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  1. Expression quantitative trait loci (eQTL) studies show how genetic variants affect downstream gene expression. Single-cell data allows reconstruction of personalized co-expression networks and therefore the id...

    Authors: Shuang Li, Katharina T. Schmid, Dylan H. de Vries, Maryna Korshevniuk, Corinna Losert, Roy Oelen, Irene V. van Blokland, Hilde E. Groot, Morris A. Swertz, Pim van der Harst, Harm-Jan Westra, Monique G.P. van der Wijst, Matthias Heinig and Lude Franke
    Citation: Genome Biology 2023 24:80
  2. A promising alternative to comprehensively performing genomics experiments is to, instead, perform a subset of experiments and use computational methods to impute the remainder. However, identifying the best i...

    Authors: Jacob Schreiber, Carles Boix, Jin wook Lee, Hongyang Li, Yuanfang Guan, Chun-Chieh Chang, Jen-Chien Chang, Alex Hawkins-Hooker, Bernhard Schölkopf, Gabriele Schweikert, Mateo Rojas Carulla, Arif Canakoglu, Francesco Guzzo, Luca Nanni, Marco Masseroli, Mark James Carman…
    Citation: Genome Biology 2023 24:79
  3. Changes in microbial community composition as a function of human health and disease states have sparked remarkable interest in the human gut microbiome. However, establishing reproducible insights into the de...

    Authors: Andrea R. Watson, Jessika Füssel, Iva Veseli, Johanna Zaal DeLongchamp, Marisela Silva, Florian Trigodet, Karen Lolans, Alon Shaiber, Emily Fogarty, Joseph M. Runde, Christopher Quince, Michael K. Yu, Arda Söylev, Hilary G. Morrison, Sonny T. M. Lee, Dina Kao…
    Citation: Genome Biology 2023 24:78
  4. We present RCRUNCH, an end-to-end solution to CLIP data analysis for identification of binding sites and sequence specificity of RNA-binding proteins. RCRUNCH can analyze not only reads that map uniquely to th...

    Authors: Maria Katsantoni, Erik van Nimwegen and Mihaela Zavolan
    Citation: Genome Biology 2023 24:77
  5. Whole -genome sequencing projects of millions of subjects contain enormous genotypes, entailing a huge memory burden and time for computation. Here, we present GBC, a toolkit for rapidly compressing large-scal...

    Authors: Liubin Zhang, Yangyang Yuan, Wenjie Peng, Bin Tang, Mulin Jun Li, Hongsheng Gui, Qiang Wang and Miaoxin Li
    Citation: Genome Biology 2023 24:76
  6. Single-molecule detection and phasing of A-to-I RNA editing events remain an unresolved problem. Long-read and PCR-free nanopore native RNA sequencing offers a great opportunity for direct RNA editing detectio...

    Authors: Longxian Chen, Liang Ou, Xinyun Jing, Yimeng Kong, Bingran Xie, Niubing Zhang, Han Shi, Hang Qin, Xuan Li and Pei Hao
    Citation: Genome Biology 2023 24:75
  7. We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary relationships. It retains core features of JBrowse while addin...

    Authors: Colin Diesh, Garrett J Stevens, Peter Xie, Teresa De Jesus Martinez, Elliot A. Hershberg, Angel Leung, Emma Guo, Shihab Dider, Junjun Zhang, Caroline Bridge, Gregory Hogue, Andrew Duncan, Matthew Morgan, Tia Flores, Benjamin N. Bimber, Robin Haw…
    Citation: Genome Biology 2023 24:74
  8. Tibetans are genetically adapted to high-altitude environments. Though many studies have been conducted, the genetic basis of the adaptation remains elusive due to the poor reproducibility for detecting select...

    Authors: Wangshan Zheng, Yaoxi He, Yongbo Guo, Tian Yue, Hui Zhang, Jun Li, Bin Zhou, Xuerui Zeng, Liya Li, Bin Wang, Jingxin Cao, Li Chen, Chunxia Li, Hongyan Li, Chaoying Cui, Caijuan Bai…
    Citation: Genome Biology 2023 24:73
  9. Single-cell RNA sequencing methods focusing on the 5′-end of transcripts can reveal promoter and enhancer activity and efficiently profile immune receptor repertoire. However, ultra-high-throughput 5′-end sing...

