accurately classifies variants for clinical diagnostic purposes. Classifications are based on gene-specific calibrations of allele freque...

    Authors: K. Joeri van der Velde, Eddy N. de Boer, Cleo C. van Diemen, Birgit Sikkema-Raddatz, Kristin M. Abbott, Alain Knopperts, Lude Franke, Rolf H. Sijmons, Tom J. de Koning, Cisca Wijmenga, Richard J. Sinke and Morris A. Swertz

    Citation: Genome Biology 2017 18:6

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  8. Content type: MEETING REPORT

    A report on the Genome Informatics conference, held at the Wellcome Genome Campus Conference Centre, Hinxton, United Kingdom, 19–22 September 2016.

    Authors: Davide Chicco and Michael M. Hoffman

    Citation: Genome Biology 2017 18:5

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  9. Content type: Research

    Slow-growing prostate cancer (PC) can be aggressive in a subset of cases. Therefore, prognostic tools to guide clinical decision-making and avoid overtreatment of indolent PC and undertreatment of aggressive d...

    Authors: Kamilla Mundbjerg, Sameer Chopra, Mehrdad Alemozaffar, Christopher Duymich, Ranjani Lakshminarasimhan, Peter W. Nichols, Manju Aron, Kimberly D. Siegmund, Osamu Ukimura, Monish Aron, ‬Mariana Stern, Parkash Gill, John D. Carpten, Torben F. Ørntoft, Karina D. Sørensen, Daniel J. Weisenberger…

    Citation: Genome Biology 2017 18:3

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  10. Content type: Research

    Recent work has identified and mapped a range of posttranscriptional modifications in mRNA, including methylation of the N6 and N1 positions in adenine, pseudouridylation, and methylation of carbon 5 in cytosi...

    Authors: Thomas Amort, Dietmar Rieder, Alexandra Wille, Daria Khokhlova-Cubberley, Christian Riml, Lukas Trixl, Xi-Yu Jia, Ronald Micura and Alexandra Lusser

    Citation: Genome Biology 2017 18:1

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  11. Content type: Research

    Gene annotations, such as those in GENCODE, are derived primarily from alignments of spliced cDNA sequences and protein sequences. The impact of RNA-seq data on annotation has been confined to major projects l...

    Authors: Abhinav Nellore, Andrew E. Jaffe, Jean-Philippe Fortin, José Alquicira-Hernández, Leonardo Collado-Torres, Siruo Wang, Robert A. Phillips III, Nishika Karbhari, Kasper D. Hansen, Ben Langmead and Jeffrey T. Leek

    Citation: Genome Biology 2016 17:266

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  12. Content type: Research Highlight

    Alternative splice isoforms are common and important and have been shown to impact many human diseases. A new study by Nellore et al. offers a comprehensive study of splice junctions in humans by re-analyzing ...

    Authors: Christelle Robert and Mick Watson

    Citation: Genome Biology 2016 17:265

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  13. Content type: Review

    Despite major progress in dissecting the molecular pathways that control DNA methylation patterns in plants, little is known about the mechanisms that shape plant methylomes over evolutionary time. Drawing on ...

    Authors: Amaryllis Vidalis, Daniel Živković, René Wardenaar, David Roquis, Aurélien Tellier and Frank Johannes

    Citation: Genome Biology 2016 17:264

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    The Erratum to this article has been published in Genome Biology 2017 18:41

  14. Content type: Research

    Evolutionary origins of derived morphologies ultimately stem from changes in protein structure, gene regulation, and gene content. A well-assembled, annotated reference genome is a central resource for pursuin...

