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Page 5 of 152

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

  10. 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
  11. 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
  12. 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
  13. 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
  14. 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

  15. 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
  16. 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
  17. 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
  18. 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
  19. Cohesin is a chromosome-associated SMC–kleisin complex that mediates sister chromatid cohesion, recombination, and most chromosomal processes during mitosis and meiosis. However, it remains unclear whether mei...

    Authors: Eui-Hwan Choi, Seobin Yoon, Young Eun Koh, Tae Kyung Hong, Jeong Tae Do, Bum-Kyu Lee, Yoonsoo Hahn and Keun P. Kim
    Citation: Genome Biology 2022 23:70
  20. The detection of physiologically relevant protein isoforms encoded by the human genome is critical to biomedicine. Mass spectrometry (MS)-based proteomics is the preeminent method for protein detection, but is...

    Authors: Rachel M. Miller, Ben T. Jordan, Madison M. Mehlferber, Erin D. Jeffery, Christina Chatzipantsiou, Simi Kaur, Robert J. Millikin, Yunxiang Dai, Simone Tiberi, Peter J. Castaldi, Michael R. Shortreed, Chance John Luckey, Ana Conesa, Lloyd M. Smith, Anne Deslattes Mays and Gloria M. Sheynkman
    Citation: Genome Biology 2022 23:69
  21. Structural variants (SVs) are a major source of human genetic diversity and have been associated with different diseases and phenotypes. The detection of SVs is difficult, and a diverse range of detection meth...

    Authors: Zhichao Liu, Ruth Roberts, Timothy R. Mercer, Joshua Xu, Fritz J. Sedlazeck and Weida Tong
    Citation: Genome Biology 2022 23:68

    The Author Correction to this article has been published in Genome Biology 2022 23:198

  22. Vaginal bacterial communities dominated by Lactobacillus species are associated with a reduced risk of various adverse health outcomes. However, somewhat unexpectedly, many healthy women have microbiota that are ...

    Authors: Michael T. France, Li Fu, Lindsay Rutt, Hongqiu Yang, Michael S. Humphrys, Shilpa Narina, Pawel M. Gajer, Bing Ma, Larry J. Forney and Jacques Ravel
    Citation: Genome Biology 2022 23:66
  23. Nucleomorphs are remnants of secondary endosymbiotic events between two eukaryote cells wherein the endosymbiont has retained its eukaryotic nucleus. Nucleomorphs have evolved at least twice independently, in ...

    Authors: Georgi K. Marinov, Xinyi Chen, Tong Wu, Chuan He, Arthur R. Grossman, Anshul Kundaje and William James Greenleaf
    Citation: Genome Biology 2022 23:65
  24. Single-stranded DNA (ssDNA) coated with replication protein A (RPA) acts as a key platform for the recruitment and exchange of genome maintenance factors in DNA damage response. Yet, how the formation of the s...

    Authors: Kaiwen Bao, Qi Zhang, Shuai Liu, Nan Song, Qiushi Guo, Ling Liu, Shanshan Tian, Jihui Hao, Yi Zhu, Kai Zhang, Ding Ai, Jie Yang, Zhi Yao, Roland Foisner and Lei Shi
    Citation: Genome Biology 2022 23:64
  25. Identifying genomic regions with hypervariable ChIP-seq or ATAC-seq signals across given samples is essential for large-scale epigenetic studies. In particular, the hypervariable regions across tumors from dif...

    Authors: Haojie Chen, Shiqi Tu, Chongze Yuan, Feng Tian, Yijing Zhang, Yihua Sun and Zhen Shao
    Citation: Genome Biology 2022 23:62
  26. Gut microbial alteration is implicated in inflammatory bowel disease but is noted in other diseases. Systematic comparison to define similarities and specificities is hampered since most studies focus on a sin...

    Authors: Haya Abbas-Egbariya, Yael Haberman, Tzipi Braun, Rotem Hadar, Lee Denson, Ohad Gal-Mor and Amnon Amir
    Citation: Genome Biology 2022 23:61
  27. A variety of epigenetic clocks utilizing DNA methylation changes have been developed; these clocks are either tissue-independent or designed to predict chronological age based on blood or saliva samples. Wheth...

    Authors: 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 23:52

    The Author Correction to this article has been published in Genome Biology 2022 23:142

  28. Unraveling the relationship between genetic variation and phenotypic traits remains a fundamental challenge in biology. Mapping variants underlying complex traits while controlling for confounding environmenta...

    Authors: Tomas Fitzgerald, Ian Brettell, Adrien Leger, Nadeshda Wolf, Natalja Kusminski, Jack Monahan, Carl Barton, Cathrin Herder, Narendar Aadepu, Jakob Gierten, Clara Becker, Omar T. Hammouda, Eva Hasel, Colin Lischik, Katharina Lust, Natalia Sokolova…
    Citation: Genome Biology 2022 23:59
  29. The teleost medaka (Oryzias latipes) is a well-established vertebrate model system, with a long history of genetic research, and multiple high-quality reference genomes available for several inbred strains. Medak...

