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  1. Content type: Opinion

    Supplements are increasingly important to the scientific record, particularly in genomics. However, they are often underutilized. Optimally, supplements should make results findable, accessible, interoperable,...

    Authors: Dov Greenbaum, Joel Rozowsky, Victoria Stodden and Mark Gerstein

    Citation: Genome Biology 2017 18:64

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  2. Content type: Erratum

    Authors: Thomas C. Mathers, Yazhou Chen, Gemy Kaithakottil, Fabrice Legeai, Sam T. Mugford, Patrice Baa-Puyoulet, Anthony Bretaudeau, Bernardo Clavijo, Stefano Colella, Olivier Collin, Tamas Dalmay, Thomas Derrien, Honglin Feng, Toni Gabaldón, Anna Jordan, Irene Julca…

    Citation: Genome Biology 2017 18:63

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    The original article was published in Genome Biology 2017 18:27

  3. Content type: Q & A

    Continuing with our Q&A series discussing issues of diversity in STEM fields, Genome Biology spoke with three openly LGBT+ researchers on their experiences in biology.

    Authors: Ben Barres, Beth Montague-Hellen and Jeremy Yoder

    Citation: Genome Biology 2017 18:62

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  4. Content type: Research

    Modern civilization depends on only a few plant species for its nourishment. These crops were derived via several thousands of years of human selection that transformed wild ancestors into high-yielding domest...

    Authors: Martha Rendón-Anaya, Josaphat M. Montero-Vargas, Soledad Saburido-Álvarez, Anna Vlasova, Salvador Capella-Gutierrez, José Juan Ordaz-Ortiz, O. Mario Aguilar, Rosana P. Vianello-Brondani, Marta Santalla, Luis Delaye, Toni Gabaldón, Paul Gepts, Robert Winkler, Roderic Guigó, Alfonso Delgado-Salinas and Alfredo Herrera-Estrella

    Citation: Genome Biology 2017 18:60

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  5. Content type: Research

    Age-associated epigenetic changes are implicated in aging. Notably, age-associated DNA methylation changes comprise a so-called aging “clock”, a robust biomarker of aging. However, while genetic, dietary and d...

    Authors: John J. Cole, Neil A. Robertson, Mohammed Iqbal Rather, John P. Thomson, Tony McBryan, Duncan Sproul, Tina Wang, Claire Brock, William Clark, Trey Ideker, Richard R. Meehan, Richard A. Miller, Holly M. Brown-Borg and Peter D. Adams

    Citation: Genome Biology 2017 18:58

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  6. Content type: Research

    Dietary restriction (DR), a reduction in food intake without malnutrition, increases most aspects of health during aging and extends lifespan in diverse species, including rodents. However, the mechanisms by w...

    Authors: Oliver Hahn, Sebastian Grönke, Thomas M. Stubbs, Gabriella Ficz, Oliver Hendrich, Felix Krueger, Simon Andrews, Qifeng Zhang, Michael J. Wakelam, Andreas Beyer, Wolf Reik and Linda Partridge

    Citation: Genome Biology 2017 18:56

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  7. Content type: Research

    Global but predictable changes impact the DNA methylome as we age, acting as a type of molecular clock. This clock can be hastened by conditions that decrease lifespan, raising the question of whether it can a...

    Authors: Tina Wang, Brian Tsui, Jason F. Kreisberg, Neil A. Robertson, Andrew M. Gross, Michael Ku Yu, Hannah Carter, Holly M. Brown-Borg, Peter D. Adams and Trey Ideker

    Citation: Genome Biology 2017 18:57

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  8. Content type: METHOD

    It is important for large-scale epigenomic studies to determine and explore the nature of hidden confounding variation, most importantly cell composition. We developed MeDeCom as a novel reference-free computa...

    Authors: Pavlo Lutsik, Martin Slawski, Gilles Gasparoni, Nikita Vedeneev, Matthias Hein and Jörn Walter

    Citation: Genome Biology 2017 18:55

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  9. Content type: Method

    We propose a probabilistic method, CancerLocator, which exploits the diagnostic potential of cell-free DNA by determining not only the presence but also the location of tumors. CancerLocator simultaneously inf...

    Authors: Shuli Kang, Qingjiao Li, Quan Chen, Yonggang Zhou, Stacy Park, Gina Lee, Brandon Grimes, Kostyantyn Krysan, Min Yu, Wei Wang, Frank Alber, Fengzhu Sun, Steven M. Dubinett, Wenyuan Li and Xianghong Jasmine Zhou

    Citation: Genome Biology 2017 18:53

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  10. Content type: Research Highlight

    A recently published study in Genome Biology shows that cells isolated from cryopreserved tissues are a reliable source of genetic material for single-cell RNA-sequencing experiments.