    Authors: C. M. Small, S. Bassham, J. Catchen, A. Amores, A. M. Fuiten, R. S. Brown, A. G. Jones and W. A. Cresko

    Citation: Genome Biology 2016 17:258

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  15. Content type: Erratum

    Authors: Linda Szabo, Robert Morey, Nathan J. Palpant, Peter L. Wang, Nastaran Afari, Chuan Jiang, Mana M. Parast, Charles E. Murry, Louise C. Laurent and Julia Salzman

    Citation: Genome Biology 2016 17:263

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    The original article was published in Genome Biology 2015 16:126

  16. Content type: METHOD

    In cancer, mutually exclusive or co-occurring somatic alterations across genes can suggest functional interactions. Existing tests for such patterns make the unrealistic assumption of identical gene alteration...

    Authors: Sander Canisius, John W. M. Martens and Lodewyk F. A. Wessels

    Citation: Genome Biology 2016 17:261

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  17. Content type: Software

    Existing workflows for the analysis of multi-omic microbiome datasets are lab-specific and often result in sub-optimal data usage. Here we present IMP, a reproducible and modular pipeline for the integrated an...

    Authors: Shaman Narayanasamy, Yohan Jarosz, Emilie E. L. Muller, Anna Heintz-Buschart, Malte Herold, Anne Kaysen, Cédric C. Laczny, Nicolás Pinel, Patrick May and Paul Wilmes

    Citation: Genome Biology 2016 17:260

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  18. Content type: Research

    Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective con...

    Authors: Federico Abascal, André Corvelo, Fernando Cruz, José L. Villanueva-Cañas, Anna Vlasova, Marina Marcet-Houben, Begoña Martínez-Cruz, Jade Yu Cheng, Pablo Prieto, Víctor Quesada, Javier Quilez, Gang Li, Francisca García, Miriam Rubio-Camarillo, Leonor Frias, Paolo Ribeca…

    Citation: Genome Biology 2016 17:251

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  19. Content type: Research

    The relationship between monogenic and polygenic forms of epilepsy is poorly understood and the extent to which the genetic and acquired epilepsies share common pathways is unclear. Here, we use an integrated ...

    Authors: Andree Delahaye-Duriez, Prashant Srivastava, Kirill Shkura, Sarah R. Langley, Liisi Laaniste, Aida Moreno-Moral, Bénédicte Danis, Manuela Mazzuferi, Patrik Foerch, Elena V. Gazina, Kay Richards, Steven Petrou, Rafal M. Kaminski, Enrico Petretto and Michael R. Johnson

    Citation: Genome Biology 2016 17:245

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  20. Content type: Method

    Chronic low-grade inflammation reflects a subclinical immune response implicated in the pathogenesis of complex diseases. Identifying genetic loci where DNA methylation is associated with chronic low-grade inf...

    Authors: Symen Ligthart, Carola Marzi, Stella Aslibekyan, Michael M. Mendelson, Karen N. Conneely, Toshiko Tanaka, Elena Colicino, Lindsay L. Waite, Roby Joehanes, Weihua Guan, Jennifer A. Brody, Cathy Elks, Riccardo Marioni, Min A. Jhun, Golareh Agha, Jan Bressler…

    Citation: Genome Biology 2016 17:255

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  21. Content type: Research

    Single-cell micro-metastases of solid tumors often occur in the bone marrow. These disseminated tumor cells (DTCs) may resist therapy and lay dormant or progress to cause overt bone and visceral metastases. Th...

    Authors: Jonas Demeulemeester, Parveen Kumar, Elen K. Møller, Silje Nord, David C. Wedge, April Peterson, Randi R. Mathiesen, Renathe Fjelldal, Masoud Zamani Esteki, Koen Theunis, Elia Fernandez Gallardo, A. Jason Grundstad, Elin Borgen, Lars O. Baumbusch, Anne-Lise Børresen-Dale, Kevin P. White…

    Citation: Genome Biology 2016 17:250

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  22. Content type: Research

    Despite their nearly identical genomes, males and females differ in risk, incidence, prevalence, severity and age-at-onset of many diseases. Sexual dimorphism is also seen in human autosomal gene expression, a...

