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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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

  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. The advancement of highly multiplexed spatial technologies requires scalable methods that can leverage spatial information. We present MISTy, a flexible, scalable, and explainable machine learning framework fo...

    Authors: Jovan Tanevski, Ricardo Omar Ramirez Flores, Attila Gabor, Denis Schapiro and Julio Saez-Rodriguez
    Citation: Genome Biology 2022 23:97
  18. 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
  19. Biases of DNA repair can shape the nucleotide landscape of genomes at evolutionary timescales. The molecular mechanisms of those biases are still poorly understood because it is difficult to isolate the contri...

    Authors: Victoria O. Pokusaeva, Aránzazu Rosado Diez, Lorena Espinar, Albert Torelló Pérez and Guillaume J. Filion
    Citation: Genome Biology 2022 23:93
  20. Prime editing can induce a desired base substitution, insertion, or deletion in a target gene using reverse transcriptase after nick formation by CRISPR nickase. In this study, we develop a technology that can...

    Authors: Yeounsun Oh, Wi-jae Lee, Junho K. Hur, Woo Jeung Song, Youngjeon Lee, Hanseop Kim, Lee Wha Gwon, Young-Hyun Kim, Young-Ho Park, Chan Hyoung Kim, Kyung-Seob Lim, Bong-Seok Song, Jae-Won Huh, Sun-Uk Kim, Bong-Hyun Jun, Cheulhee Jung…
    Citation: Genome Biology 2022 23:92
  21. Interactions of chromatin with the nuclear lamina via lamina-associated domains (LADs) confer structural stability to the genome. The dynamics of positioning of LADs during differentiation, and how LADs imping...

    Authors: Julia Madsen-Østerbye, Mohamed Abdelhalim, Marie-Odile Baudement and Philippe Collas
    Citation: Genome Biology 2022 23:91
  22. Cardiac differentiation of human-induced pluripotent stem (hiPS) cells consistently produces a mixed population of cardiomyocytes and non-cardiac cell types, even when using well-characterized protocols. We so...

    Authors: Connie L. Jiang, Yogesh Goyal, Naveen Jain, Qiaohong Wang, Rachel E. Truitt, Allison J. Coté, Benjamin Emert, Ian A. Mellis, Karun Kiani, Wenli Yang, Rajan Jain and Arjun Raj
    Citation: Genome Biology 2022 23:90
  23. Promoters are sites of transcription initiation that harbour a high concentration of phenotype-associated genetic variation. The evolutionary gain and loss of promoters between species (collectively, termed tu...

    Authors: Robert S. Young, Lana Talmane, Sophie Marion de Procé and Martin S. Taylor
    Citation: Genome Biology 2022 23:89
  24. Cost-efficient library generation by early barcoding has been central in propelling single-cell RNA sequencing. Here, we optimize and validate prime-seq, an early barcoding bulk RNA-seq method. We show that it...

    Authors: Aleksandar Janjic, Lucas E. Wange, Johannes W. Bagnoli, Johanna Geuder, Phong Nguyen, Daniel Richter, Beate Vieth, Binje Vick, Irmela Jeremias, Christoph Ziegenhain, Ines Hellmann and Wolfgang Enard
    Citation: Genome Biology 2022 23:88
  25. Vascular invasion with tumor thrombus frequently occurs in advanced renal cell carcinoma (RCC). Thrombectomy is one of the most challenging surgeries with high rate of perioperative morbidity and mortality. Ho...

    Authors: Yue Shi, Qi Zhang, Hai Bi, Min Lu, Yezhen Tan, Daojia Zou, Liyuan Ge, Zhigang Chen, Cheng Liu, Weimin Ci and Lulin Ma
    Citation: Genome Biology 2022 23:87
  26. Brassica napus is an important vegetable oil source worldwide. Seed coat content is a complex quantitative trait that negatively correlates with the seed oil content in B. napus.

    Authors: Yuting Zhang, Hui Zhang, Hu Zhao, Yefan Xia, Xiangbo Zheng, Ruyi Fan, Zengdong Tan, Chenhua Duan, Yansong Fu, Long Li, Jiang Ye, Shan Tang, Honghong Hu, Weibo Xie, Xuan Yao and Liang Guo
    Citation: Genome Biology 2022 23:86
  27. Determining the evolutionary relationships between genes is fundamental to comparative biological research. Here, we present SHOOT. SHOOT searches a user query sequence against a database of phylogenetic trees...

    Authors: David Mark Emms and Steven Kelly
    Citation: Genome Biology 2022 23:85
  28. Most animals and plants have more than one set of chromosomes and package these haplotypes into a single nucleus within each cell. In contrast, many fungal species carry multiple haploid nuclei per cell. Rust ...

