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  1. 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 2024 25:5

    The original article was published in Genome Biology 2021 22:26

  2. Transposable elements (TEs) are important drivers of genome evolution. Nonetheless, TE annotation remains a complex and challenging task. As more genomes from phylogenetically diverse species are published, a ...

    Authors: Landen Gozashti and Hopi E. Hoekstra
    Citation: Genome Biology 2024 25:4

    The original article was published in Genome Biology 2019 20:275

    The Correspondence to this article has been published in Genome Biology 2024 25:6

  3. The majority of disease-associated variants identified through genome-wide association studies are located outside of protein-coding regions. Prioritizing candidate regulatory variants and gene targets to iden...

    Authors: Charles E. Breeze, Eric Haugen, María Gutierrez-Arcelus, Xiaozheng Yao, Andrew Teschendorff, Stephan Beck, Ian Dunham, John Stamatoyannopoulos, Nora Franceschini, Mitchell J. Machiela and Sonja I. Berndt
    Citation: Genome Biology 2024 25:3
  4. Formation of tissue-specific transcriptional programs underlies multicellular development, including dorsoventral (DV) patterning of the Drosophila embryo. This involves interactions between transcriptional enhan...

    Authors: George Hunt, Roshan Vaid, Sergei Pirogov, Alexander Pfab, Christoph Ziegenhain, Rickard Sandberg, Johan Reimegård and Mattias Mannervik
    Citation: Genome Biology 2024 25:2
  5. Capturing the genetic diversity of wild relatives is crucial for improving crops because wild species are valuable sources of agronomic traits that are essential to enhance the sustainability and adaptability ...

    Authors: Noé Cochetel, Andrea Minio, Andrea Guarracino, Jadran F. Garcia, Rosa Figueroa-Balderas, Mélanie Massonnet, Takao Kasuga, Jason P. Londo, Erik Garrison, Brandon S. Gaut and Dario Cantu
    Citation: Genome Biology 2023 24:290
  6. Many deep learning-based methods have been proposed to handle complex single-cell data. Deep learning approaches may also prove useful to jointly analyze single-cell RNA sequencing (scRNA-seq) and single-cell ...

    Authors: Biqing Zhu, Yuge Wang, Li-Ting Ku, David van Dijk, Le Zhang, David A. Hafler and Hongyu Zhao
    Citation: Genome Biology 2023 24:292
  7. Spatial omics technologies can help identify spatially organized biological processes, but existing computational approaches often overlook structural dependencies in the data. Here, we introduce Smoother, a u...

    Authors: Jiayu Su, Jean-Baptiste Reynier, Xi Fu, Guojie Zhong, Jiahao Jiang, Rydberg Supo Escalante, Yiping Wang, Luis Aparicio, Benjamin Izar, David A. Knowles and Raul Rabadan
    Citation: Genome Biology 2023 24:291
  8. Metabolites play critical roles in regulating nutritional qualities of plants, thereby influencing their consumption and human health. However, the genetic basis underlying the metabolite-based nutrient qualit...

    Authors: Zehong Ding, Lili Fu, Bin Wang, Jianqiu Ye, Wenjun Ou, Yan Yan, Meiying Li, Liwang Zeng, Xuekui Dong, Weiwei Tie, Xiaoxue Ye, Jinghao Yang, Zhengnan Xie, Yu Wang, Jianchun Guo, Songbi Chen…
    Citation: Genome Biology 2023 24:289
  9. Deconvolution of cell mixtures in “bulk” transcriptomic samples from homogenate human tissue is important for understanding disease pathologies. However, several experimental and computational challenges imped...

    Authors: Sean K. Maden, Sang Ho Kwon, Louise A. Huuki-Myers, Leonardo Collado-Torres, Stephanie C. Hicks and Kristen R. Maynard
    Citation: Genome Biology 2023 24:288
  10. The coordinated transcriptional regulation of activated T-cells is based on a complex dynamic behavior of signaling networks. Given an external stimulus, T-cell gene expression is characterized by impulse and ...