    Authors: Felipe A. Vieira Braga, Sarah A. Teichmann and Michael J. T. Stubbington

    Citation: Genome Biology 2017 18:54

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  11. Content type: Method

    It remains challenging to predict regulatory variants in particular tissues or cell types due to highly context-specific gene regulation. By connecting large-scale epigenomic profiles to expression quantitativ...

    Authors: Mulin Jun Li, Miaoxin Li, Zipeng Liu, Bin Yan, Zhicheng Pan, Dandan Huang, Qian Liang, Dingge Ying, Feng Xu, Hongcheng Yao, Panwen Wang, Jean-Pierre A. Kocher, Zhengyuan Xia, Pak Chung Sham, Jun S. Liu and Junwen Wang

    Citation: Genome Biology 2017 18:52

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  12. Content type: Software

    Intron retention (IR) occurs when an intron is transcribed into pre-mRNA and remains in the final mRNA. We have developed a program and database called IRFinder to accurately detect IR from mRNA sequencing dat...

    Authors: Robert Middleton, Dadi Gao, Aubin Thomas, Babita Singh, Amy Au, Justin J-L Wong, Alexandra Bomane, Bertrand Cosson, Eduardo Eyras, John E. J. Rasko and William Ritchie

    Citation: Genome Biology 2017 18:51

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  13. Content type: Research

    The functional impact of genetic variation has been extensively surveyed, revealing that genetic changes correlated to phenotypes lie mostly in non-coding genomic regions. Studies have linked allele-specific g...

    Authors: Warren A. Cheung, Xiaojian Shao, Andréanne Morin, Valérie Siroux, Tony Kwan, Bing Ge, Dylan Aïssi, Lu Chen, Louella Vasquez, Fiona Allum, Frédéric Guénard, Emmanuelle Bouzigon, Marie-Michelle Simon, Elodie Boulier, Adriana Redensek, Stephen Watt…

    Citation: Genome Biology 2017 18:50

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  14. Content type: Research

    Gene innovation by duplication is a fundamental evolutionary process but is difficult to study in humans due to the large size, high sequence identity, and mosaic nature of segmental duplication blocks. The hu...

    Authors: Max L. Dougherty, Xander Nuttle, Osnat Penn, Bradley J. Nelson, John Huddleston, Carl Baker, Lana Harshman, Michael H. Duyzend, Mario Ventura, Francesca Antonacci, Richard Sandstrom, Megan Y. Dennis and Evan E. Eichler

    Citation: Genome Biology 2017 18:49

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  15. Content type: Research

    Hirschsprung disease (HSCR), which is congenital obstruction of the bowel, results from a failure of enteric nervous system (ENS) progenitors to migrate, proliferate, differentiate, or survive within the dista...

    Authors: Hongsheng Gui, Duco Schriemer, William W. Cheng, Rajendra K. Chauhan, Guillermo Antiňolo, Courtney Berrios, Marta Bleda, Alice S. Brooks, Rutger W. W. Brouwer, Alan J. Burns, Stacey S. Cherny, Joaquin Dopazo, Bart J. L. Eggen, Paola Griseri, Binta Jalloh, Thuy-Linh Le…

    Citation: Genome Biology 2017 18:48

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  16. Content type: Research

    Proteases represent one of the most abundant classes of enzymes in eukaryotes and are known to play key roles in many biological processes in plants. However, little is known about their functions in fruit rip...

    Authors: Weihao Wang, Jianghua Cai, Peiwen Wang, Shiping Tian and Guozheng Qin

    Citation: Genome Biology 2017 18:47

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  17. Content type: Research

    Structural variation (SV) influences genome organization and contributes to human disease. However, the complete mutational spectrum of SV has not been routinely captured in disease association studies.

    Authors: Ryan L. Collins, Harrison Brand, Claire E. Redin, Carrie Hanscom, Caroline Antolik, Matthew R. Stone, Joseph T. Glessner, Tamara Mason, Giulia Pregno, Naghmeh Dorrani, Giorgia Mandrile, Daniela Giachino, Danielle Perrin, Cole Walsh, Michelle Cipicchio, Maura Costello…

    Citation: Genome Biology 2017 18:36

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  18. Content type: METHOD

    Next-generation sequencing (NGS) of bulk tumour tissue can identify constituent cell populations in cancers and measure their abundance. This requires computational deconvolution of allelic counts from somatic...