    Authors: Yun Li, Zheng Huang, Zhaojun Zhang, Qifei Wang, Fengxian Li, Shufang Wang, Xin Ji, Shaokun Shu, Xiangdong Fang and Lan Jiang
    Citation: Genome Biology 2023 24:70

    The Publisher Correction to this article has been published in Genome Biology 2023 24:88

  10. Nanopore sequencing is being rapidly adopted in genomics. We recently developed SLOW5, a new file format with advantages for storage and analysis of raw signal data from nanopore experiments. Here we introduce sl...

    Authors: Hiruna Samarakoon, James M. Ferguson, Sasha P. Jenner, Timothy G. Amos, Sri Parameswaran, Hasindu Gamaarachchi and Ira W. Deveson
    Citation: Genome Biology 2023 24:69
  11. Oocyte maturation arrest and early embryonic arrest are important reproductive phenotypes resulting in female infertility and cause the recurrent failure of assisted reproductive technology (ART). However, the...

    Authors: Qun Li, Lin Zhao, Yang Zeng, Yanping Kuang, Yichun Guan, Biaobang Chen, Shiru Xu, Bin Tang, Ling Wu, Xiaoyan Mao, Xiaoxi Sun, Juanzi Shi, Peng Xu, Feiyang Diao, Songguo Xue, Shihua Bao…
    Citation: Genome Biology 2023 24:68
  12. N6-methyladenosine (m6A) modification has been shown to regulate RNA metabolism. Here, we investigate m6A dynamics during maternal-to-zygotic transition (MZT) in mice through multi-omic analysis. Our results show...

    Authors: Wencheng Zhu, Yufeng Ding, Juan Meng, Lei Gu, Wenjun Liu, Li Li, Hongyu Chen, Yining Wang, Ziyi Li, Chen Li, Yidi Sun and Zhen Liu
    Citation: Genome Biology 2023 24:67
  13. Long-read single-cell RNA sequencing (scRNA-seq) enables the quantification of RNA isoforms in individual cells. However, long-read scRNA-seq using the Oxford Nanopore platform has largely relied upon matched ...

    Authors: Yupei You, Yair D. J. Prawer, Ricardo De Paoli-Iseppi, Cameron P. J. Hunt, Clare L. Parish, Heejung Shim and Michael B. Clark
    Citation: Genome Biology 2023 24:66
  14. Homoeologs are defined as homologous genes resulting from allopolyploidy. Bread wheat, Triticum aestivum, is an allohexaploid species with many homoeologs. Homoeolog expression bias, referring to the relative con...

    Authors: Lihua Zhang, Chao He, Yuting Lai, Yating Wang, Lu Kang, Ankui Liu, Caixia Lan, Handong Su, Yuwen Gao, Zeqing Li, Fang Yang, Qiang Li, Hailiang Mao, Dijun Chen, Wei Chen, Kerstin Kaufmann…
    Citation: Genome Biology 2023 24:65
  15. The NSD2 p.E1099K (EK) mutation is shown to be enriched in patients with relapsed acute lymphoblastic leukemia (ALL), indicating a role in clonal evolution and drug resistance.

    Authors: Sonali Narang, Nikki A. Evensen, Jason Saliba, Joanna Pierro, Mignon L. Loh, Patrick A. Brown, Pandurang Kolekar, Heather Mulder, Ying Shao, John Easton, Xiaotu Ma, Aristotelis Tsirigos and William L. Carroll
    Citation: Genome Biology 2023 24:64
  16. Transposable Element MOnitoring with LOng-reads (TrEMOLO) is a new software that combines assembly- and mapping-based approaches to robustly detect genetic elements called transposable elements (TEs). Using hi...

    Authors: Mourdas Mohamed, François Sabot, Marion Varoqui, Bruno Mugat, Katell Audouin, Alain Pélisson, Anna-Sophie Fiston-Lavier and Séverine Chambeyron
    Citation: Genome Biology 2023 24:63
  17. With the emergence of hundreds of single-cell RNA-sequencing (scRNA-seq) datasets, the number of computational tools to analyze aspects of the generated data has grown rapidly. As a result, there is a recurrin...

    Authors: Helena L. Crowell, Sarah X. Morillo Leonardo, Charlotte Soneson and Mark D. Robinson
    Citation: Genome Biology 2023 24:62

    The Author Correction to this article has been published in Genome Biology 2024 25:178

  18. Epigenetic modifications of histones are associated with development and pathogenesis of disease. Existing approaches cannot provide insights into long-range interactions and represent the average chromatin st...

