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  1. Plant metabolites reshaped by nature and human beings are crucial for both their lives and human health. However, which metabolites respond most strongly to selection pressure at different evolutionary stages ...

    Authors: Ke Cao, Bin Wang, Weichao Fang, Gengrui Zhu, Changwen Chen, Xinwei Wang, Yong Li, Jinlong Wu, Tang Tang, Zhangjun Fei, Jie Luo and Lirong Wang
    Citation: Genome Biology 2022 23:146
  2. Persian walnut, Juglans regia, occurs naturally from Greece to western China, while its closest relative, the iron walnut, Juglans sigillata, is endemic in southwest China; both species are cultivated for their n...

    Authors: Ya-Mei Ding, Yu Cao, Wei-Ping Zhang, Jun Chen, Jie Liu, Pan Li, Susanne S. Renner, Da-Yong Zhang and Wei-Ning Bai
    Citation: Genome Biology 2022 23:145
  3. We developed Bookend, a package for transcript assembly that incorporates data from different RNA-seq techniques, with a focus on identifying and utilizing RNA 5′ and 3′ ends. We demonstrate that correct ident...

    Authors: Michael A. Schon, Stefan Lutzmayer, Falko Hofmann and Michael D. Nodine
    Citation: Genome Biology 2022 23:143

    The Publisher Correction to this article has been published in Genome Biology 2022 23:157

  4. Authors: J. James E. Barrett, Chiara Herzog, Yoo-Na Kim, Thomas E. Bartlett, Allison Jones, Iona Evans, David Cibula, Michal Zikan, Line Bjørge, Nadia Harbeck, Nicoletta Colombo, Sacha J. Howell, Angelique Flöter Rådestad, Kristina Gemzell-Danielsson and Martin Widschwendter
    Citation: Genome Biology 2022 23:142

    The original article was published in Genome Biology 2022 23:52

  5. Clinical laboratories routinely use formalin-fixed paraffin-embedded (FFPE) tissue or cell block cytology samples in oncology panel sequencing to identify mutations that can predict patient response to targete...

    Authors: Yifan Zhang, Thomas M. Blomquist, Rebecca Kusko, Daniel Stetson, Zhihong Zhang, Lihui Yin, Robert Sebra, Binsheng Gong, Jennifer S. Lococo, Vinay K. Mittal, Natalia Novoradovskaya, Ji-Youn Yeo, Nicole Dominiak, Jennifer Hipp, Amelia Raymond, Fujun Qiu…
    Citation: Genome Biology 2022 23:141
  6. Coessentiality networks derived from CRISPR screens in cell lines provide a powerful framework for identifying functional modules in the cell and for inferring the roles of uncharacterized genes. However, thes...

    Authors: Eiru Kim, Lance C. Novak, Chenchu Lin, Medina Colic, Lori L. Bertolet, Veronica Gheorghe, Christopher A. Bristow and Traver Hart
    Citation: Genome Biology 2022 23:140
  7. There are major efforts underway to make genome sequencing a routine part of clinical practice. A critical barrier to these is achieving practical solutions for data ownership and integrity. Blockchain provide...

    Authors: Gamze Gürsoy, Charlotte M. Brannon, Eric Ni, Sarah Wagner, Amol Khanna and Mark Gerstein
    Citation: Genome Biology 2022 23:134
  8. In studies of cellular function in cancer, researchers are increasingly able to choose from many -omics assays as functional readouts. Choosing the correct readout for a given study can be difficult, and which...

    Authors: Jake Crawford, Brock C. Christensen, Maria Chikina and Casey S. Greene
    Citation: Genome Biology 2022 23:137
  9. Chromatin states and enhancers associate gene expression, cell identity and disease. Here, we systematically delineate the acute innate immune response to endotoxin in terms of human macrophage enhancer activi...

    Authors: Ping Zhang, Harindra E. Amarasinghe, Justin P. Whalley, Chwen Tay, Hai Fang, Gabriele Migliorini, Andrew C. Brown, Alice Allcock, Giuseppe Scozzafava, Phalguni Rath, Benjamin Davies and Julian C. Knight
    Citation: Genome Biology 2022 23:136
  10. The COVID-19 pandemic has emphasized the importance of accurate detection of known and emerging pathogens. However, robust characterization of pathogenic sequences remains an open challenge. To address this ne...