    Authors: Sohrab Salehi, Adi Steif, Andrew Roth, Samuel Aparicio, Alexandre Bouchard-Côté and Sohrab P. Shah

    Citation: Genome Biology 2017 18:44

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  19. Content type: Method

    A variety of single-cell RNA preparation procedures have been described. So far, protocols require fresh material, which hinders complex study designs. We describe a sample preservation method that maintains t...

    Authors: Amy Guillaumet-Adkins, Gustavo Rodríguez-Esteban, Elisabetta Mereu, Maria Mendez-Lago, Diego A. Jaitin, Alberto Villanueva, August Vidal, Alex Martinez-Marti, Enriqueta Felip, Ana Vivancos, Hadas Keren-Shaul, Simon Heath, Marta Gut, Ido Amit, Ivo Gut and Holger Heyn

    Citation: Genome Biology 2017 18:45

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  20. Content type: Erratum

    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 2017 18:46

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    The original article was published in Genome Biology 2016 17:231

  21. Content type: Research Highlight

    Selection-free genome editing using Cas9 ribonucleoprotein embryo bombardment has been achieved for maize and wheat. This is a breakthrough that should make new breeding technologies more acceptable for worldw...

    Authors: Felix Wolter and Holger Puchta

    Citation: Genome Biology 2017 18:43

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  22. Content type: Correspondence

    In a recent study, Petrovski and Goldstein reported that (non-Finnish) Europeans have significantly fewer nonsynonymous singletons in Online Mendelian Inheritance in Man (OMIM) disease genes compared with Afri...

    Authors: Michael D. Kessler and Timothy D. O’Connor

    Citation: Genome Biology 2017 18:42

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  23. Content type: METHOD

    Allele-specific measurements of transcription factor binding from ChIP-seq data are key to dissecting the allelic effects of non-coding variants and their contribution to phenotypic diversity. However, most me...

    Authors: Ines de Santiago, Wei Liu, Ke Yuan, Martin O’Reilly, Chandra Sekhar Reddy Chilamakuri, Bruce A. J. Ponder, Kerstin B. Meyer and Florian Markowetz

    Citation: Genome Biology 2017 18:39

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  24. Content type: METHOD

    The study of epigenetic heterogeneity at the level of individual cells and in whole populations is the key to understanding cellular differentiation, organismal development, and the evolution of cancer. We dev...

    Authors: Martin Vincent, Kamilla Mundbjerg, Jakob Skou Pedersen, Gangning Liang, Peter A. Jones, Torben Falck Ørntoft, Karina Dalsgaard Sørensen and Carsten Wiuf

    Citation: Genome Biology 2017 18:38

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  25. Content type: Research

    The history of African indigenous cattle and their adaptation to environmental and human selection pressure is at the root of their remarkable diversity. Characterization of this diversity is an essential step...

    Authors: Jaemin Kim, Olivier Hanotte, Okeyo Ally Mwai, Tadelle Dessie, Salim Bashir, Boubacar Diallo, Morris Agaba, Kwondo Kim, Woori Kwak, Samsun Sung, Minseok Seo, Hyeonsoo Jeong, Taehyung Kwon, Mengistie Taye, Ki-Duk Song, Dajeong Lim…

    Citation: Genome Biology 2017 18:34

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  26. Content type: Research

    Distinct RNA species may compete for binding to microRNAs (miRNAs). This competition creates an indirect interaction between miRNA targets, which behave as miRNA sponges and eventually influence each other’s e...

    Authors: Carla Bosia, Francesco Sgrò, Laura Conti, Carlo Baldassi, Davide Brusa, Federica Cavallo, Ferdinando Di Cunto, Emilia Turco, Andrea Pagnani and Riccardo Zecchina

    Citation: Genome Biology 2017 18:37

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  27. Content type: Research

    Cotton has been cultivated and used to make fabrics for at least 7000 years. Two allotetraploid species of great commercial importance, Gossypium hirsutum and Gossypium barbadense, were domesticated after polyplo...

    Authors: Lei Fang, Hao Gong, Yan Hu, Chunxiao Liu, Baoliang Zhou, Tao Huang, Yangkun Wang, Shuqi Chen, David D. Fang, Xiongming Du, Hong Chen, Jiedan Chen, Sen Wang, Qiong Wang, Qun Wan, Bingliang Liu…

    Citation: Genome Biology 2017 18:33

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  28. Content type: Research

    Precise genome editing via homology-directed repair (HDR) after double-stranded DNA (dsDNA) cleavage facilitates functional genomic research and holds promise for gene therapy. However, HDR efficiency remains ...

