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  1. Small nucleolar RNAs (snoRNAs) are abundant noncoding RNAs best known for their involvement in ribosomal RNA maturation. In mammals, most expressed snoRNAs are embedded in introns of longer genes and produced ...

    Authors: Danny Bergeron, Laurence Faucher-Giguère, Ann-Kathrin Emmerichs, Karine Choquet, Kristina Sungeun Song, Gabrielle Deschamps-Francoeur, Étienne Fafard-Couture, Andrea Rivera, Sonia Couture, L. Stirling Churchman, Florian Heyd, Sherif Abou Elela and Michelle S. Scott
    Citation: Genome Biology 2023 24:160
  2. Intestinal barrier dysfunction plays a central role in the pathological onset of Crohn’s disease. We identify the cadherin superfamily member protocadherin 20 (PCDH20) as a crucial factor in Crohn’s disease. H...

    Authors: Shanshan Huang, Zhuo Xie, Jing Han, Huiling Wang, Guang Yang, Manying Li, Gaoshi Zhou, Ying Wang, Lixuan Li, Li Li, Zhirong Zeng, Jun Yu, Minhu Chen and Shenghong Zhang
    Citation: Genome Biology 2023 24:159
  3. The first telomere-to-telomere (T2T) human genome assembly (T2T-CHM13) release is a milestone in human genomics. The T2T-CHM13 genome assembly extends our understanding of telomeres, centromeres, segmental dup...

    Authors: Xiangyu Yang, Xuankai Wang, Yawen Zou, Shilong Zhang, Manying Xia, Lianting Fu, Mitchell R. Vollger, Nae-Chyun Chen, Dylan J. Taylor, William T. Harvey, Glennis A. Logsdon, Dan Meng, Junfeng Shi, Rajiv C. McCoy, Michael C. Schatz, Weidong Li…
    Citation: Genome Biology 2023 24:157
  4. Sequencing has revealed hundreds of millions of human genetic variants, and continued efforts will only add to this variant avalanche. Insufficient information exists to interpret the effects of most variants,...

    Authors: Douglas M. Fowler, David J. Adams, Anna L. Gloyn, William C. Hahn, Debora S. Marks, Lara A. Muffley, James T. Neal, Frederick P. Roth, Alan F. Rubin, Lea M. Starita and Matthew E. Hurles
    Citation: Genome Biology 2023 24:147
  5. Prime editing is limited by low efficiency in plants. Here, we develop an upgraded engineered plant prime editor in hexaploid wheat, ePPEplus, by introducing a V223A substitution into reverse transcriptase in ...

    Authors: Pei Ni, Yidi Zhao, Ximeng Zhou, Zehua Liu, Zhengwei Huang, Zhongfu Ni, Qixin Sun and Yuan Zong
    Citation: Genome Biology 2023 24:156
  6. The ring-shaped cohesin complex is an important factor for the formation of chromatin loops and topologically associating domains (TADs) by loop extrusion. However, the regulation of association between cohesi...

    Authors: Yuao Sun, Xin Xu, Wenxue Zhao, Yu Zhang, Keyang Chen, Yongzheng Li, Xiaotian Wang, Mengling Zhang, Boxin Xue, Wanting Yu, Yingping Hou, Chaobin Wang, Wei Xie, Cheng Li, Daochun Kong, Shu Wang…
    Citation: Genome Biology 2023 24:155
  7. Deep learning models such as convolutional neural networks (CNNs) excel in genomic tasks but lack interpretability. We introduce ExplaiNN, which combines the expressiveness of CNNs with the interpretability of...

    Authors: Gherman Novakovsky, Oriol Fornes, Manu Saraswat, Sara Mostafavi and Wyeth W. Wasserman
    Citation: Genome Biology 2023 24:154
  8. A large-scale application of the “stacked modeling” approach for chromatin state discovery previously provides a single “universal” chromatin state annotation of the human genome based jointly on data from many c...

    Authors: Ha Vu and Jason Ernst
    Citation: Genome Biology 2023 24:153
  9. Platelets and erythrocytes constitute over 95% of all hematopoietic stem cell output. However, the clonal dynamics of HSC contribution to these lineages remains largely unexplored.

    Authors: Edyta E. Wojtowicz, Jayna J. Mistry, Vladimir Uzun, Charlotte Hellmich, Anita Scoones, Desmond W. Chin, Laura M. Kettyle, Francesca Grasso, Allegra M. Lord, David J. Wright, Graham J. Etherington, Petter S. Woll, Mirjam E. Belderbos, Kristian M. Bowles, Claus Nerlov, Wilfried Haerty…
    Citation: Genome Biology 2023 24:152
  10. Human papillomavirus (HPV) drives almost all cervical cancers and up to 70% of head and neck cancers. Frequent integration into the host genome occurs predominantly in tumorigenic types of HPV. We hypothesize ...