    Authors: Zhe Weng, Fengying Ruan, Weitian Chen, Zhichao Chen, Yeming Xie, Meng Luo, Zhe Xie, Chen Zhang, Juan Wang, Yuxin Sun, Yitong Fang, Mei Guo, Chen Tan, Wenfang Chen, Yiqin Tong, Yaning Li…
    Citation: Genome Biology 2023 24:61
  19. Maize (Zea mays L.) is one of the most important crops worldwide. Although sophisticated maize gene regulatory networks (GRNs) have been constructed for functional genomics and phenotypic dissection, a multi-omic...

    Authors: Wanchao Zhu, Xinxin Miao, Jia Qian, Sijia Chen, Qixiao Jin, Mingzhu Li, Linqian Han, Wanshun Zhong, Dan Xie, Xiaoyang Shang and Lin Li
    Citation: Genome Biology 2023 24:60
  20. Genome-wide association studies (GWAS) have identified > 200 loci associated with breast cancer risk. The majority of candidate causal variants are in non-coding regions and likely modulate cancer risk by regu...

    Authors: Natasha K. Tuano, Jonathan Beesley, Murray Manning, Wei Shi, Laura Perlaza-Jimenez, Luis F. Malaver-Ortega, Jacob M. Paynter, Debra Black, Andrew Civitarese, Karen McCue, Aaron Hatzipantelis, Kristine Hillman, Susanne Kaufmann, Haran Sivakumaran, Jose M. Polo, Roger R. Reddel…
    Citation: Genome Biology 2023 24:59
  21. Significant improvements in long-read sequencing technologies have unlocked complex genomic areas, such as centromeres, in the genome and introduced the centromere annotation problem. Currently, centromeres ar...

    Authors: Shenghan Gao, Xiaofei Yang, Hongtao Guo, Xixi Zhao, Bo Wang and Kai Ye
    Citation: Genome Biology 2023 24:58
  22. The annual Genome Informatics conference was held at the Wellcome Genome Campus on September 21–23, 2022. The conference covered a remarkable range of topics of which we highlight a few in this report.

    Authors: Iman Hajirasouliha and Stefan Semrau
    Citation: Genome Biology 2023 24:57
  23. Ageing is inherent to all human beings, yet why we age remains a hotly contested topic. Most mechanistic explanations of ageing posit that ageing is caused by the accumulation of one or more forms of molecular...

    Authors: João Pedro de Magalhães
    Citation: Genome Biology 2023 24:51
  24. The largest sequence-based models of transcription control to date are obtained by predicting genome-wide gene regulatory assays across the human genome. This setting is fundamentally correlative, as those mod...

    Authors: Alexander Karollus, Thomas Mauermeier and Julien Gagneur
    Citation: Genome Biology 2023 24:56
  25. Transcription bridges genetic information and phenotypes. Here, we evaluated how changes in transcriptional regulation enable maize (Zea mays), a crop originally domesticated in the tropics, to adapt to temperate...

    Authors: Guangchao Sun, Huihui Yu, Peng Wang, Martha Lopez-Guerrero, Ravi V. Mural, Olivier N. Mizero, Marcin Grzybowski, Baoxing Song, Karin van Dijk, Daniel P. Schachtman, Chi Zhang and James C. Schnable
    Citation: Genome Biology 2023 24:55
  26. We present GenEra (https://​github.​com/​josuebarrera/​GenEra), a DIAMOND-fueled gene-family founder inference framework that addresses previously raised limitations a...

    Authors: Josué Barrera-Redondo, Jaruwatana Sodai Lotharukpong, Hajk-Georg Drost and Susana M. Coelho
    Citation: Genome Biology 2023 24:54
  27. Alternative splicing is a widespread regulatory phenomenon that enables a single gene to produce multiple transcripts. Among the different types of alternative splicing, intron retention is one of the least ex...

    Authors: Fahad Ullah, Saira Jabeen, Maayan Salton, Anireddy S. N. Reddy and Asa Ben-Hur
    Citation: Genome Biology 2023 24:53
  28. Phosphorylation of proteins is a key step in the regulation of many cellular processes including activation of enzymes and signaling cascades. The abundance of a phosphorylated peptide (phosphopeptide) is dete...

