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  1. We propose a polynomial algorithm computing a minimum plain-text representation of k-mer sets, as well as an efficient near-minimum greedy heuristic. When compressing read sets of large model organisms or bacteri...

    Authors: Sebastian Schmidt, Shahbaz Khan, Jarno N. Alanko, Giulio E. Pibiri and Alexandru I. Tomescu
    Citation: Genome Biology 2023 24:136
  2. Recent deep learning models that predict the Hi-C contact map from DNA sequence achieve promising accuracy but cannot generalize to new cell types and or even capture differences among training cell types. We ...

    Authors: Rui Yang, Arnav Das, Vianne R. Gao, Alireza Karbalayghareh, William S. Noble, Jeffery A. Bilmes and Christina S. Leslie
    Citation: Genome Biology 2023 24:134
  3. It has been over a decade since the first publication of a method dedicated entirely to mapping long-reads. The distinctive characteristics of long reads resulted in methods moving from the seed-and-extend fra...

    Authors: Kristoffer Sahlin, Thomas Baudeau, Bastien Cazaux and Camille Marchet
    Citation: Genome Biology 2023 24:133
  4. Multiplexed assays of variant effect (MAVE) experimentally measure the effect of large numbers of sequence variants by selective enrichment of sequences with desirable properties followed by quantification by ...

    Authors: Charlotte Soneson, Alexandra M. Bendel, Guillaume Diss and Michael B. Stadler
    Citation: Genome Biology 2023 24:132
  5. Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central...

    Authors: Benjamin Noel, France Denoeud, Alice Rouan, Carol Buitrago-López, Laura Capasso, Julie Poulain, Emilie Boissin, Mélanie Pousse, Corinne Da Silva, Arnaud Couloux, Eric Armstrong, Quentin Carradec, Corinne Cruaud, Karine Labadie, Julie Lê-Hoang, Sylvie Tambutté…
    Citation: Genome Biology 2023 24:123
  6. We present a novel data structure for searching sequences in large databases: the Hierarchical Interleaved Bloom Filter (HIBF). It is extremely fast and space efficient, yet so general that it could serve as t...

    Authors: Svenja Mehringer, Enrico Seiler, Felix Droop, Mitra Darvish, René Rahn, Martin Vingron and Knut Reinert
    Citation: Genome Biology 2023 24:131
  7. Genetic variation influences both chromatin accessibility, assessed in chromatin accessibility quantitative trait loci (caQTL) studies, and gene expression, assessed in expression QTL (eQTL) studies. Genetic v...

    Authors: Nil Aygün, Dan Liang, Wesley L. Crouse, Gregory R. Keele, Michael I. Love and Jason L. Stein
    Citation: Genome Biology 2023 24:130
  8. Transcriptional regulation is a key aspect of environmental stress responses. Heat stress induces transcriptional memory, i.e., sustained induction or enhanced re-induction of transcription, that allows plants...

    Authors: Christian Kappel, Thomas Friedrich, Vicky Oberkofler, Li Jiang, Tim Crawford, Michael Lenhard and Isabel Bäurle
    Citation: Genome Biology 2023 24:129
  9. Therapy resistance in cancer is often driven by a subpopulation of cells that are temporarily arrested in a non-proliferative G0 state, which is difficult to capture and whose mutational drivers remain largely...

    Authors: Anna J. Wiecek, Stephen J. Cutty, Daniel Kornai, Mario Parreno-Centeno, Lucie E. Gourmet, Guidantonio Malagoli Tagliazucchi, Daniel H. Jacobson, Ping Zhang, Lingyun Xiong, Gareth L. Bond, Alexis R. Barr and Maria Secrier
    Citation: Genome Biology 2023 24:128
  10. Understanding the variation between well and poorly adapted cattle breeds to local environments and pathogens is essential for breeding cattle with improved climate and disease-resistant phenotypes. Although c...

    Authors: Jessica Powell, Andrea Talenti, Andressa Fisch, Johanneke D. Hemmink, Edith Paxton, Philip Toye, Isabel Santos, Beatriz R. Ferreira, Tim K. Connelley, Liam J. Morrison and James G. D. Prendergast
    Citation: Genome Biology 2023 24:127
  11. Single nucleotide variants (SNVs) contribute to human genomic diversity. Synonymous SNVs are previously considered to be “silent,” but mounting evidence has revealed that these variants can cause RNA and prote...

