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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. “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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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

  23. 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
  24. 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
  25. 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
  26. A key step for comparative genomics is to group open reading frames into functionally and evolutionarily meaningful gene clusters. Gene clustering is complicated by intraspecific duplications and horizontal ge...

    Authors: Saioa Manzano-Morales, Yang Liu, Sara González-Bodí, Jaime Huerta-Cepas and Jaime Iranzo
    Citation: Genome Biology 2023 24:250
  27. CHESS 3 represents an improved human gene catalog based on nearly 10,000 RNA-seq experiments across 54 body sites. It significantly improves current genome annotation by integrating the latest reference data a...

    Authors: Ales Varabyou, Markus J. Sommer, Beril Erdogdu, Ida Shinder, Ilia Minkin, Kuan-Hao Chao, Sukhwan Park, Jakob Heinz, Christopher Pockrandt, Alaina Shumate, Natalia Rincon, Daniela Puiu, Martin Steinegger, Steven L. Salzberg and Mihaela Pertea
    Citation: Genome Biology 2023 24:249
  28. The high mutation rate throughout the entire melanoma genome presents a major challenge in stratifying true driver events from the background mutations. Numerous recurrent non-coding alterations, such as those...

    Authors: Zhao Wang, Menghan Luo, Qian Liang, Ke Zhao, Yuelin Hu, Wei Wang, Xiangling Feng, Bolang Hu, Jianjin Teng, Tianyi You, Ran Li, Zhengkai Bao, Wenhao Pan, Tielong Yang, Chao Zhang, Ting Li…
    Citation: Genome Biology 2023 24:248
  29. Genomic abnormalities are strongly associated with cancer and infertility. In this study, we develop a simple and efficient method — multiple genetic abnormality sequencing (MGA-Seq) — to simultaneously detect...

    Authors: Da Lin, Yanyan Zou, Xinyu Li, Jinyue Wang, Qin Xiao, Xiaochen Gao, Fei Lin, Ningyuan Zhang, Ming Jiao, Yu Guo, Zhaowei Teng, Shiyi Li, Yongchang Wei, Fuling Zhou, Rong Yin, Siheng Zhang…
    Citation: Genome Biology 2023 24:247
  30. RNA velocity analysis of single cells offers the potential to predict temporal dynamics from gene expression. In many systems, RNA velocity has been observed to produce a vector field that qualitatively reflec...

    Authors: Shijie C. Zheng, Genevieve Stein-O’Brien, Leandros Boukas, Loyal A. Goff and Kasper D. Hansen
    Citation: Genome Biology 2023 24:246
  31. The Quartet Data Portal facilitates community access to well-characterized reference materials, reference datasets, and related resources established based on a family of four individuals with identical twins ...

    Authors: Jingcheng Yang, Yaqing Liu, Jun Shang, Qiaochu Chen, Qingwang Chen, Luyao Ren, Naixin Zhang, Ying Yu, Zhihui Li, Yueqiang Song, Shengpeng Yang, Andreas Scherer, Weida Tong, Huixiao Hong, Wenming Xiao, Leming Shi…
    Citation: Genome Biology 2023 24:245
  32. The endogenous adenosine deaminases acting on RNA (ADAR) have been harnessed to facilitate precise adenosine-to-inosine editing on RNAs. However, the practicability of this approach for therapeutic purposes is...

    Authors: Zongyi Yi, Yanxia Zhao, Zexuan Yi, Yongjian Zhang, Gangbin Tang, Xiaoxue Zhang, Huixian Tang, Wei Zhang, Ying Zhao, Huayuan Xu, Yuyang Nie, Xueqing Sun, Lijun Xing, Lian Dai, Pengfei Yuan and Wensheng Wei
    Citation: Genome Biology 2023 24:243
  33. Analysis of microbial data from archaeological samples is a growing field with great potential for understanding ancient environments, lifestyles, and diseases. However, high error rates have been a challenge ...

    Authors: Zoé Pochon, Nora Bergfeldt, Emrah Kırdök, Mário Vicente, Thijessen Naidoo, Tom van der Valk, N. Ezgi Altınışık, Maja Krzewińska, Love Dalén, Anders Götherström, Claudio Mirabello, Per Unneberg and Nikolay Oskolkov
    Citation: Genome Biology 2023 24:242
  34. Properly integrating spatially resolved transcriptomics (SRT) generated from different batches into a unified gene-spatial coordinate system could enable the construction of a comprehensive spatial transcripto...

