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  1. Authors: Teppo Felin, Jan Koenderink, Joachim I. Krueger, Denis Noble and George F. R. Ellis

    Citation: Genome Biology 2021 22:59

    Content type: Correspondence

    Published on:

    The original article was published in Genome Biology 2021 22:58

  2. Transcription in mammalian cells is a complex stochastic process involving shuttling of polymerase between genes and phase-separated liquid condensates. It occurs in bursts, which results in vastly different n...

    Authors: Massimo Cavallaro, Mark D. Walsh, Matt Jones, James Teahan, Simone Tiberi, Bärbel Finkenstädt and Daniel Hebenstreit

    Citation: Genome Biology 2021 22:56

    Content type: Research

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  3. A bottleneck in high-throughput functional genomics experiments is identifying the most important genes and their relevant functions from a list of gene hits. Gene Ontology (GO) enrichment methods provide insi...

    Authors: Robert Ietswaart, Benjamin M. Gyori, John A. Bachman, Peter K. Sorger and L. Stirling Churchman

    Citation: Genome Biology 2021 22:55

    Content type: Research

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  4. Frequent activation of the co-transcriptional factor YAP is observed in a large number of solid tumors. Activated YAP associates with enhancer loci via TEAD4-DNA-binding protein and stimulates cancer aggressiv...

    Authors: Li Li, Alejandro P. Ugalde, Colinda L. G. J. Scheele, Sebastian M. Dieter, Remco Nagel, Jin Ma, Abhijeet Pataskar, Gozde Korkmaz, Ran Elkon, Miao-Ping Chien, Li You, Pin-Rui Su, Onno B. Bleijerveld, Maarten Altelaar, Lyubomir Momchev, Zohar Manber…

    Citation: Genome Biology 2021 22:54

    Content type: Research

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  5. Massive genome sequencing data have inspired new challenges in personalized treatments and facilitated oncological drug discovery. We present a comprehensive database, My Personal Mutanome (MPM), for accelerat...

    Authors: Yadi Zhou, Junfei Zhao, Jiansong Fang, William Martin, Lang Li, Ruth Nussinov, Timothy A. Chan, Charis Eng and Feixiong Cheng

    Citation: Genome Biology 2021 22:53

    Content type: Database

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  6. N6-methyladenosine (m6A) and adenosine-to-inosine (A-to-I) RNA editing are two of the most abundant RNA modification events affecting adenosines in mammals. Both these RNA modifications determine mRNA fate and p....

    Authors: Valentina Tassinari, Valeriana Cesarini, Sara Tomaselli, Zaira Ianniello, Domenico Alessandro Silvestris, Lavinia Ceci Ginistrelli, Maurizio Martini, Biagio De Angelis, Gabriele De Luca, Lucia Ricci Vitiani, Alessandro Fatica, Franco Locatelli and Angela Gallo

    Citation: Genome Biology 2021 22:51

    Content type: Research

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  7. Macrophages are innate immune cells with diverse functional and molecular phenotypes. This diversity is largely unexplored at the level of single-cell proteomes because of the limitations of quantitative singl...

    Authors: Harrison Specht, Edward Emmott, Aleksandra A. Petelski, R. Gray Huffman, David H. Perlman, Marco Serra, Peter Kharchenko, Antonius Koller and Nikolai Slavov

    Citation: Genome Biology 2021 22:50

    Content type: Research

    Published on:

  8. The resources generated by the GTEx consortium offer unprecedented opportunities to advance our understanding of the biology of human diseases. Here, we present an in-depth examination of the phenotypic conseq...

    Authors: Alvaro N. Barbeira, Rodrigo Bonazzola, Eric R. Gamazon, Yanyu Liang, YoSon Park, Sarah Kim-Hellmuth, Gao Wang, Zhuoxun Jiang, Dan Zhou, Farhad Hormozdiari, Boxiang Liu, Abhiram Rao, Andrew R. Hamel, Milton D. Pividori, François Aguet, Lisa Bastarache…

    Citation: Genome Biology 2021 22:49

    Content type: Research

    Published on:

  9. Alternative splicing is a rich source of tumor-specific neoantigen targets for immunotherapy. This holds promise for glioblastomas (GBMs), the most common primary tumors of the adult brain, which are resistant...