    Authors: Michael Rade, Sebastian Böhlen, Vanessa Neuhaus, Dennis Löffler, Conny Blumert, Maximilian Merz, Ulrike Köhl, Susann Dehmel, Katherina Sewald and Kristin Reiche
    Citation: Genome Biology 2023 24:287
  11. Expression quantitative trait locus (eQTL) analysis has emerged as an important tool in elucidating the link between genetic variants and gene expression, thereby bridging the gap between risk SNPs and associa...

    Authors: Yong Zeng, Rahi Jain, Magnus Lam, Musaddeque Ahmed, Haiyang Guo, Wenjie Xu, Yuan Zhong, Gong-Hong Wei, Wei Xu and Housheng Hansen He
    Citation: Genome Biology 2023 24:285
  12. Point mutations in histone variant H3.3 (H3.3K27M, H3.3G34R) and the H3.3-specific ATRX/DAXX chaperone complex are frequent events in pediatric gliomas. These H3.3 point mutations affect many chromatin modific...

    Authors: Hsiao P. J. Voon, Linda Hii, Andrew Garvie, Maheshi Udugama, Brian Krug, Caterina Russo, Anderly C. Chüeh, Roger J. Daly, Alison Morey, Toby D. M. Bell, Stephen J. Turner, Joseph Rosenbluh, Paul Daniel, Ron Firestein, Jeffrey R. Mann, Philippe Collas…
    Citation: Genome Biology 2023 24:284
  13. Strain-level diversity is widespread among bacterial species and can expand the functional potential of natural microbial communities. However, to what extent communities undergo consistent shifts in strain co...

    Authors: Gilles L. C. Baud, Aiswarya Prasad, Kirsten M. Ellegaard and Philipp Engel
    Citation: Genome Biology 2023 24:283
  14. Many elite genes have been identified from the available cotton genomic data, providing various genetic resources for gene-driven breeding. However, backbone cultivar-driven breeding is the most widely applied...

    Authors: Shang Liu, Dongyun Zuo, Hailiang Cheng, Man He, Qiaolian Wang, Limin Lv, Youping Zhang, Javaria Ashraf, Ji Liu and Guoli Song
    Citation: Genome Biology 2023 24:282
  15. GCLiPP is a global RNA interactome capture method that detects RNA-binding protein (RBP) occupancy transcriptome-wide. GCLiPP maps RBP-occupied sites at a higher resolution than phase separation-based techniqu...

    Authors: Wandi S. Zhu, Adam J. Litterman, Harshaan S. Sekhon, Robin Kageyama, Maya M. Arce, Kimberly E. Taylor, Wenxue Zhao, Lindsey A. Criswell, Noah Zaitlen, David J. Erle and K. Mark Ansel
    Citation: Genome Biology 2023 24:281
  16. The dikaryotic stage dominates most of the life cycle in basidiomycetes, and each cell carries two different haploid nuclei. Accurate phasing of these two nuclear genomes and their interactions have long been ...

    Authors: Youjin Deng, Lin Guo, Longji Lin, Yuefeng Li, Jinxiang Zhang, Yue Zhang, Bin Yuan, Lina Ke, Baogui Xie and Ray Ming
    Citation: Genome Biology 2023 24:280
  17. Identifying host factors is key to understanding RNA virus pathogenicity. Besides proteins, RNAs can interact with virus genomes to impact replication.

    Authors: Kuo-Chieh Liao, Xuping Xie, Anna Karin Beatrice Sundstrom, Xin Ni Lim, Kiat Kee Tan, Yu Zhang, Jing Zou, Amanda Makha Bifani, Hui Xian Poh, Jia Jia Chen, Wy Ching Ng, Su Ying Lim, Eng Eong Ooi, October M. Sessions, Yvonne Tay, Pei-Yong Shi…
    Citation: Genome Biology 2023 24:279
  18. Epigenetic scores (EpiScores) can provide biomarkers of lifestyle and disease risk. Projecting new datasets onto a reference panel is challenging due to separation of technical and biological variation with ar...