    Authors: Advait Balaji, Bryce Kille, Anthony D. Kappell, Gene D. Godbold, Madeline Diep, R. A. Leo Elworth, Zhiqin Qian, Dreycey Albin, Daniel J. Nasko, Nidhi Shah, Mihai Pop, Santiago Segarra, Krista L. Ternus and Todd J. Treangen
    Citation: Genome Biology 2022 23:133
  11. Proteogenomics aims to identify variant or unknown proteins in bottom-up proteomics, by searching transcriptome- or genome-derived custom protein databases. However, empirical observations reveal that these la...

    Authors: Laura Fancello and Thomas Burger
    Citation: Genome Biology 2022 23:132
  12. Genetic studies of human traits have revolutionized our understanding of the variation between individuals, and yet, the genetics of most traits is still poorly understood. In this review, we highlight the maj...

    Authors: Nadav Brandes, Omer Weissbrod and Michal Linial
    Citation: Genome Biology 2022 23:131
  13. A challenge in bulk gene differential expression analysis is to differentiate changes due to cell type-specific gene expression and cell type proportions. SCADIE is an iterative algorithm that simultaneously e...

    Authors: Daiwei Tang, Seyoung Park and Hongyu Zhao
    Citation: Genome Biology 2022 23:129
  14. Copy number alterations constitute important phenomena in tumor evolution. Whole genome single-cell sequencing gives insight into copy number profiles of individual cells, but is highly noisy. Here, we propose...

    Authors: Magda Markowska, Tomasz Cąkała, BłaŻej Miasojedow, Bogac Aybey, Dilafruz Juraeva, Johanna Mazur, Edith Ross, Eike Staub and Ewa Szczurek
    Citation: Genome Biology 2022 23:128
  15. Multiple sclerosis (MS) is an autoimmune condition of the central nervous system with a well-characterized genetic background. Prior analyses of MS genetics have identified broad enrichments across peripheral ...

    Authors: Michael H. Guo, Prashanth Sama, Brenna A. LaBarre, Hrishikesh Lokhande, John Balibalos, Ci Chu, Xiaomi Du, Pouya Kheradpour, Charles C. Kim, Taylor Oniskey, Thomas Snyder, Damien Z. Soghoian, Howard L. Weiner, Tanuja Chitnis and Nikolaos A. Patsopoulos
    Citation: Genome Biology 2022 23:127
  16. SARS-CoV-2 infection results in a broad spectrum of COVID-19 disease, from mild or no symptoms to hospitalization and death. COVID-19 disease severity has been associated with some pre-existing conditions and ...

    Authors: Matthew C. Pahl, Carole Le Coz, Chun Su, Prabhat Sharma, Rajan M. Thomas, James A. Pippin, Emylette Cruz Cabrera, Matthew E. Johnson, Michelle E. Leonard, Sumei Lu, Alessandra Chesi, Kathleen E. Sullivan, Neil Romberg, Struan F. A. Grant and Andrew D. Wells
    Citation: Genome Biology 2022 23:125
  17. Tumors are complex tissues of cancerous cells surrounded by a heterogeneous cellular microenvironment with which they interact. Single-cell sequencing enables molecular characterization of single cells within ...

    Authors: Jan Dohmen, Artem Baranovskii, Jonathan Ronen, Bora Uyar, Vedran Franke and Altuna Akalin
    Citation: Genome Biology 2022 23:123
  18. DNA methylation plays vital roles in both prokaryotes and eukaryotes. There are three forms of DNA methylation in prokaryotes: N6-methyladenine (6mA), N4-methylcytosine (4mC), and 5-methylcytosine (5mC). Although...