    Authors: Lin Wang, Karin Shamardani, Husam Babikir, Francisca Catalan, Takahide Nejo, Susan Chang, Joanna J. Phillips, Hideho Okada and Aaron A. Diaz

    Citation: Genome Biology 2021 22:48

    Content type: Research

    Published on:

  10. Genes contain multiple promoters that can drive the expression of various transcript isoforms. Although transcript isoforms from the same gene could have diverse and non-overlapping functions, current loss-of-...

    Authors: Rebecca Davies, Ling Liu, Sheng Taotao, Natasha Tuano, Richa Chaturvedi, Kie Kyon Huang, Catherine Itman, Amit Mandoli, Aditi Qamra, Changyuan Hu, David Powell, Roger J. Daly, Patrick Tan and Joseph Rosenbluh

    Citation: Genome Biology 2021 22:47

    Content type: Research

    Published on:

    The Author Correction to this article has been published in Genome Biology 2021 22:88

  11. An amendment to this paper has been published and can be accessed via the original article.

    Authors: Minghao Chia, Cai Li, Sueli Marques, Vicente Pelechano, Nicholas M. Luscombe and Folkert J. van Werven

    Citation: Genome Biology 2021 22:46

    Content type: Author Correction

    Published on:

    The original article was published in Genome Biology 2021 22:34

  12. There is currently no method to precisely measure the errors that occur in the sequencing instrument/sequencer, which is critical for next-generation sequencing applications aimed at discovering the genetic ma...

    Authors: Eric M. Davis, Yu Sun, Yanling Liu, Pandurang Kolekar, Ying Shao, Karol Szlachta, Heather L. Mulder, Dongren Ren, Stephen V. Rice, Zhaoming Wang, Joy Nakitandwe, Alexander M. Gout, Bridget Shaner, Salina Hall, Leslie L. Robison, Stanley Pounds…

    Citation: Genome Biology 2021 22:37

    Content type: Research

    Published on:

  13. Deregulated gene expression is a hallmark of cancer; however, most studies to date have analyzed short-read RNA sequencing data with inherent limitations. Here, we combine PacBio long-read isoform sequencing (...

    Authors: Kie Kyon Huang, Jiawen Huang, Jeanie Kar Leng Wu, Minghui Lee, Su Ting Tay, Vikrant Kumar, Kalpana Ramnarayanan, Nisha Padmanabhan, Chang Xu, Angie Lay Keng Tan, Charlene Chan, Dennis Kappei, Jonathan Göke and Patrick Tan

    Citation: Genome Biology 2021 22:44

    Content type: Research

    Published on:

  14. Microexons, exons that are ≤ 30 nucleotides, are a highly conserved and dynamically regulated set of cassette exons. They have key roles in nervous system development and function, as evidenced by recent resul...

    Authors: Guillermo E. Parada, Roberto Munita, Ilias Georgakopoulos-Soares, Hugo J. R. Fernandes, Veronika R. Kedlian, Emmanouil Metzakopian, Maria Estela Andres, Eric A. Miska and Martin Hemberg

    Citation: Genome Biology 2021 22:43

    Content type: Research

    Published on:

  15. Recently, efforts have been made toward the harmonization of transcriptomic data structures and workflows using the concept of data tidiness, to facilitate modularisation. We present tidybulk, a modular framew...

    Authors: Stefano Mangiola, Ramyar Molania, Ruining Dong, Maria A. Doyle and Anthony T. Papenfuss

    Citation: Genome Biology 2021 22:42

    Content type: Software

    Published on:

  16. Short hairpin RNAs (shRNAs) are used to deplete circRNAs by targeting back-splicing junction (BSJ) sites. However, frequent discrepancies exist between shRNA-mediated circRNA knockdown and the corresponding bi...