    Authors: Tian Zhang, Gregory R. Keele, Isabela Gerdes Gyuricza, Matthew Vincent, Catherine Brunton, Timothy A. Bell, Pablo Hock, Ginger D. Shaw, Steven C. Munger, Fernando Pardo-Manuel de Villena, Martin T. Ferris, Joao A. Paulo, Steven P. Gygi and Gary A. Churchill
    Citation: Genome Biology 2023 24:52
  29. Cis-regulatory elements are coordinated to regulate the expression of their targeted genes. However, the joint measurement of cis-regulatory elements’ activities and their interactions in spatial proximity is ...

    Authors: Hailu Fu, Haizi Zheng, Xiaoting Chen, Matthew T. Weirauch, Louis J. Muglia, Li Wang and Yaping Liu
    Citation: Genome Biology 2023 24:50
  30. The epidermis of cotton ovule produces fibers, the most important natural cellulose source for the global textile industry. However, the molecular mechanism of fiber cell growth is still poorly understood.

    Authors: Dehe Wang, Xiao Hu, Hanzhe Ye, Yue Wang, Qian Yang, Xiaodong Liang, Zilin Wang, Yifan Zhou, Miaomiao Wen, Xueyan Yuan, Xiaomin Zheng, Wen Ye, Boyu Guo, Mayila Yusuyin, Eugenia Russinova, Yu Zhou…
    Citation: Genome Biology 2023 24:49
  31. Genomic imprinting affects gene expression in a parent-of-origin manner and has a profound impact on complex traits including growth and behavior. While the rat is widely used to model human pathophysiology, f...

    Authors: Julien Richard Albert, Toshihiro Kobayashi, Azusa Inoue, Ana Monteagudo-Sánchez, Soichiro Kumamoto, Tomoya Takashima, Asuka Miura, Mami Oikawa, Fumihito Miura, Shuji Takada, Masumi Hirabayashi, Keegan Korthauer, Kazuki Kurimoto, Maxim V. C. Greenberg, Matthew Lorincz and Hisato Kobayashi
    Citation: Genome Biology 2023 24:48
  32. The mutational landscape of SARS-CoV-2 varies at the dominant viral genome sequence and minor genomic variant population. During the COVID-19 pandemic, an early substitution in the genome was the D614G change ...

    Authors: Hannah Goldswain, Xiaofeng Dong, Rebekah Penrice-Randal, Muhannad Alruwaili, Ghada T. Shawli, Tessa Prince, Maia Kavanagh Williamson, Jayna Raghwani, Nadine Randle, Benjamin Jones, I’ah Donovan-Banfield, Francisco J. Salguero, Julia A. Tree, Yper Hall, Catherine Hartley, Maximilian Erdmann…
    Citation: Genome Biology 2023 24:47
  33. Reptiles exhibit a wide variety of skin colors, which serve essential roles in survival and reproduction. However, the molecular basis of these conspicuous colors remains unresolved.

    Authors: Chen-Yang Tang, Xiaohu Zhang, Xiao Xu, Shijie Sun, Changjun Peng, Meng-Huan Song, Chaochao Yan, Huaqin Sun, Mingfeng Liu, Liang Xie, Shu-Jin Luo and Jia-Tang Li
    Citation: Genome Biology 2023 24:46
  34. Inference and analysis of gene regulatory networks (GRNs) require software that integrates multi-omic data from various sources. The Network Zoo (netZoo; netzoo.github.io) is a collection of open-source method...

    Authors: Marouen Ben Guebila, Tian Wang, Camila M. Lopes-Ramos, Viola Fanfani, Des Weighill, Rebekka Burkholz, Daniel Schlauch, Joseph N. Paulson, Michael Altenbuchinger, Katherine H. Shutta, Abhijeet R. Sonawane, James Lim, Genis Calderer, David G.P. van IJzendoorn, Daniel Morgan, Alessandro Marin…
    Citation: Genome Biology 2023 24:45
  35. It is apparent that genomes harbor much structural variation that is largely undetected for technical reasons. Such variation can cause artifacts when short-read sequencing data are mapped to a reference genom...

    Authors: Benjamin Jaegle, Rahul Pisupati, Luz Mayela Soto-Jiménez, Robin Burns, Fernando A. Rabanal and Magnus Nordborg
    Citation: Genome Biology 2023 24:44
  36. Chemical modifications of RNAs, known as the epitranscriptome, are emerging as widespread regulatory mechanisms underlying gene regulation. The field of epitranscriptomics advances recently due to improved tra...