    Authors: Xuwen Li, Shiyuan Guo, Yan Cui, Zijian Zhang, Xinlong Luo, Margarita T. Angelova, Laura F. Landweber, Yinsheng Wang and Tao P. Wu
    Citation: Genome Biology 2022 23:122
  19. The plasticity along the epithelial-mesenchymal transition (EMT) spectrum has been shown to be regulated by various epigenetic repertoires. Emerging evidence of local chromatin conformation changes suggests th...

    Authors: Qing You Pang, Tuan Zea Tan, Vignesh Sundararajan, Yi-Chia Chiu, Edward Yu Wing Chee, Vin Yee Chung, Mahesh A. Choolani and Ruby Yun-Ju Huang
    Citation: Genome Biology 2022 23:121
  20. Cancer is a set of diseases characterized by unchecked cell proliferation and invasion of surrounding tissues. The many genes that have been genetically associated with cancer or shown to directly contribute t...

    Authors: Anupama Jha, Mathieu Quesnel-Vallières, David Wang, Andrei Thomas-Tikhonenko, Kristen W Lynch and Yoseph Barash
    Citation: Genome Biology 2022 23:117
  21. Pleiotropy describes the phenomenon in which a gene affects multiple phenotypes. The extent of pleiotropy is still disputed, mainly because of issues of inadequate power of analyses. A further challenge is tha...

    Authors: Eirini Christodoulaki, Viola Nolte, Wei-Yun Lai and Christian Schlötterer
    Citation: Genome Biology 2022 23:116
  22. Several high-throughput antibody-free methods for RNA modification detection from sequencing data have been developed. We present JACUSA2 as a versatile software solution and comprehensive analysis framework f...

    Authors: Michael Piechotta, Isabel S. Naarmann-de Vries, Qi Wang, Janine Altmüller and Christoph Dieterich
    Citation: Genome Biology 2022 23:115
  23. Technological development has enabled the profiling of gene expression and chromatin accessibility from the same cell. We develop scREG, a dimension reduction methodology, based on the concept of cis-regulatory p...

    Authors: Zhana Duren, Fengge Chang, Fnu Naqing, Jingxue Xin, Qiao Liu and Wing Hung Wong
    Citation: Genome Biology 2022 23:114

    The Author Correction to this article has been published in Genome Biology 2022 23:213

  24. Colorectal cancer (CRC) consensus molecular subtypes (CMS) have different immunological, stromal cell, and clinicopathological characteristics. Single-cell characterization of CMS subtype tumor microenvironmen...

    Authors: Ateeq M. Khaliq, Cihat Erdogan, Zeyneb Kurt, Sultan Sevgi Turgut, Miles W. Grunvald, Tim Rand, Sonal Khare, Jeffrey A. Borgia, Dana M. Hayden, Sam G. Pappas, Henry R. Govekar, Audrey E. Kam, Jochen Reiser, Kiran Turaga, Milan Radovich, Yong Zang…
    Citation: Genome Biology 2022 23:113

    The Author Correction to this article has been published in Genome Biology 2022 23:156

  25. Integration of single-cell multiomics profiles generated by different single-cell technologies from the same biological sample is still challenging. Previous approaches based on shared features have only provi...

    Authors: Jinzhuang Dou, Shaoheng Liang, Vakul Mohanty, Qi Miao, Yuefan Huang, Qingnan Liang, Xuesen Cheng, Sangbae Kim, Jongsu Choi, Yumei Li, Li Li, May Daher, Rafet Basar, Katayoun Rezvani, Rui Chen and Ken Chen
    Citation: Genome Biology 2022 23:112
  26. Recent proteogenomic studies revealed extensive translation outside of annotated protein coding regions, such as non-coding RNAs and untranslated regions of mRNAs. This non-canonical translation is largely due...

    Authors: Dmitry E. Andreev, Gary Loughran, Alla D. Fedorova, Maria S. Mikhaylova, Ivan N. Shatsky and Pavel V. Baranov
    Citation: Genome Biology 2022 23:111
  27. The precise spatiotemporal gene expression is orchestrated by enhancers that lack general sequence features and thus are difficult to be computationally identified. By nascent RNA sequencing combined with epig...