    Authors: Jian-Ping Zhang, Xiao-Lan Li, Guo-Hua Li, Wanqiu Chen, Cameron Arakaki, Gary D. Botimer, David Baylink, Lu Zhang, Wei Wen, Ya-Wen Fu, Jing Xu, Noah Chun, Weiping Yuan, Tao Cheng and Xiao-Bing Zhang

    Citation: Genome Biology 2017 18:35

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  29. Content type: Research

    Monoubiquitination of H2B (H2Bub1) is a largely enigmatic histone modification that has been linked to transcriptional elongation. Because of this association, it has been commonly assumed that H2Bub1 is an ex...

    Authors: Wanhua Xie, Sankari Nagarajan, Simon J. Baumgart, Robyn Laura Kosinsky, Zeynab Najafova, Vijayalakshmi Kari, Magali Hennion, Daniela Indenbirken, Stefan Bonn, Adam Grundhoff, Florian Wegwitz, Ahmed Mansouri and Steven A. Johnsen

    Citation: Genome Biology 2017 18:32

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  30. Content type: Research Highlight

    Tumor cells have to overcome challenges in the host tissue microenvironment to metastasize successfully to distant organs. In a recent Nature study, a genome-wide functional screen demonstrated that deficiency of...

    Authors: Toni Celià-Terrassa and Yibin Kang

    Citation: Genome Biology 2017 18:31

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  31. Content type: Research

    Comparative transcriptomics can answer many questions in developmental and evolutionary developmental biology. Most transcriptomic studies start by showing global patterns of variation in transcriptomes that d...

    Authors: Sophie Pantalacci, Laurent Guéguen, Coraline Petit, Anne Lambert, Renata Peterkovà and Marie Sémon

    Citation: Genome Biology 2017 18:29

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  32. Content type: Research

    The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contamina...

    Authors: Ronald P. de Vries, Robert Riley, Ad Wiebenga, Guillermo Aguilar-Osorio, Sotiris Amillis, Cristiane Akemi Uchima, Gregor Anderluh, Mojtaba Asadollahi, Marion Askin, Kerrie Barry, Evy Battaglia, Özgür Bayram, Tiziano Benocci, Susanna A. Braus-Stromeyer, Camila Caldana, David Cánovas…

    Citation: Genome Biology 2017 18:28

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  33. Content type: Research

    The prevailing paradigm of host-parasite evolution is that arms races lead to increasing specialisation via genetic adaptation. Insect herbivores are no exception and the majority have evolved to colonise a sm...

    Authors: Thomas C. Mathers, Yazhou Chen, Gemy Kaithakottil, Fabrice Legeai, Sam T. Mugford, Patrice Baa-Puyoulet, Anthony Bretaudeau, Bernardo Clavijo, Stefano Colella, Olivier Collin, Tamas Dalmay, Thomas Derrien, Honglin Feng, Toni Gabaldón, Anna Jordan, Irene Julca…

    Citation: Genome Biology 2017 18:27

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    The Erratum to this article has been published in Genome Biology 2017 18:63

  34. Content type: Review

    High-throughput assays for measuring the three-dimensional (3D) configuration of DNA have provided unprecedented insights into the relationship between DNA 3D configuration and function. Data interpretation fr...

    Authors: Galip Gürkan Yardımcı and William Stafford Noble

    Citation: Genome Biology 2017 18:26

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  35. Content type: Research

    The CRISPR-Cas9 system is a widely utilized platform for transgenic animal production in various species, although its off-target effects should be addressed. Several applications of this tool have been propos...

    Authors: Yuanpeng Gao, Haibo Wu, Yongsheng Wang, Xin Liu, Linlin Chen, Qian Li, Chenchen Cui, Xu Liu, Jingcheng Zhang and Yong Zhang

    Citation: Genome Biology 2017 18:13

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  36. Content type: Method

    Current three-dimensional (3D) genome modeling platforms are limited by their inability to account for radial placement of loci in the nucleus. We present Chrom3D, a user-friendly whole-genome 3D computational...

    Authors: Jonas Paulsen, Monika Sekelja, Anja R. Oldenburg, Alice Barateau, Nolwenn Briand, Erwan Delbarre, Akshay Shah, Anita L. Sørensen, Corinne Vigouroux, Brigitte Buendia and Philippe Collas

    Citation: Genome Biology 2017 18:21

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  37. Content type: Research

    Whole-exome sequencing (WES) has been successful in identifying genes that cause familial Parkinson’s disease (PD). However, until now this approach has not been deployed to study large cohorts of unrelated pa...