    Authors: Charlotte Merzbacher, Barry Ryan, Thibaut Goldsborough, Robert F. Hillary, Archie Campbell, Lee Murphy, Andrew M. McIntosh, David Liewald, Sarah E. Harris, Allan F. McRae, Simon R. Cox, Timothy I. Cannings, Catalina A. Vallejos, Daniel L. McCartney and Riccardo E. Marioni
    Citation: Genome Biology 2023 24:278
  19. MALDI-TOF MS-based microbial identification relies on reference spectral libraries, which limits the screening of diverse isolates, including uncultured lineages. We present a new strategy for broad-spectrum i...

    Authors: Yuji Sekiguchi, Kanae Teramoto, Dieter M. Tourlousse, Akiko Ohashi, Mayu Hamajima, Daisuke Miura, Yoshihiro Yamada, Shinichi Iwamoto and Koichi Tanaka
    Citation: Genome Biology 2023 24:257
  20. Recent state-of-the-art sequencing technologies enable the investigation of challenging regions in the human genome and expand the scope of variant benchmarking datasets. Herein, we sequence a Chinese Quartet,...

    Authors: Peng Jia, Lianhua Dong, Xiaofei Yang, Bo Wang, Stephen J. Bush, Tingjie Wang, Jiadong Lin, Songbo Wang, Xixi Zhao, Tun Xu, Yizhuo Che, Ningxin Dang, Luyao Ren, Yujing Zhang, Xia Wang, Fan Liang…
    Citation: Genome Biology 2023 24:277
  21. Although generally superior, hybrid approaches for correcting errors in third-generation sequencing (TGS) reads, using next-generation sequencing (NGS) reads, mistake haplotype-specific variants for errors in ...

    Authors: Xiongbin Kang, Jialu Xu, Xiao Luo and Alexander Schönhuth
    Citation: Genome Biology 2023 24:275
  22. Spatial transcriptomic technologies, such as the Visium platform, measure gene expression in different regions of tissues. Here, we describe new software, STmut, to visualize somatic point mutations, allelic i...

    Authors: Limin Chen, Darwin Chang, Bishal Tandukar, Delahny Deivendran, Joanna Pozniak, Noel Cruz-Pacheco, Raymond J. Cho, Jeffrey Cheng, Iwei Yeh, Chris Marine, Boris C. Bastian, Andrew L. Ji and A. Hunter Shain
    Citation: Genome Biology 2023 24:273
  23. A tumor contains a diverse collection of somatic mutations that reflect its past evolutionary history and that range in scale from single nucleotide variants (SNVs) to large-scale copy-number aberrations (CNAs...

    Authors: Palash Sashittal, Haochen Zhang, Christine A. Iacobuzio-Donahue and Benjamin J. Raphael
    Citation: Genome Biology 2023 24:272
  24. Common diseases manifest differentially between patients, but the genetic origin of this variation remains unclear. To explore possible involvement of gene transcriptional-variation, we produce a DNA methylati...

    Authors: Yifat Edrei, Revital Levy, Daniel Kaye, Anat Marom, Bernhard Radlwimmer and Asaf Hellman
    Citation: Genome Biology 2023 24:264
  25. Genomic DNA reference materials are widely recognized as essential for ensuring data quality in omics research. However, relying solely on reference datasets to evaluate the accuracy of variant calling results...

    Authors: Luyao Ren, Xiaoke Duan, Lianhua Dong, Rui Zhang, Jingcheng Yang, Yuechen Gao, Rongxue Peng, Wanwan Hou, Yaqing Liu, Jingjing Li, Ying Yu, Naixin Zhang, Jun Shang, Fan Liang, Depeng Wang, Hui Chen…
    Citation: Genome Biology 2023 24:270
  26. Systematic characterization of how  genetic variation modulates gene regulation in a cell type-specific context is essential for understanding complex traits. To address this question, we profile gene expressi...