    Authors: Yilin Xie, Yan Chen, Zijuan Li, Jiafu Zhu, Min Liu, Yijing Zhang and Zhicheng Dong
    Citation: Genome Biology 2022 23:109
  28. Despite recent improvements in basecalling accuracy, nanopore sequencing still has higher error rates on short-tandem repeats (STRs). Instead of using basecalled reads, we developed DeepRepeat which converts i...

    Authors: Li Fang, Qian Liu, Alex Mas Monteys, Pedro Gonzalez-Alegre, Beverly L. Davidson and Kai Wang
    Citation: Genome Biology 2022 23:108
  29. Authors: Panagiotis Galanos, George Pappas, Alexander Polyzos, Athanassios Kotsinas, Ioanna Svolaki, Nickolaos N. Giakoumakis, Christina Glytsou, Ioannis S. Pateras, Umakanta Swain, Vassilis L. Souliotis, Alexandros G. Georgakilas, Nicholas Geacintov, Luca Scorrano, Claudia Lukas, Jiri Lukas, Zvi Livneh…
    Citation: Genome Biology 2022 23:107

    The original article was published in Genome Biology 2018 19:37

  30. Patient-derived organoid culture is a powerful system for studying the molecular mechanisms of cancers, especially colorectal cancer (CRC), one of the most prevalent cancers worldwide. There are two main types...

    Authors: Rui Wang, Yunuo Mao, Wendong Wang, Xin Zhou, Wei Wang, Shuai Gao, Jingyun Li, Lu Wen, Wei Fu and Fuchou Tang
    Citation: Genome Biology 2022 23:106
  31. Revealing the gene targets of distal regulatory elements is challenging yet critical for interpreting regulome data. Experiment-derived enhancer-gene links are restricted to a small set of enhancers and/or cel...

    Authors: Tingting Qin, Christopher Lee, Shiting Li, Raymond G. Cavalcante, Peter Orchard, Heming Yao, Hanrui Zhang, Shuze Wang, Snehal Patil, Alan P. Boyle and Maureen A. Sartor
    Citation: Genome Biology 2022 23:105
  32. Recent progress in deep learning has greatly improved the prediction of RNA splicing from DNA sequence. Here, we present Pangolin, a deep learning model to predict splice site strength in multiple tissues. Pan...

    Authors: Tony Zeng and Yang I Li
    Citation: Genome Biology 2022 23:103
  33. Genome-wide association studies (GWAS) aim to correlate phenotypic changes with genotypic variation. Upon transcription, single nucleotide variants (SNVs) may alter mRNA structure, with potential impacts on tr...

    Authors: Ángel Ferrero-Serrano, Megan M. Sylvia, Peter C. Forstmeier, Andrew J. Olson, Doreen Ware, Philip C. Bevilacqua and Sarah M. Assmann
    Citation: Genome Biology 2022 23:101
  34. Reproducibility is a significant challenge in (epi)genomic research due to the complexity of experiments composed of traditional biochemistry and informatics. Recent advances have exacerbated this as high-thro...

    Authors: Danying Shao, Gretta D. Kellogg, Ali Nematbakhsh, Prashant K. Kuntala, Shaun Mahony, B. Franklin Pugh and William K. M. Lai
    Citation: Genome Biology 2022 23:99
  35. Multiplex assays of variant effect (MAVEs) are a family of methods that includes deep mutational scanning experiments on proteins and massively parallel reporter assays on gene regulatory sequences. Despite th...

    Authors: Ammar Tareen, Mahdi Kooshkbaghi, Anna Posfai, William T. Ireland, David M. McCandlish and Justin B. Kinney
    Citation: Genome Biology 2022 23:98
  36. Genome-wide association studies have identified 3p21.31 as the main risk locus for severe COVID-19, although underlying mechanisms remain elusive. We perform an epigenomic dissection of 3p21.31, identifying a ...

    Authors: Bernard S. Stikker, Grégoire Stik, Antoinette F. van Ouwerkerk, Lianne Trap, Salvatore Spicuglia, Rudi W. Hendriks and Ralph Stadhouders
    Citation: Genome Biology 2022 23:96

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