    Authors: Yang Zhang, Tuan M. Nguyen, Xiao-Ou Zhang, Limei Wang, Tin Phan, John G. Clohessy and Pier Paolo Pandolfi

    Citation: Genome Biology 2021 22:41

    Content type: Method

    Published on:

  17. CRISPR guide RNA libraries have been iteratively improved to provide increasingly efficient reagents, although their large size is a barrier for many applications. We design an optimised minimal genome-wide hu...

    Authors: Emanuel Gonçalves, Mark Thomas, Fiona M. Behan, Gabriele Picco, Clare Pacini, Felicity Allen, Alessandro Vinceti, Mamta Sharma, David A. Jackson, Stacey Price, Charlotte M. Beaver, Oliver Dovey, David Parry-Smith, Francesco Iorio, Leopold Parts, Kosuke Yusa…

    Citation: Genome Biology 2021 22:40

    Content type: Short Report

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  18. The Environmental Determinants of Diabetes in the Young (TEDDY) is a prospective birth cohort designed to study type 1 diabetes (T1D) by following children with high genetic risk. An integrative multi-omics ap...

    Authors: Leandro Balzano-Nogueira, Ricardo Ramirez, Tatyana Zamkovaya, Jordan Dailey, Alexandria N. Ardissone, Srikar Chamala, Joan Serrano-Quílez, Teresa Rubio, Michael J. Haller, Patrick Concannon, Mark A. Atkinson, Desmond A. Schatz, Eric W. Triplett and Ana Conesa

    Citation: Genome Biology 2021 22:39

    Content type: Research

    Published on:

  19. Although genome-wide DNA methylomes have demonstrated their clinical value as reliable biomarkers for tumor detection, subtyping, and classification, their direct biological impacts at the individual gene leve...

    Authors: Justin Williams, Beisi Xu, Daniel Putnam, Andrew Thrasher, Chunliang Li, Jun Yang and Xiang Chen

    Citation: Genome Biology 2021 22:24

    Content type: Method

    Published on:

  20. We report SPIN, an integrative computational method to reveal genome-wide intranuclear chromosome positioning and nuclear compartmentalization relative to multiple nuclear structures, which are pivotal for mod...

    Authors: Yuchuan Wang, Yang Zhang, Ruochi Zhang, Tom van Schaik, Liguo Zhang, Takayo Sasaki, Daniel Peric-Hupkes, Yu Chen, David M. Gilbert, Bas van Steensel, Andrew S. Belmont and Jian Ma

    Citation: Genome Biology 2021 22:36

    Content type: Method

    Published on:

  21. Alternative splicing (AS) is a widespread regulatory mechanism in multicellular organisms. Numerous transcriptomic and single-gene studies in plants have investigated AS in response to specific conditions, esp...

    Authors: Guiomar Martín, Yamile Márquez, Federica Mantica, Paula Duque and Manuel Irimia

    Citation: Genome Biology 2021 22:35

    Content type: Research

    Published on:

  22. The start and end sites of messenger RNAs (TSSs and TESs) are highly regulated, often in a cell-type-specific manner. Yet the contribution of transcript diversity in regulating gene expression remains largely ...

    Authors: Minghao Chia, Cai Li, Sueli Marques, Vicente Pelechano, Nicholas M. Luscombe and Folkert J. van Werven

    Citation: Genome Biology 2021 22:34

    Content type: Research

    Published on:

    The Author Correction to this article has been published in Genome Biology 2021 22:46

  23. Aberrant activation of the Hedgehog pathway drives tumorigenesis of many cancers, including glioblastoma. However, the sensitization mechanism of the G protein-coupled-like receptor smoothened (SMO), a key com...