    Authors: Brian C. Lin, Upendra Katneni, Katarzyna I. Jankowska, Douglas Meyer and Chava Kimchi-Sarfaty
    Citation: Genome Biology 2023 24:126
  12. Several models and algorithms have been proposed to build pangenomes from multiple input assemblies, but their impact on variant representation, and consequently downstream analyses, is largely unknown.

    Authors: Alexander S. Leonard, Danang Crysnanto, Xena M. Mapel, Meenu Bhati and Hubert Pausch
    Citation: Genome Biology 2023 24:124
  13. We present RabbitTClust, a fast and memory-efficient genome clustering tool based on sketch-based distance estimation. Our approach enables efficient processing of large-scale datasets by combining dimensional...

    Authors: Xiaoming Xu, Zekun Yin, Lifeng Yan, Hao Zhang, Borui Xu, Yanjie Wei, Beifang Niu, Bertil Schmidt and Weiguo Liu
    Citation: Genome Biology 2023 24:121
  14. Spatial transcriptomics maps gene expression across tissues, posing the challenge of determining the spatial arrangement of different cell types. However, spatial transcriptomics spots contain multiple cells. ...

    Authors: Agnieszka Geras, Shadi Darvish Shafighi, Kacper Domżał, Igor Filipiuk, Alicja Rączkowska, Paulina Szymczak, Hosein Toosi, Leszek Kaczmarek, Łukasz Koperski, Jens Lagergren, Dominika Nowis and Ewa Szczurek
    Citation: Genome Biology 2023 24:120
  15. Computational methods represent the lifeblood of modern molecular biology. Benchmarking is important for all methods, but with a focus here on computational methods, benchmarking is critical to dissect importa...

    Authors: Anthony Sonrel, Almut Luetge, Charlotte Soneson, Izaskun Mallona, Pierre-Luc Germain, Sergey Knyazev, Jeroen Gilis, Reto Gerber, Ruth Seurinck, Dominique Paul, Emanuel Sonder, Helena L. Crowell, Imran Fanaswala, Ahmad Al-Ajami, Elyas Heidari, Stephan Schmeing…
    Citation: Genome Biology 2023 24:119
  16. Predicting the impact of coding and noncoding variants on splicing is challenging, particularly in non-canonical splice sites, leading to missed diagnoses in patients. Existing splice prediction tools are comp...

    Authors: Patricia J. Sullivan, Velimir Gayevskiy, Ryan L. Davis, Marie Wong, Chelsea Mayoh, Amali Mallawaarachchi, Yvonne Hort, Mark J. McCabe, Sarah Beecroft, Matilda R. Jackson, Peer Arts, Andrew Dubowsky, Nigel Laing, Marcel E. Dinger, Hamish S. Scott, Emily Oates…
    Citation: Genome Biology 2023 24:118
  17. The variation in the rate at which humans age may be rooted in early events acting through the genomic regions that are influenced by such events and subsequently are related to health phenotypes in later life...

    Authors: Chenhao Gao, Carmen Amador, Rosie M. Walker, Archie Campbell, Rebecca A. Madden, Mark J. Adams, Xiaomeng Bai, Ying Liu, Miaoxin Li, Caroline Hayward, David J. Porteous, Xueyi Shen, Kathryn L. Evans, Chris S. Haley, Andrew M. McIntosh, Pau Navarro…
    Citation: Genome Biology 2023 24:117
  18. The Vertebrate Gene Nomenclature Committee (VGNC) was established in 2016 as a sister project to the HUGO Gene Nomenclature Committee, to approve gene nomenclature in vertebrate species without an existing ded...

    Authors: Tamsin E. M. Jones, Bethan Yates, Bryony Braschi, Kristian Gray, Susan Tweedie, Ruth L. Seal and Elspeth A. Bruford
    Citation: Genome Biology 2023 24:115
  19. Plant architecture associated with increased grain yield and adaptation to the local environments is selected during wheat (Triticum aestivum) breeding. The internode length of individual stems and tiller length ...

    Authors: Yangyang Liu, Kuocheng Shen, Changbin Yin, Xiaowan Xu, Xuchang Yu, Botao Ye, Zhiwen Sun, Jiayu Dong, Aoyue Bi, Xuebo Zhao, Daxing Xu, Zhonghu He, Xueyong Zhang, Chenyang Hao, Jianhui Wu, Ziying Wang…
    Citation: Genome Biology 2023 24:114
  20. Protein annotation is a major goal in molecular biology, yet experimentally determined knowledge is typically limited to a few model organisms. In non-model species, the sequence-based prediction of gene ortho...