    Authors: Irfahan Kassam, Luke Lloyd-Jones, Alexander Holloway, Kerrin S. Small, Biao Zeng, Andrew Bakshi, Andres Metspalu, Greg Gibson, Tim D. Spector, Tonu Esko, Grant W. Montgomery, Joseph E. Powell, Jian Yang, Peter M. Visscher and Allan F. McRae

    Citation: Genome Biology 2016 17:248

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  23. Content type: Erratum

    Authors: Etienne Becht, Nicolas A. Giraldo, Laetitia Lacroix, Bénédicte Buttard, Nabila Elarouci, Florent Petitprez, Janick Selves, Pierre Laurent-Puig, Catherine Sautès-Fridman, Wolf H. Fridman and Aurélien de Reyniès

    Citation: Genome Biology 2016 17:249

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    The original article was published in Genome Biology 2016 17:218

  24. Content type: Research

    Genome-wide association studies (GWAS) have revealed many susceptibility loci for complex genetic diseases. For most loci, the causal genes have not been identified. Currently, the identification of candidate ...

    Authors: Claartje A. Meddens, Magdalena Harakalova, Noortje A. M. van den Dungen, Hassan Foroughi Asl, Hemme J. Hijma, Edwin P. J. G. Cuppen, Johan L. M. Björkegren, Folkert W. Asselbergs, Edward E. S. Nieuwenhuis and Michal Mokry

    Citation: Genome Biology 2016 17:247

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  25. Content type: Research

    Disorders of sex development (DSD) are congenital conditions in which chromosomal, gonadal, or phenotypic sex is atypical. Clinical management of DSD is often difficult and currently only 13% of patients recei...

    Authors: Stefanie Eggers, Simon Sadedin, Jocelyn A. van den Bergen, Gorjana Robevska, Thomas Ohnesorg, Jacqueline Hewitt, Luke Lambeth, Aurore Bouty, Ingrid M. Knarston, Tiong Yang Tan, Fergus Cameron, George Werther, John Hutson, Michele O’Connell, Sonia R. Grover, Yves Heloury…

    Citation: Genome Biology 2016 17:243

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  26. Content type: Research

    The 2’-5’ oligoadenylate synthetase (OAS) locus encodes for three OAS enzymes (OAS1-3) involved in innate immune response. This region harbors high amounts of Neandertal ancestry in non-African populations; ye...

    Authors: Aaron J. Sams, Anne Dumaine, Yohann Nédélec, Vania Yotova, Carolina Alfieri, Jerome E. Tanner, Philipp W. Messer and Luis B. Barreiro

    Citation: Genome Biology 2016 17:246

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  27. Content type: Research

    The papaya Y-linked region showed clear population structure, resulting in the detection of the ancestral male population that domesticated hermaphrodite papayas were selected from. The same populations were u...

    Authors: Robert VanBuren, Ching Man Wai, Jisen Zhang, Jennifer Han, Jie Arro, Zhicong Lin, Zhenyang Liao, Qingyi Yu, Ming-Li Wang, Francis Zee, Richard C. Moore, Deborah Charlesworth and Ray Ming

    Citation: Genome Biology 2016 17:230

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  28. Content type: Research

    Ciliopathies are clinically diverse disorders of the primary cilium. Remarkable progress has been made in understanding the molecular basis of these genetically heterogeneous conditions; however, our knowledge...

    Authors: Ranad Shaheen, Katarzyna Szymanska, Basudha Basu, Nisha Patel, Nour Ewida, Eissa Faqeih, Amal Al Hashem, Nada Derar, Hadeel Alsharif, Mohammed A. Aldahmesh, Anas M. Alazami, Mais Hashem, Niema Ibrahim, Firdous M. Abdulwahab, Rawda Sonbul, Hisham Alkuraya…

    Citation: Genome Biology 2016 17:242

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  29. Content type: Software

    Genome-wide association studies (GWAS) have become indispensable in human medicine and genomics, but very few have been carried out on bacteria. Here we introduce Scoary, an ultra-fast, easy-to-use, and widely...