    Authors: Adrien Leger, Ian Brettell, Jack Monahan, Carl Barton, Nadeshda Wolf, Natalja Kusminski, Cathrin Herder, Narendar Aadepu, Clara Becker, Jakob Gierten, Omar T. Hammouda, Eva Hasel, Colin Lischik, Katharina Lust, Natalia Sokolova, Risa Suzuki…
    Citation: Genome Biology 2022 23:58
  30. Computational biology provides software tools for testing and making inferences about biological data. In the face of increasing volumes of data, heuristic methods that trade software speed for accuracy may be...

    Authors: Paul P. Gardner, James M. Paterson, Stephanie McGimpsey, Fatemeh Ashari-Ghomi, Sinan U. Umu, Aleksandra Pawlik, Alex Gavryushkin and Michael A. Black
    Citation: Genome Biology 2022 23:56
  31. Multiplexing of samples in single-cell RNA-seq studies allows a significant reduction of the experimental costs, straightforward identification of doublets, increased cell throughput, and reduction of sample-s...

    Authors: Viacheslav Mylka, Irina Matetovici, Suresh Poovathingal, Jeroen Aerts, Niels Vandamme, Ruth Seurinck, Kevin Verstaen, Gert Hulselmans, Silvie Van den Hoecke, Isabelle Scheyltjens, Kiavash Movahedi, Hans Wils, Joke Reumers, Jeroen Van Houdt, Stein Aerts and Yvan Saeys
    Citation: Genome Biology 2022 23:55
  32. Autism spectrum disorder (ASD) involves complex genetics interacting with the perinatal environment, complicating the discovery of common genetic risk. The epigenetic layer of DNA methylation shows dynamic dev...

    Authors: Yihui Zhu, J. Antonio Gomez, Benjamin I. Laufer, Charles E. Mordaunt, Julia S. Mouat, Daniela C. Soto, Megan Y. Dennis, Kelly S. Benke, Kelly M. Bakulski, John Dou, Ria Marathe, Julia M. Jianu, Logan A. Williams, Orangel J. Gutierrez Fugón, Cheryl K. Walker, Sally Ozonoff…
    Citation: Genome Biology 2022 23:46
  33. Ribosomal DNA (rDNA) displays substantial inter-individual genetic variation in human and mouse. A systematic analysis of how this variation impacts epigenetic states and expression of the rDNA has thus far no...

    Authors: Francisco Rodriguez-Algarra, Robert A. E. Seaborne, Amy F. Danson, Selin Yildizoglu, Harunori Yoshikawa, Pui Pik Law, Zakaryya Ahmad, Victoria A. Maudsley, Ama Brew, Nadine Holmes, Mateus Ochôa, Alan Hodgkinson, Sarah J. Marzi, Madapura M. Pradeepa, Matthew Loose, Michelle L. Holland…
    Citation: Genome Biology 2022 23:54
  34. Hybridization and backcrossing are commonly used in animal and plant breeding to induce heritable variation including epigenetic changes such as paramutation. However, the molecular basis for hybrid-induced ep...

    Authors: Shuai Cao, Longfei Wang, Tongwen Han, Wenxue Ye, Yang Liu, Yi Sun, Stephen P. Moose, Qingxin Song and Z. Jeffrey Chen
    Citation: Genome Biology 2022 23:53
  35. The high-activity adenine base editors (ABEs), engineered with the recently-developed tRNA adenosine deaminases (TadA8e and TadA9), show robust base editing activity but raise concerns about off-target effects.

    Authors: Shaofang Li, Lang Liu, Wenxian Sun, Xueping Zhou and Huanbin Zhou
    Citation: Genome Biology 2022 23:51
  36. Circular RNAs (circRNAs), a novel class of poorly conserved non-coding RNAs that regulate gene expression, are highly enriched in the human brain. Despite increasing discoveries of circRNA function in human ne...

    Authors: Yangping Li, Feng Wang, Peng Teng, Li Ku, Li Chen, Yue Feng and Bing Yao
    Citation: Genome Biology 2022 23:48
  37. High-throughput single-cell analysis today is facilitated by protocols like the 10X Genomics platform or Drop-Seq which generate cDNA pools in which the origin of a transcript is encoded at its 5′ or 3′ end. H...

    Authors: Roger Volden and Christopher Vollmers
    Citation: Genome Biology 2022 23:47
  38. Despite remarkable advances in our knowledge of epigenetically mediated transcriptional programming of cell differentiation in plants, little is known about chromatin topology and its functional implications i...

    Authors: Liuling Pei, Xianhui Huang, Zhenping Liu, Xuehan Tian, Jiaqi You, Jianying Li, David D. Fang, Keith Lindsey, Longfu Zhu, Xianlong Zhang and Maojun Wang
    Citation: Genome Biology 2022 23:45
  39. The human pathogen Haemophilus influenzae was the main cause of bacterial meningitis in children and a major cause of worldwide infant mortality before the introduction of a vaccine in the 1980s. Although the occ...

    Authors: Meriam Guellil, Marcel Keller, Jenna M. Dittmar, Sarah A. Inskip, Craig Cessford, Anu Solnik, Toomas Kivisild, Mait Metspalu, John E. Robb and Christiana L. Scheib
    Citation: Genome Biology 2022 23:22
  40. Clonal analysis of tumour sequencing data enables the evaluation of the relationship of histologically distinct synchronous lesions, such as co-existing benign areas, and temporally distinct tumours, such as p...

    Authors: Tanjina Kader, Magnus Zethoven and Kylie L. Gorringe
    Citation: Genome Biology 2022 23:43

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