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  1. The encoding of cell intrinsic drug resistance states in breast cancer reflects the contributions of genomic and non-genomic variations and requires accurate estimation of clonal fitness from co-measurement of...

    Authors: Farhia Kabeer, Hoa Tran, Mirela Andronescu, Gurdeep Singh, Hakwoo Lee, Sohrab Salehi, Beixi Wang, Justina Biele, Jazmine Brimhall, David Gee, Viviana Cerda, Ciara O’Flanagan, Teresa Algara, Takako Kono, Sean Beatty, Elena Zaikova…
    Citation: Genome Biology 2024 25:191
  2. Interactions among cis-regulatory elements (CREs) play a crucial role in gene regulation. Various approaches have been developed to map these interactions genome-wide, including those relying on interindividual e...

    Authors: Olga Pushkarev, Guido van Mierlo, Judith Franziska Kribelbauer, Wouter Saelens, Vincent Gardeux and Bart Deplancke
    Citation: Genome Biology 2024 25:190
  3. Single-cell RNA-sequencing enables testing for differential expression (DE) between conditions at a cell type level. While powerful, one of the limitations of such approaches is that the sensitivity of DE test...

    Authors: Alsu Missarova, Emma Dann, Leah Rosen, Rahul Satija and John Marioni
    Citation: Genome Biology 2024 25:189
  4. We recently identified ~ 10,000 correlated regions of systemic interindividual epigenetic variation (CoRSIVs) in the human genome. These methylation variants are amenable to population studies, as DNA methylat...

    Authors: Wen-Jou Chang, Maria S. Baker, Eleonora Laritsky, Chathura J. Gunasekara, Uditha Maduranga, Justine C. Galliou, Joseph W. McFadden, Jessica R. Waltemyer, Bruce Berggren-Thomas, Brianna N. Tate, Hanxue Zhang, Benjamin D. Rosen, Curtis P. Van Tassell, George E. Liu, Cristian Coarfa, Yi Athena Ren…
    Citation: Genome Biology 2024 25:185
  5. Characterizing the binding preferences of transcription factors (TFs) in different cell types and conditions is key to understand how they orchestrate gene expression. Here, we develop TFscope, a machine learn...

    Authors: Raphaël Romero, Christophe Menichelli, Christophe Vroland, Jean-Michel Marin, Sophie Lèbre, Charles-Henri Lecellier and Laurent Bréhélin
    Citation: Genome Biology 2024 25:187
  6. DNA methylation is a key component of the mammalian epigenome, playing a regulatory role in development, disease, and other processes. Robust, high-throughput single-cell DNA methylation assays are now possibl...

    Authors: Sonia N. Acharya, Ruth V. Nichols, Lauren E. Rylaarsdam, Brendan L. O’Connell, Theodore P. Braun and Andrew C. Adey
    Citation: Genome Biology 2024 25:186
  7. Although disease-causal genetic variants have been found within silencer sequences, we still lack a comprehensive analysis of the association of silencers with diseases. Here, we profiled GWAS variants in 2.8 ...

    Authors: Di Huang and Ivan Ovcharenko
    Citation: Genome Biology 2024 25:184
  8. Recent studies uncovered pervasive transcription and translation of thousands of noncanonical open reading frames (nORFs) outside of annotated genes. The contribution of nORFs to cellular phenotypes is difficu...

    Authors: April Rich, Omer Acar and Anne-Ruxandra Carvunis
    Citation: Genome Biology 2024 25:183
  9. Single-cell multiomic analysis of the epigenome, transcriptome, and proteome allows for comprehensive characterization of the molecular circuitry that underpins cell identity and state. However, the holistic i...

    Authors: Fabiola Curion, Charlotte Rich-Griffin, Devika Agarwal, Sarah Ouologuem, Kevin Rue-Albrecht, Lilly May, Giulia E. L. Garcia, Lukas Heumos, Tom Thomas, Wojciech Lason, David Sims, Fabian J. Theis and Calliope A. Dendrou
    Citation: Genome Biology 2024 25:181
  10. Spatial transcriptomics technologies permit the study of the spatial distribution of RNA at near-single-cell resolution genome-wide. However, the feasibility of studying spatial allele-specific expression (ASE...