    Authors: Mehran Karimzadeh, Christopher Arlidge, Ariana Rostami, Mathieu Lupien, Scott V. Bratman and Michael M. Hoffman
    Citation: Genome Biology 2023 24:142
  11. The pathophysiological causes of kidney disease are not fully understood. Here we show that the integration of genome-wide genetic, transcriptomic, and proteomic association studies can nominate causal determi...

    Authors: Pascal Schlosser, Jingning Zhang, Hongbo Liu, Aditya L. Surapaneni, Eugene P. Rhee, Dan E. Arking, Bing Yu, Eric Boerwinkle, Paul A. Welling, Nilanjan Chatterjee, Katalin Susztak, Josef Coresh and Morgan E. Grams
    Citation: Genome Biology 2023 24:150
  12. Variability of gene expression due to stochasticity of transcription or variation of extrinsic signals, termed biological noise, is a potential driving force of cellular differentiation. Utilizing single-cell ...

    Authors: Reyna Edith Rosales-Alvarez, Jasmin Rettkowski, Josip Stefan Herman, Gabrijela Dumbović, Nina Cabezas-Wallscheid and Dominic Grün
    Citation: Genome Biology 2023 24:148
  13. The efficiency of homology-directed repair (HDR) plays a crucial role in the development of animal models and gene therapy. We demonstrate that microhomology-mediated end-joining (MMEJ) constitutes a substanti...

    Authors: Hongyu Chen, Xingchen Liu, Lanxin Li, Qingtong Tan, Shiyan Li, Li Li, Chunyang Li, Jiqiang Fu, Yong Lu, Yan Wang, Yidi Sun, Zhen-Ge Luo, Zongyang Lu, Qiang Sun and Zhen Liu
    Citation: Genome Biology 2023 24:146
  14. The CRISPR/Cas12a and CRISPR/Cas13d systems are widely used for fundamental research and hold great potential for future clinical applications. However, the short half-life of guide RNAs (gRNAs), particularly ...

    Authors: Xin Zhang, Xinlong Wang, Jie Lv, Hongxin Huang, Jiahong Wang, Ma Zhuo, Zhihong Tan, Guanjie Huang, Jiawei Liu, Yuchen Liu, Mengrao Li, Qixiao Lin, Lian Li, Shufeng Ma, Tao Huang, Ying Lin…
    Citation: Genome Biology 2023 24:145
  15. Phylogenetic trees based on copy number profiles from multiple samples of a patient are helpful to understand cancer evolution. Here, we develop a new maximum likelihood method, CNETML, to infer phylogenies fr...

    Authors: Bingxin Lu, Kit Curtius, Trevor A. Graham, Ziheng Yang and Chris P. Barnes
    Citation: Genome Biology 2023 24:144
  16. Seed oil content is an important agronomic trait of Brassica napus (B. napus), and metabolites are considered as the bridge between genotype and phenotype for physical traits.

    Authors: Long Li, Zhitao Tian, Jie Chen, Zengdong Tan, Yuting Zhang, Hu Zhao, Xiaowei Wu, Xuan Yao, Weiwei Wen, Wei Chen and Liang Guo
    Citation: Genome Biology 2023 24:141
  17. In droplet-based single-cell and single-nucleus RNA-seq experiments, not all reads associated with one cell barcode originate from the encapsulated cell. Such background noise is attributed to spillage from ce...

    Authors: Philipp Janssen, Zane Kliesmete, Beate Vieth, Xian Adiconis, Sean Simmons, Jamie Marshall, Cristin McCabe, Holger Heyn, Joshua Z. Levin, Wolfgang Enard and Ines Hellmann
    Citation: Genome Biology 2023 24:140
  18. The Bovine Pangenome Consortium (BPC) is an international collaboration dedicated to the assembly of cattle genomes to develop a more complete representation of cattle genomic diversity. The goal of the BPC is...

    Authors: Timothy P. L. Smith, Derek M. Bickhart, Didier Boichard, Amanda J. Chamberlain, Appolinaire Djikeng, Yu Jiang, Wai Y. Low, Hubert Pausch, Sebastian Demyda-Peyrás, James Prendergast, Robert D. Schnabel and Benjamin D. Rosen
    Citation: Genome Biology 2023 24:139
  19. 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
  20. 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, Jeffrey A. Bilmes and Christina S. Leslie
    Citation: Genome Biology 2023 24:134

    The Author Correction to this article has been published in Genome Biology 2024 25:132

  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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

    The Author Correction to this article has been published in Genome Biology 2024 25:50

  39. 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

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