    Authors: Fabian Ruperti, Nikolaos Papadopoulos, Jacob M. Musser, Milot Mirdita, Martin Steinegger and Detlev Arendt
    Citation: Genome Biology 2023 24:113
  21. Verticillium wilt is one of the most devasting diseases for many plants, leading to global economic loss. Cotton is known to be vulnerable to its fungal pathogen, Verticillium dahliae, yet the related genetic mec...

    Authors: Yihao Zhang, Yaning Zhang, Xiaoyang Ge, Yuan Yuan, Yuying Jin, Ye Wang, Lihong Zhao, Xiao Han, Wei Hu, Lan Yang, Chenxu Gao, Xi Wei, Fuguang Li and Zhaoen Yang
    Citation: Genome Biology 2023 24:111
  22. Genetic variation in regulatory sequences that alter transcription factor (TF) binding is a major cause of phenotypic diversity. Brassinosteroid is a growth hormone that has major effects on plant phenotypes. ...

    Authors: Thomas Hartwig, Michael Banf, Gisele Passaia Prietsch, Jia-Ying Zhu, Isabel Mora-Ramírez, Jos H. M. Schippers, Samantha J. Snodgrass, Arun S. Seetharam, Bruno Huettel, Judith M. Kolkman, Jinliang Yang, Julia Engelhorn and Zhi-Yong Wang
    Citation: Genome Biology 2023 24:108
  23. Group heteroscedasticity is commonly observed in pseudo-bulk single-cell RNA-seq datasets and its presence can hamper the detection of differentially expressed genes. Since most bulk RNA-seq methods assume equ...

    Authors: Yue You, Xueyi Dong, Yong Kiat Wee, Mhairi J. Maxwell, Monther Alhamdoosh, Gordon K. Smyth, Peter F. Hickey, Matthew E. Ritchie and Charity W. Law
    Citation: Genome Biology 2023 24:107

    The Publisher Correction to this article has been published in Genome Biology 2023 24:112

  24. Plants memorize previous pathogen attacks and are “primed” to produce a faster and stronger defense response, which is critical for defense against pathogens. In plants, cytosines in transposons and gene bodie...

    Authors: Seungchul Lee, Jaemyung Choi, Jihwan Park, Chang Pyo Hong, Daeseok Choi, Soeun Han, Kyuha Choi, Tae-Young Roh, Daehee Hwang and Ildoo Hwang
    Citation: Genome Biology 2023 24:106
  25. Deep neural networks (DNNs) hold promise for functional genomics prediction, but their generalization capability may be limited by the amount of available data. To address this, we propose EvoAug, a suite of e...

    Authors: Nicholas Keone Lee, Ziqi Tang, Shushan Toneyan and Peter K. Koo
    Citation: Genome Biology 2023 24:105
  26. RNA N6-methyladenosine (m6A) modification is critical for plant growth and crop yield. m6A reader proteins can recognize m6A modifications to facilitate the functions of m6A in gene regulation. ECT2, ECT3, and EC...

    Authors: Peizhe Song, Lianhuan Wei, Zixin Chen, Zhihe Cai, Qiang Lu, Chunling Wang, Enlin Tian and Guifang Jia
    Citation: Genome Biology 2023 24:103
  27. Cas12a (formerly known as Cpf1), the class II type V CRISPR nuclease, has been widely used for genome editing in mammalian cells and plants due to its distinct characteristics from Cas9. Despite being one of t...

    Authors: Liyang Zhang, Gen Li, Yingxiao Zhang, Yanhao Cheng, Nathaniel Roberts, Steve E. Glenn, Diane DeZwaan-McCabe, H. Tomas Rube, Jeff Manthey, Gary Coleman, Christopher A. Vakulskas and Yiping Qi
    Citation: Genome Biology 2023 24:102
  28. The telomere-to-telomere (T2T) complete human reference has significantly improved our ability to characterize genome structural variation. To understand its impact on inversion polymorphisms, we remapped data...

    Authors: David Porubsky, William T. Harvey, Allison N. Rozanski, Jana Ebler, Wolfram Höps, Hufsah Ashraf, Patrick Hasenfeld, Benedict Paten, Ashley D. Sanders, Tobias Marschall, Jan O. Korbel and Evan E. Eichler
    Citation: Genome Biology 2023 24:100
  29. Circulating tumor DNA detection using next-generation sequencing (NGS) data of plasma DNA is promising for cancer identification and characterization. However, the tumor signal in the blood is often low and di...