    Authors: Tiantian Guo, Zhiyuan Yuan, Yan Pan, Jiakang Wang, Fengling Chen, Michael Q. Zhang and Xiangyu Li
    Citation: Genome Biology 2023 24:241
  35. Single-cell gene expression profiling provides unique opportunities to understand tumor heterogeneity and the tumor microenvironment. Because of cost and feasibility, profiling bulk tumors remains the primary ...

    Authors: Ariel A. Hippen, Dalia K. Omran, Lukas M. Weber, Euihye Jung, Ronny Drapkin, Jennifer A. Doherty, Stephanie C. Hicks and Casey S. Greene
    Citation: Genome Biology 2023 24:239
  36. Single-cell RNA-sequencing (scRNA-seq) technologies enable the capture of gene expression heterogeneity and consequently facilitate the study of cell-to-cell variability at the cell type level. Although differ...

    Authors: Huiwen Zheng, Jan Vijg, Atefeh Taherian Fard and Jessica Cara Mar
    Citation: Genome Biology 2023 24:238
  37. Technologies to study localized host–pathogen interactions are urgently needed. Here, we present a spatial transcriptomics approach to simultaneously capture host and pathogen transcriptome-wide spatial gene e...

    Authors: Hailey Sounart, Enikő Lázár, Yuvarani Masarapu, Jian Wu, Tibor Várkonyi, Tibor Glasz, András Kiss, Erik Borgström, Andrew Hill, Sefanit Rezene, Soham Gupta, Aleksandra Jurek, Anezka Niesnerová, Henrik Druid, Olaf Bergmann and Stefania Giacomello
    Citation: Genome Biology 2023 24:237
  38. Parts-based representations, such as non-negative matrix factorization and topic modeling, have been used to identify structure from single-cell sequencing data sets, in particular structure that is not as wel...

    Authors: Peter Carbonetto, Kaixuan Luo, Abhishek Sarkar, Anthony Hung, Karl Tayeb, Sebastian Pott and Matthew Stephens
    Citation: Genome Biology 2023 24:236
  39. When analyzing data from in situ RNA detection technologies, cell segmentation is an essential step in identifying cell boundaries, assigning RNA reads to cells, and studying the gene expression and morphologi...

    Authors: Yuxing Wang, Wenguan Wang, Dongfang Liu, Wenpin Hou, Tianfei Zhou and Zhicheng Ji
    Citation: Genome Biology 2023 24:235
  40. Xenobiotics are primarily metabolized by hepatocytes in the liver, and primary human hepatocytes are the gold standard model for the assessment of drug efficacy, safety, and toxicity in the early phases of dru...

    Authors: Eva Sanchez-Quant, Maria Lucia Richter, Maria Colomé-Tatché and Celia Pilar Martinez-Jimenez
    Citation: Genome Biology 2023 24:234
  41. We define and identify a new class of control genes for next-generation sequencing called total RNA expression genes (TREGs), which correlate with total RNA abundance in cell types of different sizes and trans...

    Authors: Louise A. Huuki-Myers, Kelsey D. Montgomery, Sang Ho Kwon, Stephanie C. Page, Stephanie C. Hicks, Kristen R. Maynard and Leonardo Collado-Torres
    Citation: Genome Biology 2023 24:233
  42. The evolution of genomic regulatory regions plays a critical role in shaping the diversity of life. While this process is primarily sequence-dependent, the enormous complexity of biological systems complicates...

    Authors: Samuel Khodursky, Eric B. Zheng, Nicolas Svetec, Sylvia M. Durkin, Sigi Benjamin, Alice Gadau, Xia Wu and Li Zhao
    Citation: Genome Biology 2023 24:232
  43. Malaria remains one of the deadliest infectious diseases. Transcriptional regulation effects of noncoding variants in this unusual genome of malaria parasites remain elusive. We developed a sequence-based, ab ...

    Authors: Chengqi Wang, Yibo Dong, Chang Li, Jenna Oberstaller, Min Zhang, Justin Gibbons, Camilla Valente Pires, Mianli Xiao, Lei Zhu, Rays H. Y. Jiang, Kami Kim, Jun Miao, Thomas D. Otto, Liwang Cui, John H. Adams and Xiaoming Liu
    Citation: Genome Biology 2023 24:231
  44. In several eukaryotes, DNA methylation occurs within the coding regions of many genes, termed gene body methylation (GbM). Whereas the role of DNA methylation on the silencing of transposons and repetitive DNA...

    Authors: Clara J. Williams, Dawei Dai, Kevin A. Tran, J. Grey Monroe and Ben P. Williams
    Citation: Genome Biology 2023 24:227

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