    Authors: Jun Wang, Xuesen Cheng, Qingnan Liang, Leah A. Owen, Jiaxiong Lu, Yiqiao Zheng, Meng Wang, Shiming Chen, Margaret M. DeAngelis, Yumei Li and Rui Chen
    Citation: Genome Biology 2023 24:269
  27. Enhancer dysregulation is one of the important features for cancer cells. Enhancers enriched with H3K4me3 have been implicated to play important roles in cancer. However, their detailed features and regulatory...

    Authors: Xiang Lin, Ji-Dong Chen, Chen-Yu Wang, Zhen Cai, Rui Zhan, Chen Yang, La-Ying Zhang, Lian-Yun Li, Yong Xiao, Ming-Kai Chen and Min Wu
    Citation: Genome Biology 2023 24:268
  28. RNA editing has been described as promoting genetic heterogeneity, leading to the development of multiple disorders, including cancer. The cytosine deaminase APOBEC3B is implicated in tumor evolution through D...

    Authors: Alicia Alonso de la Vega, Nuri Alpay Temiz, Rafail Tasakis, Kalman Somogyi, Lorena Salgueiro, Eleni Zimmer, Maria Ramos, Alberto Diaz-Jimenez, Sara Chocarro, Mirian Fernández-Vaquero, Bojana Stefanovska, Eli Reuveni, Uri Ben-David, Albrecht Stenzinger, Tanja Poth, Mathias Heikenwälder…
    Citation: Genome Biology 2023 24:267
  29. Linking cis-regulatory sequences to target genes has been a long-standing challenge. In this study, we introduce CREaTor, an attention-based deep neural network designed to model cis-regulatory patterns for genom...

    Authors: Yongge Li, Fusong Ju, Zhiyuan Chen, Yiming Qu, Huanhuan Xia, Liang He, Lijun Wu, Jianwei Zhu, Bin Shao and Pan Deng
    Citation: Genome Biology 2023 24:266
  30. “Red tides” are harmful algal blooms caused by dinoflagellate microalgae that accumulate toxins lethal to other organisms, including humans via consumption of contaminated seafood. These algal blooms are drive...

    Authors: Katherine E. Dougan, Zhi-Luo Deng, Lars Wöhlbrand, Carsten Reuse, Boyke Bunk, Yibi Chen, Juliane Hartlich, Karsten Hiller, Uwe John, Jana Kalvelage, Johannes Mansky, Meina Neumann-Schaal, Jörg Overmann, Jörn Petersen, Selene Sanchez-Garcia, Kerstin Schmidt-Hohagen…
    Citation: Genome Biology 2023 24:265
  31. Differential analysis of bulk RNA-seq data often suffers from lack of good controls. Here, we present a generative model that replaces controls, trained solely on healthy tissues. The unsupervised model learns...

    Authors: Iñigo Prada-Luengo, Viktoria Schuster, Yuhu Liang, Thilde Terkelsen, Valentina Sora and Anders Krogh
    Citation: Genome Biology 2023 24:263
  32. Recently, many analysis tools have been devised to offer insights into data generated via cytometry by time-of-flight (CyTOF). However, objective evaluations of these methods remain absent as most evaluations ...

    Authors: Yuqiu Yang, Kaiwen Wang, Zeyu Lu, Tao Wang and Xinlei Wang
    Citation: Genome Biology 2023 24:262
  33. Using mouse genetic studies and systematic assessments of brain neuroanatomical phenotypes, we set out to identify which of the 30 genes causes brain defects at the autism-associated 16p11.2 locus.