    Authors: Xujia Wu, Songhua Xiao, Maolei Zhang, Lixuan Yang, Jian Zhong, Bo Li, Fanying Li, Xin Xia, Xixi Li, Huangkai Zhou, Dawei Liu, Nunu Huang, Xuesong Yang, Feizhe Xiao and Nu Zhang

    Citation: Genome Biology 2021 22:33

    Content type: Research

    Published on:

  24. GWAS summary statistics are fundamental for a variety of research applications yet no common storage format has been widely adopted. Existing tabular formats ambiguously or incompletely store information about...

    Authors: Matthew S. Lyon, Shea J. Andrews, Ben Elsworth, Tom R. Gaunt, Gibran Hemani and Edoardo Marcora

    Citation: Genome Biology 2021 22:32

    Content type: Method

    Published on:

  25. Tartary buckwheat (Fagopyrum tataricum) is a nutritionally balanced and flavonoid-rich crop plant that has been in cultivation for 4000 years and is now grown globally. Despite its nutraceutical and agricultural ...

    Authors: Kaixuan Zhang, Ming He, Yu Fan, Hui Zhao, Bin Gao, Keli Yang, Faliang Li, Yu Tang, Qiang Gao, Tao Lin, Muriel Quinet, Dagmar Janovská, Vladimir Meglič, Jacek Kwiatkowski, Olga Romanova, Nikhil Chrungoo…

    Citation: Genome Biology 2021 22:23

    Content type: Research

    Published on:

  26. Animal genomes contain thousands of long noncoding RNA (lncRNA) genes, a growing subset of which are thought to be functionally important. This functionality is often mediated by short sequence elements scatte...

    Authors: Caroline Jane Ross, Aviv Rom, Amit Spinrad, Dikla Gelbard-Solodkin, Neta Degani and Igor Ulitsky

    Citation: Genome Biology 2021 22:29

    Content type: Research

    Published on:

  27. A major challenge to long read sequencing data is their high error rate of up to 15%. We present Ratatosk, a method to correct long reads with short read data. We demonstrate on 5 human genome trios that Ratat...

    Authors: Guillaume Holley, Doruk Beyter, Helga Ingimundardottir, Peter L. Møller, Snædis Kristmundsdottir, Hannes P. Eggertsson and Bjarni V. Halldorsson

    Citation: Genome Biology 2021 22:28

    Content type: Method

    Published on:

  28. Polyploidization and introgression are major events driving plant genome evolution and influencing crop breeding. However, the mechanisms underlying the higher-order chromatin organization of subgenomes and al...

    Authors: Jizeng Jia, Yilin Xie, Jingfei Cheng, Chuizheng Kong, Meiyue Wang, Lifeng Gao, Fei Zhao, Jingyu Guo, Kai Wang, Guangwei Li, Dangqun Cui, Tiezhu Hu, Guangyao Zhao, Daowen Wang, Zhengang Ru and Yijing Zhang

    Citation: Genome Biology 2021 22:26

    Content type: Research

    Published on:

  29. Seminal studies of vertebrate protein evolution speculated that gene regulatory changes can drive anatomical innovations. However, very little is known about gene regulatory network (GRN) evolution associated ...

    Authors: Tarang K. Mehta, Christopher Koch, Will Nash, Sara A. Knaack, Padhmanand Sudhakar, Marton Olbei, Sarah Bastkowski, Luca Penso-Dolfin, Tamas Korcsmaros, Wilfried Haerty, Sushmita Roy and Federica Di-Palma

    Citation: Genome Biology 2021 22:25

    Content type: Research

    Published on:

  30. There are no comprehensive methods to identify N6-methyladenosine (m6A) at single-base resolution for every single transcript, which is necessary for the estimation of m6A abundance. We develop a new pipeline cal...

    Authors: Yubang Gao, Xuqing Liu, Bizhi Wu, Huihui Wang, Feihu Xi, Markus V. Kohnen, Anireddy S. N. Reddy and Lianfeng Gu

    Citation: Genome Biology 2021 22:22

    Content type: Method

    Published on:

  31. In any ‘omics study, the scale of analysis can dramatically affect the outcome. For instance, when clustering single-cell transcriptomes, is the analysis tuned to discover broad or specific cell types? Likewis...