    Authors: Luli S. Zou, Dylan M. Cable, Irving A. Barrera-Lopez, Tongtong Zhao, Evan Murray, Martin J. Aryee, Fei Chen and Rafael A. Irizarry
    Citation: Genome Biology 2024 25:180
  11. Pathogenic allele silencing is a promising treatment for genetic hereditary diseases. Here, we develop an RNA-cleaving tool, TaqTth-hpRNA, consisting of a small, chimeric TaqTth, and a hairpin RNA guiding prob...

    Authors: Chong Xu, Jiyanuo Cao, Huanran Qiang, Yu Liu, Jialin Wu, Qiudan Luo, Meng Wan, Yujie Wang, Peiliang Wang, Qian Cheng, Guohua Zhou, Jian Sima, Yongjian Guo and Shu Xu
    Citation: Genome Biology 2024 25:179
  12. Tandem repeats are frequent across the human genome, and variation in repeat length has been linked to a variety of traits. Recent improvements in long read sequencing technologies have the potential to greatl...

    Authors: Helyaneh Ziaei Jam, Justin M. Zook, Sara Javadzadeh, Jonghun Park, Aarushi Sehgal and Melissa Gymrek
    Citation: Genome Biology 2024 25:176
  13. Transposable elements play a critical role in maintaining genome architecture during neurodevelopment. Short Interspersed Nuclear Elements (SINEs), a major subtype of transposable elements, are known to harbor...

    Authors: Daijing Sun, Yueyan Zhu, Wenzhu Peng, Shenghui Zheng, Jie Weng, Shulong Dong, Jiaqi Li, Qi Chen, Chuanhui Ge, Liyong Liao, Yuhao Dong, Yun Liu, Weida Meng and Yan Jiang
    Citation: Genome Biology 2024 25:175
  14. The gut microbiota controls broad aspects of human metabolism and feeding behavior, but the basis for this control remains largely unclear. Given the key role of human dipeptidyl peptidase 4 (DPP4) in host met...

    Authors: Marta Olivares, Paula Hernández-Calderón, Sonia Cárdenas-Brito, Rebeca Liébana-García, Yolanda Sanz and Alfonso Benítez-Páez
    Citation: Genome Biology 2024 25:174
  15. RNA-seq has brought forth significant discoveries regarding aberrations in RNA processing, implicating these RNA variants in a variety of diseases. Aberrant splicing and single nucleotide variants (SNVs) in RN...

    Authors: Alison D. Tang, Colette Felton, Eva Hrabeta-Robinson, Roger Volden, Christopher Vollmers and Angela N. Brooks
    Citation: Genome Biology 2024 25:173
  16. Computational variant effect predictors offer a scalable and increasingly reliable means of interpreting human genetic variation, but concerns of circularity and bias have limited previous methods for evaluati...

    Authors: Daniel R. Tabet, Da Kuang, Megan C. Lancaster, Roujia Li, Karen Liu, Jochen Weile, Atina G. Coté, Yingzhou Wu, Robert A. Hegele, Dan M. Roden and Frederick P. Roth
    Citation: Genome Biology 2024 25:172
  17. The massive structural variations and frequent introgression highly contribute to the genetic diversity of wheat, while the huge and complex genome of polyploid wheat hinders efficient genotyping of abundant v...

    Authors: Jianxia Niu, Wenxi Wang, Zihao Wang, Zhe Chen, Xiaoyu Zhang, Zhen Qin, Lingfeng Miao, Zhengzhao Yang, Chaojie Xie, Mingming Xin, Huiru Peng, Yingyin Yao, Jie Liu, Zhongfu Ni, Qixin Sun and Weilong Guo
    Citation: Genome Biology 2024 25:171
  18. Microbial pangenome analysis identifies present or absent genes in prokaryotic genomes. However, current tools are limited when analyzing species with higher sequence diversity or higher taxonomic orders such ...

    Authors: Kevin Lamkiewicz, Lisa-Marie Barf, Konrad Sachse and Martin Hölzer
    Citation: Genome Biology 2024 25:170
  19. Variable number tandem repeats (VNTRs) are highly polymorphic DNA regions harboring many potentially disease-causing variants. However, VNTRs often appear unresolved (“dark”) in variation databases due to thei...