    Authors: Hongyu Duan, Ashley W. Jones, Tim Hewitt, Amy Mackenzie, Yiheng Hu, Anna Sharp, David Lewis, Rohit Mago, Narayana M. Upadhyaya, John P. Rathjen, Eric A. Stone, Benjamin Schwessinger, Melania Figueroa, Peter N. Dodds, Sambasivam Periyannan and Jana Sperschneider
    Citation: Genome Biology 2022 23:84
  29. The increasing number of scRNA-seq data emphasizes the need for integrative analysis to interpret similarities and differences between single-cell samples. Although different batch effect removal methods have ...

    Authors: Kun Qian, Shiwei Fu, Hongwei Li and Wei Vivian Li
    Citation: Genome Biology 2022 23:82

    The Author Correction to this article has been published in Genome Biology 2022 23:104

  30. Cleavage Under Targets and Tagmentation (CUT&Tag) is an antibody-directed transposase tethering strategy for in situ chromatin profiling in small samples and single cells. We describe a modified CUT&Tag protoc...

    Authors: Derek H. Janssens, Dominik J. Otto, Michael P. Meers, Manu Setty, Kami Ahmad and Steven Henikoff
    Citation: Genome Biology 2022 23:81
  31. Genomic prediction in crop breeding is hindered by modeling on limited phenotypic traits. We propose an integrative multi-trait breeding strategy via machine learning algorithm, target-oriented prioritization ...

    Authors: Wenyu Yang, Tingting Guo, Jingyun Luo, Ruyang Zhang, Jiuran Zhao, Marilyn L. Warburton, Yingjie Xiao and Jianbing Yan
    Citation: Genome Biology 2022 23:80
  32. When identifying differentially expressed genes between two conditions using human population RNA-seq samples, we found a phenomenon by permutation analysis: two popular bioinformatics methods, DESeq2 and edge...

    Authors: Yumei Li, Xinzhou Ge, Fanglue Peng, Wei Li and Jingyi Jessica Li
    Citation: Genome Biology 2022 23:79
  33. Paralogs that arise from gene duplications during genome evolution enable genetic redundancy and phenotypic robustness. Variation in the coding or regulatory sequence of paralogous transcriptional regulators d...

    Authors: Xiaozhen Huang, Nan Xiao, Yupan Zou, Yue Xie, Lingli Tang, Yueqin Zhang, Yuan Yu, Yiting Li and Cao Xu
    Citation: Genome Biology 2022 23:78
  34. Authors: Shujun Ou, Weijia Su, Yi Liao, Kapeel Chougule, Jireh R. A. Agda, Adam J. Hellinga, Carlos Santiago Blanco Lugo, Tyler A. Elliott, Doreen Ware, Thomas Peterson, Ning Jiang, Candice N. Hirsch and Matthew B. Hufford
    Citation: Genome Biology 2022 23:76

    The original article was published in Genome Biology 2021 22:332

  35. Spinach (Spinacia oleracea L.) is a dioecious species with an XY sex chromosome system, but its Y chromosome has not been fully characterized. Our knowledge about the history of its domestication and improvement ...

    Authors: Xiaokai Ma, Li’ang Yu, Mahpara Fatima, William H. Wadlington, Amanda M. Hulse-Kemp, Xingtan Zhang, Shengcheng Zhang, Xindan Xu, Jingjing Wang, Huaxing Huang, Jing Lin, Ban Deng, Zhenyang Liao, Zhenhui Yang, Yanhong Ma, Haibao Tang…
    Citation: Genome Biology 2022 23:75
  36. Human-associated microbial communities comprise not only complex mixtures of bacterial species, but also mixtures of conspecific strains, the implications of which are mostly unknown since strain level dynamic...

    Authors: Lucas R. van Dijk, Bruce J. Walker, Timothy J. Straub, Colin J. Worby, Alexandra Grote, Henry L. Schreiber IV, Christine Anyansi, Amy J. Pickering, Scott J. Hultgren, Abigail L. Manson, Thomas Abeel and Ashlee M. Earl
    Citation: Genome Biology 2022 23:74
  37. A major advantage of single cell RNA-sequencing (scRNA-Seq) data is the ability to reconstruct continuous ordering and trajectories for cells. Here we present TraSig, a computational method for improving the i...

    Authors: Dongshunyi Li, Jeremy J. Velazquez, Jun Ding, Joshua Hislop, Mo R. Ebrahimkhani and Ziv Bar-Joseph
    Citation: Genome Biology 2022 23:73
  38. Neuroblastoma is a pediatric malignancy with a high frequency of metastatic disease at initial diagnosis. Neuroblastoma tumors have few recurrent protein-coding mutations but contain extensive somatic copy num...

    Authors: Arko Sen, Yuchen Huo, Jennifer Elster, Peter E. Zage and Graham McVicker
    Citation: Genome Biology 2022 23:71

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