    Authors: Fan Zheng, She Zhang, Christopher Churas, Dexter Pratt, Ivet Bahar and Trey Ideker

    Citation: Genome Biology 2021 22:21

    Content type: Short Report

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  32. Transcription factor (TF) binding specificity is determined via a complex interplay between the transcription factor’s DNA binding preference and cell type-specific chromatin environments. The chromatin featur...

    Authors: Divyanshi Srivastava, Begüm Aydin, Esteban O. Mazzoni and Shaun Mahony

    Citation: Genome Biology 2021 22:20

    Content type: Research

    Published on:

  33. Metastatic progress is the primary cause of death in most cancers, yet the regulatory dynamics driving the cellular changes necessary for metastasis remain poorly understood. Multi-omics approaches hold great ...

    Authors: Saba Ghaffari, Casey Hanson, Remington E. Schmidt, Kelly J. Bouchonville, Steven M. Offer and Saurabh Sinha

    Citation: Genome Biology 2021 22:19

    Content type: Research

    Published on:

  34. Although the genomes of monozygotic twins are practically identical, their methylomes may evolve divergently throughout their lifetime as a consequence of factors such as the environment or aging. Particularly...

    Authors: Benjamin Planterose Jiménez, Fan Liu, Amke Caliebe, Diego Montiel González, Jordana T. Bell, Manfred Kayser and Athina Vidaki

    Citation: Genome Biology 2021 22:18

    Content type: Research

    Published on:

  35. N6-methyladenosine (m6A) modification is known to impact many aspects of RNA metabolism, including mRNA stability and translation, and is highly prevalent in the brain.

    Authors: Andrew M. Shafik, Feiran Zhang, Zhenxing Guo, Qing Dai, Kinga Pajdzik, Yangping Li, Yunhee Kang, Bing Yao, Hao Wu, Chuan He, Emily G. Allen, Ranhui Duan and Peng Jin

    Citation: Genome Biology 2021 22:17

    Content type: Research

    Published on:

  36. The folding of proteins is challenging in the highly crowded and sticky environment of a cell. Regulation of translation elongation may play a crucial role in ensuring the correct folding of proteins. Much of ...

    Authors: Taolan Zhao, Yan-Ming Chen, Yu Li, Jia Wang, Siyu Chen, Ning Gao and Wenfeng Qian

    Citation: Genome Biology 2021 22:16

    Content type: Research

    Published on:

  37. Small RNAs (sRNAs) including microRNAs (miRNAs) and small interfering RNAs (siRNAs) serve as core players in gene silencing at transcriptional and post-transcriptional levels in plants, but their subcellular l...

    Authors: Xiaoyu Yang, Chenjiang You, Xufeng Wang, Lei Gao, Beixin Mo, Lin Liu and Xuemei Chen

    Citation: Genome Biology 2021 22:15

    Content type: Research

    Published on:

  38. The regulation of messenger RNA (mRNA) stability has a profound impact on gene expression dynamics during embryogenesis. For example, in animals, maternally deposited mRNAs are degraded after fertilization to ...

    Authors: Santiago Gerardo Medina-Muñoz, Gopal Kushawah, Luciana Andrea Castellano, Michay Diez, Michelle Lynn DeVore, María José Blanco Salazar and Ariel Alejandro Bazzini

    Citation: Genome Biology 2021 22:14

    Content type: Research

    Published on:

  39. Structural variations (SVs), a major resource of genomic variation, can have profound consequences on phenotypic variation, yet the impacts of SVs remain largely unexplored in crops.

    Authors: Jiantao Guan, Yaoguang Xu, Yang Yu, Jun Fu, Fei Ren, Jiying Guo, Jianbo Zhao, Quan Jiang, Jianhua Wei and Hua Xie

    Citation: Genome Biology 2021 22:13

    Content type: Research

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