    Authors: Mikkel H. Christensen, Simon O. Drue, Mads H. Rasmussen, Amanda Frydendahl, Iben Lyskjær, Christina Demuth, Jesper Nors, Kåre A. Gotschalck, Lene H. Iversen, Claus L. Andersen and Jakob Skou Pedersen
    Citation: Genome Biology 2023 24:99
  30. Caloric restriction (CR) has been known to promote health by reprogramming metabolism, yet little is known about how the epigenome and microbiome respond during metabolic adaptation to CR.

    Authors: Yun Fan, Hong Qian, Meijia Zhang, Chengzhe Tao, Zhi Li, Wenkai Yan, Yuna Huang, Yan Zhang, Qiaoqiao Xu, Xinru Wang, Paul A. Wade, Yankai Xia, Yufeng Qin and Chuncheng Lu
    Citation: Genome Biology 2023 24:98
  31. Glucokinase (GCK) regulates insulin secretion to maintain appropriate blood glucose levels. Sequence variants can alter GCK activity to cause hyperinsulinemic hypoglycemia or hyperglycemia associated with GCK-...

    Authors: Sarah Gersing, Matteo Cagiada, Marinella Gebbia, Anette P. Gjesing, Atina G. Coté, Gireesh Seesankar, Roujia Li, Daniel Tabet, Jochen Weile, Amelie Stein, Anna L. Gloyn, Torben Hansen, Frederick P. Roth, Kresten Lindorff-Larsen and Rasmus Hartmann-Petersen
    Citation: Genome Biology 2023 24:97
  32. The microrchidia (MORC) proteins are a family of evolutionarily conserved GHKL-type ATPases involved in chromatin compaction and gene silencing. Arabidopsis MORC proteins act in the RNA-directed DNA methylatio...

    Authors: Zhenhui Zhong, Yan Xue, C. Jake Harris, Ming Wang, Zheng Li, Yunqing Ke, Mukun Liu, Jessica Zhou, Yasaman Jami-Alahmadi, Suhua Feng, James A. Wohlschlegel and Steven E. Jacobsen
    Citation: Genome Biology 2023 24:96
  33. Apple is an economically important fruit crop. Changes in metabolism accompanying human-guided evolution can be revealed using a multiomics approach. We perform genome-wide metabolic analysis of apple fruits c...

    Authors: Qiong Lin, Jing Chen, Xuan Liu, Bin Wang, Yaoyao Zhao, Liao Liao, Andrew C. Allan, Chongde Sun, Yuquan Duan, Xuan Li, Donald Grierson, Julian C. Verdonk, Kunsong Chen, Yuepeng Han and Jinfeng Bi
    Citation: Genome Biology 2023 24:95
  34. Extensive studies have revealed the function and mechanism of lncRNAs in development and differentiation, but the majority have focused on those lncRNAs adjacent to protein-coding genes. In contrast, lncRNAs l...

    Authors: Pei Lu, Jie Yang, Mao Li, Shanshan Wen, Tianzhe Zhang, Chenchao Yan, Ran Liu, Yu Xiao, Xinghuan Wang and Wei Jiang
    Citation: Genome Biology 2023 24:92
  35. Long-read RNA sequencing (lrRNA-seq) produces detailed information about full-length transcripts, including novel and sample-specific isoforms. Furthermore, there is an opportunity to call variants directly fr...

    Authors: Vladimir B. C. de Souza, Ben T. Jordan, Elizabeth Tseng, Elizabeth A. Nelson, Karen K. Hirschi, Gloria Sheynkman and Mark D. Robinson
    Citation: Genome Biology 2023 24:91
  36. DNA double-strand breaks (DSBs) are among the most deleterious DNA lesions, and they can cause cancer if improperly repaired. Recent chromosome conformation capture techniques, such as Hi-C, have enabled the i...

    Authors: Yu Sun, Xiang Xu, Lin Lin, Kang Xu, Yang Zheng, Chao Ren, Huan Tao, Xu Wang, Huan Zhao, Weiwei Tu, Xuemei Bai, Junting Wang, Qiya Huang, Yaru Li, Hebing Chen, Hao Li…
    Citation: Genome Biology 2023 24:90
  37. Multiple genetic modifications may be required to develop potent off-the-shelf chimeric antigen receptor (CAR) T cell therapies. Conventional CRISPR-Cas nucleases install sequence-specific DNA double-strand br...

    Authors: Viktor Glaser, Christian Flugel, Jonas Kath, Weijie Du, Vanessa Drosdek, Clemens Franke, Maik Stein, Axel Pruß, Michael Schmueck-Henneresse, Hans-Dieter Volk, Petra Reinke and Dimitrios L. Wagner
    Citation: Genome Biology 2023 24:89

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