    Authors: Perrine F. Kretz, Christel Wagner, Anna Mikhaleva, Charlotte Montillot, Sylvain Hugel, Ilaria Morella, Meghna Kannan, Marie-Christine Fischer, Maxence Milhau, Ipek Yalcin, Riccardo Brambilla, Mohammed Selloum, Yann Herault, Alexandre Reymond, Stephan C. Collins and Binnaz Yalcin
    Citation: Genome Biology 2023 24:261
  34. Transposable elements (TEs) have colonized the genomes of most metazoans, and many TE-embedded sequences function as cis-regulatory elements (CREs) for genes involved in a wide range of biological processes from ...

    Authors: Cyril Pulver, Delphine Grun, Julien Duc, Shaoline Sheppard, Evarist Planet, Alexandre Coudray, Raphaël de Fondeville, Julien Pontis and Didier Trono
    Citation: Genome Biology 2023 24:258
  35. Metagenome-assembled genomes have greatly expanded the reference genomes for skin microbiome. However, the current reference genomes are largely based on samples from adults in North America and lack represent...

    Authors: Zeyang Shen, Lukian Robert, Milan Stolpman, You Che, Katrina J. Allen, Richard Saffery, Audrey Walsh, Angela Young, Jana Eckert, Clay Deming, Qiong Chen, Sean Conlan, Karen Laky, Jenny Min Li, Lindsay Chatman, Sara Saheb Kashaf…
    Citation: Genome Biology 2023 24:252
  36. Daylength is a key seasonal cue for animals and plants. In cereals, photoperiodic responses are a major adaptive trait, and alleles of clock genes such as PHOTOPERIOD1 (PPD1) and EARLY FLOWERING3 (ELF3) have been...

    Authors: Mingjun Gao, Yunlong Lu, Feng Geng, Cornelia Klose, Anne-Marie Staudt, He Huang, Duy Nguyen, Hui Lan, Han Lu, Todd C. Mockler, Dmitri A. Nusinow, Andreas Hiltbrunner, Eberhard Schäfer, Philip A. Wigge and Katja E. Jaeger
    Citation: Genome Biology 2023 24:256
  37. Authors: Jennifer R. S. Meadows, Jefrey M. Kidd, Guo-Dong Wang, Heidi G. Parker, Peter Z. Schall, Matteo Bianchi, Matthew J. Christmas, Katia Bougiouri, Reuben M. Buckley, Christophe Hitte, Anthony K. Nguyen, Chao Wang, Vidhya Jagannathan, Julia E. Niskanen, Laurent A. F. Frantz, Meharji Arumilli…
    Citation: Genome Biology 2023 24:255

    The original article was published in Genome Biology 2023 24:187

  38. We introduce DEQSeq, a nanopore sequencing approach that rationalizes the selection of favorable genome editing enzymes from directed molecular evolution experiments. With the ability to capture full-length se...

    Authors: Lukas Theo Schmitt, Aksana Schneider, Jonas Posorski, Felix Lansing, Milica Jelicic, Manavi Jain, Shady Sayed, Frank Buchholz and Duran Sürün
    Citation: Genome Biology 2023 24:254
  39. Archaea, together with Bacteria, represent the two main divisions of life on Earth, with many of the defining characteristics of the more complex eukaryotes tracing their origin to evolutionary innovations fir...

    Authors: Georgi K. Marinov, S. Tansu Bagdatli, Tong Wu, Chuan He, Anshul Kundaje and William J. Greenleaf
    Citation: Genome Biology 2023 24:253
  40. Harnessing hepatocytes for basic research and regenerative medicine demands a complete understanding of the genetic determinants underlying hepatocyte differentiation and maturation. Single-cell CRISPR screens...

    Authors: Junbo Liang, Jinsong Wei, Jun Cao, Jun Qian, Ran Gao, Xiaoyu Li, Dingding Wang, Yani Gu, Lei Dong, Jia Yu, Bing Zhao and Xiaoyue Wang
    Citation: Genome Biology 2023 24:251

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