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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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

  18. 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
  19. 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
  20. 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
  21. 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
  22. 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

  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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

  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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

  36. 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
  37. 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
  38. 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

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