    Authors: Silvia Di Maio, Peter Zöscher, Hansi Weissensteiner, Lukas Forer, Johanna F. Schachtl-Riess, Stephan Amstler, Gertraud Streiter, Cathrin Pfurtscheller, Bernhard Paulweber, Florian Kronenberg, Stefan Coassin and Sebastian Schönherr
    Citation: Genome Biology 2024 25:167
  20. Vascular endothelial growth factor (VEGF) is one of the most powerful proangiogenic factors and plays an important role in multiple diseases. Increased glycolytic rates and lactate accumulation are associated ...

    Authors: Wei Fan, Shuhao Zeng, Xiaotang Wang, Guoqing Wang, Dan Liao, Ruonan Li, Siyuan He, Wanqian Li, Jiaxing Huang, Xingran Li, Jiangyi Liu, Na Li and Shengping Hou
    Citation: Genome Biology 2024 25:165
  21. Copy number variation (CNV) is a key genetic characteristic for cancer diagnostics and can be used as a biomarker for the selection of therapeutic treatments. Using data sets established in our previous study,...

    Authors: Daniall Masood, Luyao Ren, Cu Nguyen, Francesco G. Brundu, Lily Zheng, Yongmei Zhao, Erich Jaeger, Yong Li, Seong Won Cha, Aaron Halpern, Sean Truong, Michael Virata, Chunhua Yan, Qingrong Chen, Andy Pang, Reyes Alberto…
    Citation: Genome Biology 2024 25:163
  22. The functional coupling between alternative pre-mRNA splicing (AS) and the mRNA quality control mechanism called nonsense-mediated decay (NMD) can modulate transcript abundance. Previous studies have identifie...

    Authors: Anna Zhuravskaya, Karen Yap, Fursham Hamid and Eugene V. Makeyev
    Citation: Genome Biology 2024 25:162
  23. Neuroblastoma is a common pediatric cancer, where preclinical studies suggest that a mesenchymal-like gene expression program contributes to chemotherapy resistance. However, clinical outcomes remain poor, imp...

    Authors: Richard H. Chapple, Xueying Liu, Sivaraman Natarajan, Margaret I. M. Alexander, Yuna Kim, Anand G. Patel, Christy W. LaFlamme, Min Pan, William C. Wright, Hyeong-Min Lee, Yinwen Zhang, Meifen Lu, Selene C. Koo, Courtney Long, John Harper, Chandra Savage…
    Citation: Genome Biology 2024 25:161
  24. Methylation-based liquid biopsies show promises in detecting cancer using circulating cell-free DNA; however, current limitations impede clinical application. Most assays necessitate substantial DNA inputs, po...

    Authors: Xiao-Long Cui, Ji Nie, Houxiang Zhu, Krissana Kowitwanich, Alana V. Beadell, Diana C. West-Szymanski, Zhou Zhang, Urszula Dougherty, Akushika Kwesi, Zifeng Deng, Yan Li, Danqing Meng, Kevin Roggin, Teresa Barry, Ryan Owyang, Ben Fefferman…
    Citation: Genome Biology 2024 25:157
  25. Genetic changes that modify the function of transcriptional enhancers have been linked to the evolution of biological diversity across species. Multiple studies have focused on the role of nucleotide substitut...

    Authors: Acadia A. Kocher, Emily V. Dutrow, Severin Uebbing, Kristina M. Yim, María F. Rosales Larios, Marybeth Baumgartner, Timothy Nottoli and James P. Noonan
    Citation: Genome Biology 2024 25:156
  26. Genomic data holds huge potential for medical progress but requires strict safety measures due to its sensitive nature to comply with data protection laws. This conflict is especially pronounced in genome-wide...

    Authors: Alissa Brauneck, Louisa Schmalhorst, Stefan Weiss, Linda Baumbach, Uwe Völker, David Ellinghaus, Jan Baumbach and Gabriele Buchholtz
    Citation: Genome Biology 2024 25:154

    The Author Correction to this article has been published in Genome Biology 2024 25:160

  27. Protein folding has become a tractable problem with the significant advances in deep learning-driven protein structure prediction. Here we propose FoldPAthreader, a protein folding pathway prediction method th...