    Authors: Iris E. Jansen, Hui Ye, Sasja Heetveld, Marie C. Lechler, Helen Michels, Renée I. Seinstra, Steven J. Lubbe, Valérie Drouet, Suzanne Lesage, Elisa Majounie, J. Raphael Gibbs, Mike A. Nalls, Mina Ryten, Juan A. Botia, Jana Vandrovcova, Javier Simon-Sanchez…

    Citation: Genome Biology 2017 18:22

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  38. Content type: Editorial

    We summarize the remarkable progress that has been made in the identification and functional characterization of DNA sequence variants associated with disease.

    Authors: Mark I. McCarthy and Daniel G. MacArthur

    Citation: Genome Biology 2017 18:20

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  39. Content type: Research

    5-Hydroxymethyluracil (5hmU) is a thymine base modification found in the genomes of a diverse range of organisms. To explore the functional importance of 5hmU, we develop a method for the genome-wide mapping o...

    Authors: Fumiko Kawasaki, Dario Beraldi, Robyn E. Hardisty, Gordon R. McInroy, Pieter van Delft and Shankar Balasubramanian

    Citation: Genome Biology 2017 18:23

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  40. Content type: Correspondence

    We thank Hattab and colleagues for their correspondence and their investigation of cell-type mixture correction methods in methyl-CG binding domain sequencing. Here, we speculate on why surrogate variable anal...

    Authors: Kevin McGregor, Aurélie Labbe and Celia M. T. Greenwood

    Citation: Genome Biology 2017 18:25

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  41. Content type: Correspondence

    Based on an extensive simulation study, McGregor and colleagues recently recommended the use of surrogate variable analysis (SVA) to control for the confounding effects of cell-type heterogeneity in DNA methyl...

    Authors: Mohammad W. Hattab, Andrey A. Shabalin, Shaunna L. Clark, Min Zhao, Gaurav Kumar, Robin F. Chan, Lin Ying Xie, Rick Jansen, Laura K. M. Han, Patrik K. E. Magnusson, Gerard van Grootheest, Christina M. Hultman, Brenda W. J. H. Penninx, Karolina A. Aberg and Edwin J. C. G. van den Oord

    Citation: Genome Biology 2017 18:24

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  42. Content type: METHOD

    We show that epigenome- and transcriptome-wide association studies (EWAS and TWAS) are prone to significant inflation and bias of test statistics, an unrecognized phenomenon introducing spurious findings if le...

    Authors: Maarten van Iterson, Erik W. van Zwet and Bastiaan T. Heijmans

    Citation: Genome Biology 2017 18:19

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  43. Content type: Research

    A healthy immune system requires immune cells that adapt rapidly to environmental challenges. This phenotypic plasticity can be mediated by transcriptional and epigenetic variability.

    Authors: Simone Ecker, Lu Chen, Vera Pancaldi, Frederik O. Bagger, José María Fernández, Enrique Carrillo de Santa Pau, David Juan, Alice L. Mann, Stephen Watt, Francesco Paolo Casale, Nikos Sidiropoulos, Nicolas Rapin, Angelika Merkel, Hendrik G. Stunnenberg, Oliver Stegle, Mattia Frontini…

    Citation: Genome Biology 2017 18:18

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  44. Content type: Research

    Inactivation of one X chromosome is established early in female mammalian development and can be reversed in vivo and in vitro when pluripotency factors are re-expressed. The extent of reactivation along the i...

    Authors: Irene Cantone, Gopuraja Dharmalingam, Yi-Wah Chan, Anne-Celine Kohler, Boris Lenhard, Matthias Merkenschlager and Amanda G. Fisher

    Citation: Genome Biology 2017 18:2

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  45. Content type: Research

    Identification of single nucleotide polymorphisms (SNPs) associated with gene expression levels, known as expression quantitative trait loci (eQTLs), may improve understanding of the functional role of phenoty...

    Authors: Roby Joehanes, Xiaoling Zhang, Tianxiao Huan, Chen Yao, Sai-xia Ying, Quang Tri Nguyen, Cumhur Yusuf Demirkale, Michael L. Feolo, Nataliya R. Sharopova, Anne Sturcke, Alejandro A. Schäffer, Nancy Heard-Costa, Han Chen, Po-ching Liu, Richard Wang, Kimberly A. Woodhouse…

    Citation: Genome Biology 2017 18:16

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