    Authors: Ola Brynildsrud, Jon Bohlin, Lonneke Scheffer and Vegard Eldholm

    Citation: Genome Biology 2016 17:238

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    The Erratum to this article has been published in Genome Biology 2016 17:262

  30. Content type: Research

    The control of energy metabolism is fundamental for cell growth and function and anomalies in it are implicated in complex diseases and ageing. Metabolism in yeast cells can be manipulated by supplying differe...

    Authors: Michal Malecki, Danny A. Bitton, Maria Rodríguez-López, Charalampos Rallis, Noelia Garcia Calavia, Graeme C. Smith and Jürg Bähler

    Citation: Genome Biology 2016 17:240

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  31. Content type: Opinion

    Nanopore DNA strand sequencing has emerged as a competitive, portable technology. Reads exceeding 150 kilobases have been achieved, as have in-field detection and analysis of clinical pathogens. We summarize k...

    Authors: Miten Jain, Hugh E. Olsen, Benedict Paten and Mark Akeson

    Citation: Genome Biology 2016 17:239

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    The Erratum to this article has been published in Genome Biology 2016 17:256

  32. Content type: Research

    Blood levels of amino acids are important biomarkers of disease and are influenced by synthesis, protein degradation, and gene–environment interactions. Whole genome sequence analysis of amino acid levels may ...

    Authors: Bing Yu, Paul S. de Vries, Ginger A. Metcalf, Zhe Wang, Elena V. Feofanova, Xiaoming Liu, Donna Marie Muzny, Lynne E. Wagenknecht, Richard A. Gibbs, Alanna C. Morrison and Eric Boerwinkle

    Citation: Genome Biology 2016 17:237

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  33. Content type: Research

    The pathogenicity of many Mendelian variants has been challenged by large-scale sequencing efforts. However, many rare and benign “disease mutations” are difficult to analyze due to their rarity. The Saudi Ara...

    Authors: Mohamed Abouelhoda, Tariq Faquih, Mohamed El-Kalioby and Fowzan S. Alkuraya

    Citation: Genome Biology 2016 17:235

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  34. Content type: Research

    Ten-eleven translocation (TET) enzymes oxidise DNA methylation as part of an active demethylation pathway. Despite extensive research into the role of TETs in genome regulation, little is known about their eff...

    Authors: Lorenzo de la Rica, Özgen Deniz, Kevin C. L. Cheng, Christopher D. Todd, Cristina Cruz, Jonathan Houseley and Miguel R. Branco

    Citation: Genome Biology 2016 17:234

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  35. Content type: Research

    Tumor-infiltrating immune cells have been linked to prognosis and response to immunotherapy; however, the levels of distinct immune cell subsets and the signals that draw them into a tumor, such as the express...

    Authors: Yasin Şenbabaoğlu, Ron S. Gejman, Andrew G. Winer, Ming Liu, Eliezer M. Van Allen, Guillermo de Velasco, Diana Miao, Irina Ostrovnaya, Esther Drill, Augustin Luna, Nils Weinhold, William Lee, Brandon J. Manley, Danny N. Khalil, Samuel D. Kaffenberger, Yingbei Chen…

    Citation: Genome Biology 2016 17:231

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    The Erratum to this article has been published in Genome Biology 2017 18:46

  36. Content type: Opinion

    Studies of human genetic disorders have traditionally followed a reductionist paradigm. Traits are defined as Mendelian or complex based on family pedigree and population data, whereas alleles are deemed rare,...

    Authors: Nicholas Katsanis

    Citation: Genome Biology 2016 17:233

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  37. Content type: METHOD

    Due to the high cost of sequencing-based genomics assays such as ChIP-seq and DNase-seq, the epigenomic characterization of a cell type is typically carried out using a small panel of assay types. Deciding a p...

    Authors: Kai Wei, Maxwell W. Libbrecht, Jeffrey A. Bilmes and William Stafford Noble

    Citation: Genome Biology 2016 17:229

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