    Authors: Kailong Zhao, Pengxin Zhao, Suhui Wang, Yuhao Xia and Guijun Zhang
    Citation: Genome Biology 2024 25:152
  28. Deconvolution methods infer quantitative cell type estimates from bulk measurement of mixed samples including blood and tissue. DNA methylation sequencing measures multiple CpGs per read, but few existing deco...

    Authors: Irene Unterman, Dana Avrahami, Efrat Katsman, Timothy J. Triche Jr., Benjamin Glaser and Benjamin P. Berman
    Citation: Genome Biology 2024 25:151

    The Author Correction to this article has been published in Genome Biology 2024 25:182

  29. Cancer is a complex disease composing systemic alterations in multiple scales. In this study, we develop the Tumor Multi-Omics pre-trained Network (TMO-Net) that integrates multi-omics pan-cancer datasets for ...

    Authors: Feng-ao Wang, Zhenfeng Zhuang, Feng Gao, Ruikun He, Shaoting Zhang, Liansheng Wang, Junwei Liu and Yixue Li
    Citation: Genome Biology 2024 25:149
  30. Sheep and goats have undergone domestication and improvement to produce similar phenotypes, which have been greatly impacted by structural variants (SVs). Here, we report a high-quality chromosome-level refere...

    Authors: Ji Yang, Dong-Feng Wang, Jia-Hui Huang, Qiang-Hui Zhu, Ling-Yun Luo, Ran Lu, Xing-Long Xie, Hosein Salehian-Dehkordi, Ali Esmailizadeh, George E. Liu and Meng-Hua Li
    Citation: Genome Biology 2024 25:148
  31. Current clustering analysis of spatial transcriptomics data primarily relies on molecular information and fails to fully exploit the morphological features present in histology images, leading to compromised a...

    Authors: Xi Jiang, Shidan Wang, Lei Guo, Bencong Zhu, Zhuoyu Wen, Liwei Jia, Lin Xu, Guanghua Xiao and Qiwei Li
    Citation: Genome Biology 2024 25:147
  32. DNA methylation is an important epigenetic modification which has numerous roles in modulating genome function. Its levels are spatially correlated across the genome, typically high in repressed regions but lo...

    Authors: Martina Rimoldi, Ning Wang, Jilin Zhang, Diego Villar, Duncan T. Odom, Jussi Taipale, Paul Flicek and Maša Roller
    Citation: Genome Biology 2024 25:146
  33. Single-cell RNA sequencing (scRNA-seq) and spatially resolved transcriptomics (SRT) have led to groundbreaking advancements in life sciences. To develop bioinformatics tools for scRNA-seq and SRT data and perf...

    Authors: Hongrui Duo, Yinghong Li, Yang Lan, Jingxin Tao, Qingxia Yang, Yingxue Xiao, Jing Sun, Lei Li, Xiner Nie, Xiaoxi Zhang, Guizhao Liang, Mingwei Liu, Youjin Hao and Bo Li
    Citation: Genome Biology 2024 25:145
  34. Like its parent base 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) is a direct epigenetic modification of cytosines in the context of CpG dinucleotides. 5hmC is the most abundant oxidized form of 5mC,...

    Authors: Edahi Gonzalez-Avalos, Atsushi Onodera, Daniela Samaniego-Castruita, Anjana Rao and Ferhat Ay
    Citation: Genome Biology 2024 25:142
  35. Variation in X chromosome inactivation (XCI) in human-induced pluripotent stem cells (hiPSCs) can impact their ability to model biological sex biases. The gene-wise landscape of X chromosome gene dosage remain...

    Authors: Hande Topa, Clara Benoit-Pilven, Taru Tukiainen and Olli Pietiläinen
    Citation: Genome Biology 2024 25:144
  36. Targeted therapies exploiting vulnerabilities of cancer cells hold promise for improving patient outcome and reducing side-effects of chemotherapy. However, efficacy of precision therapies is limited in part b...

    Authors: Alena Malyukova, Mari Lahnalampi, Ton Falqués-Costa, Petri Pölönen, Mikko Sipola, Juha Mehtonen, Susanna Teppo, Karen Akopyan, Johanna Viiliainen, Olli Lohi, Anna K. Hagström-Andersson, Merja Heinäniemi and Olle Sangfelt
    Citation: Genome Biology 2024 25:143

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

    Usage 2023
    Downloads: 6,688,476
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