    Authors: Lisha Shen, Jinqi Ma, Ping Li, Yujin Wu and Hao Yu
    Citation: Genome Biology 2023 24:43
  37. Increased expression of the complement component 4A (C4A) gene is associated with a greater lifetime risk of schizophrenia. In the brain, C4A is involved in synaptic pruning; yet, it remains unclear the extent to...

    Authors: Leanna M. Hernandez, Minsoo Kim, Pan Zhang, Richard A. I. Bethlehem, Gil Hoftman, Robert Loughnan, Diana Smith, Susan Y. Bookheimer, Chun Chieh Fan, Carrie E. Bearden, Wesley K. Thompson and Michael J. Gandal
    Citation: Genome Biology 2023 24:42
  38. Enhancers are essential in defining cell fates through the control of cell-type-specific gene expression. Enhancer activation is a multi-step process involving chromatin remodelers and histone modifiers includ...

    Authors: Ryan M. Boileau, Kevin X. Chen and Robert Blelloch
    Citation: Genome Biology 2023 24:41
  39. There is widespread interest in the three-dimensional chromatin conformation of the genome and its impact on gene expression. However, these studies frequently do not consider parent-of-origin differences, suc...

    Authors: Stephen Richer, Yuan Tian, Stefan Schoenfelder, Laurence Hurst, Adele Murrell and Giuseppina Pisignano
    Citation: Genome Biology 2023 24:40
  40. Kinship analysis from very low-coverage ancient sequences has been possible up to the second degree with large uncertainties. We propose a new, accurate, and fast method, correctKin, to estimate the kinship co...

    Authors: Emil Nyerki, Tibor Kalmár, Oszkár Schütz, Rui M. Lima, Endre Neparáczki, Tibor Török and Zoltán Maróti
    Citation: Genome Biology 2023 24:38
  41. Insertions and deletions (indels) enable evolution and cause disease. Due to technical challenges, indels are left out of most mutational scans, limiting our understanding of them in disease, biology, and evol...

    Authors: Christian B. Macdonald, David Nedrud, Patrick Rockefeller Grimes, Donovan Trinidad, James S. Fraser and Willow Coyote-Maestas
    Citation: Genome Biology 2023 24:36
  42. Mapping of quantitative trait loci (QTL) associated with molecular phenotypes is a powerful approach for identifying the genes and molecular mechanisms underlying human traits and diseases, though most studies...

    Authors: Derek E. Kelly, Shweta Ramdas, Rong Ma, Renata A. Rawlings-Goss, Gregory R. Grant, Alessia Ranciaro, Jibril B. Hirbo, William Beggs, Meredith Yeager, Stephen Chanock, Thomas B. Nyambo, Sabah A. Omar, Dawit Woldemeskel, Gurja Belay, Hongzhe Li, Christopher D. Brown…
    Citation: Genome Biology 2023 24:35
  43. Codon usage and nucleotide composition of coding sequences have profound effects on protein expression. However, while it is recognized that different tissues have distinct tRNA profiles and codon usages in th...

    Authors: Xavier Hernandez-Alias, Hannah Benisty, Leandro G. Radusky, Luis Serrano and Martin H. Schaefer
    Citation: Genome Biology 2023 24:34
  44. The current version of the human reference genome, GRCh38, contains a number of errors including 1.2 Mbp of falsely duplicated and 8.04 Mbp of collapsed regions. These errors impact the variant calling of 33 p...

    Authors: Sairam Behera, Jonathon LeFaive, Peter Orchard, Medhat Mahmoud, Luis F. Paulin, Jesse Farek, Daniela C. Soto, Stephen C. J. Parker, Albert V. Smith, Megan Y. Dennis, Justin M. Zook and Fritz J. Sedlazeck
    Citation: Genome Biology 2023 24:31

Annual Journal Metrics

  • Citation Impact 2023
    Journal Impact Factor: 10.1
    5-year Journal Impact Factor: 16.5
    Source Normalized Impact per Paper (SNIP): 2.521
    SCImago Journal Rank (SJR): 7.197

    Speed 2023
    Submission to first editorial decision (median days): 22
    Submission to acceptance (median days): 277

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