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  1. Clustering is a critical component of single-cell RNA sequencing (scRNA-seq) data analysis and can help reveal cell types and infer cell lineages. Despite considerable successes, there are few methods tailored...

    Authors: Yang Li, Mingcong Wu, Shuangge Ma and Mengyun Wu
    Citation: Genome Biology 2023 24:208
  2. Comparative gene expression studies in apes are fundamentally limited by the challenges associated with sampling across different tissues. Here, we used single-cell RNA sequencing of embryoid bodies to collect...

    Authors: Kenneth A. Barr, Katherine L. Rhodes and Yoav Gilad
    Citation: Genome Biology 2023 24:207
  3. Resolving complex genomic regions rich in segmental duplications (SDs) is challenging due to the high error rate of long-read sequencing. Here, we describe a targeted approach with a novel genome assembler Pha...

    Authors: Barbara Poszewiecka, Krzysztof Gogolewski, Justyna A. Karolak, Paweł Stankiewicz and Anna Gambin
    Citation: Genome Biology 2023 24:205
  4. Various computational approaches have been developed to annotate epigenomes on a per-position basis by modeling combinatorial and spatial patterns within epigenomic data. However, such annotations are less sui...

    Authors: Artur Jaroszewicz and Jason Ernst
    Citation: Genome Biology 2023 24:203
  5. Quantitative proteomics is an indispensable tool in life science research. However, there is a lack of reference materials for evaluating the reproducibility of label-free liquid chromatography-tandem mass spe...

    Authors: Sha Tian, Dongdong Zhan, Ying Yu, Yunzhi Wang, Mingwei Liu, Subei Tan, Yan Li, Lei Song, Zhaoyu Qin, Xianju Li, Yang Liu, Yao Li, Shuhui Ji, Shanshan Wang, Yuanting Zheng, Fuchu He…
    Citation: Genome Biology 2023 24:202
  6. Batch effects are notoriously common technical variations in multiomics data and may result in misleading outcomes if uncorrected or over-corrected. A plethora of batch-effect correction algorithms are propose...

    Authors: Ying Yu, Naixin Zhang, Yuanbang Mai, Luyao Ren, Qiaochu Chen, Zehui Cao, Qingwang Chen, Yaqing Liu, Wanwan Hou, Jingcheng Yang, Huixiao Hong, Joshua Xu, Weida Tong, Lianhua Dong, Leming Shi, Xiang Fang…
    Citation: Genome Biology 2023 24:201
  7. Complex traits, such as growth and fitness, are typically controlled by a very large number of variants, which can interact in both additive and non-additive fashion. In an attempt to gauge the relative import...

    Authors: Wei Yuan, Fiona Beitel, Thanvi Srikant, Ilja Bezrukov, Sabine Schäfer, Robin Kraft and Detlef Weigel
    Citation: Genome Biology 2023 24:200
  8. Cancer patients can achieve dramatic responses to chemotherapy yet retain resistant tumor cells, which ultimately results in relapse. Although xenograft model studies have identified several cellular and molec...

    Authors: Yongping Zhang, Shuting Jiang, Fuhong He, Yuanyuan Tian, Haiyang Hu, Li Gao, Lin Zhang, Aili Chen, Yixin Hu, Liyan Fan, Chun Yang, Bi Zhou, Dan Liu, Zihan Zhou, Yanxun Su, Lei Qin…
    Citation: Genome Biology 2023 24:199
  9. The Fe (II)- and α-ketoglutarate-dependent AlkB family dioxygenases are implicated in nucleotide demethylation. AlkB homolog1 (ALKBH1) is shown to demethylate DNA adenine methylation (6mA) preferentially from ...

    Authors: Qingxiao Jia, Xinran Zhang, Qian Liu, Junjie Li, Wentao Wang, Xuan Ma, Bo Zhu, Sheng Li, Shicheng Gong, Jingjing Tian, Meng Yuan, Yu Zhao and Dao-Xiu Zhou
    Citation: Genome Biology 2023 24:198
  10. Large-scale genotype–phenotype association studies of crop germplasm are important for identifying alleles associated with favorable traits. The limited number of single-nucleotide polymorphisms (SNPs) in most...

    Authors: Yangyang Liu, Jun Chen, Changbin Yin, Ziying Wang, He Wu, Kuocheng Shen, Zhiliang Zhang, Lipeng Kang, Song Xu, Aoyue Bi, Xuebo Zhao, Daxing Xu, Zhonghu He, Xueyong Zhang, Chenyang Hao, Jianhui Wu…
    Citation: Genome Biology 2023 24:196
  11. In humans, muscle-invasive bladder cancer (MIBC) is highly aggressive and associated with a poor prognosis. With a high mutation load and large number of altered genes, strategies to delineate key driver event...

    Authors: Kim Wong, Federico Abascal, Latasha Ludwig, Heike Aupperle-Lellbach, Julia Grassinger, Colin W. Wright, Simon J. Allison, Emma Pinder, Roger M. Phillips, Laura P. Romero, Arnon Gal, Patrick J. Roady, Isabel Pires, Franco Guscetti, John S. Munday, Maria C. Peleteiro…
    Citation: Genome Biology 2023 24:191
  12. Dimensionality reduction summarizes the complex transcriptomic landscape of single-cell datasets for downstream analyses. Current approaches favor large cellular populations defined by many genes, at the expen...

    Authors: Benjamin DeMeo and Bonnie Berger
    Citation: Genome Biology 2023 24:195

    The Protocol to this article has been published in Nature Protocols 2024 :s41596-024-00991-3

  13. Somatic embryogenesis is a major process for plant regeneration. However, cell communication and the gene regulatory network responsible for cell reprogramming during somatic embryogenesis are still largely un...

    Authors: Xiangqian Zhu, Zhongping Xu, Guanying Wang, Yulong Cong, Lu Yu, Ruoyu Jia, Yuan Qin, Guangyu Zhang, Bo Li, Daojun Yuan, Lili Tu, Xiyan Yang, Keith Lindsey, Xianlong Zhang and Shuangxia Jin
    Citation: Genome Biology 2023 24:194

    The Author Correction to this article has been published in Genome Biology 2023 24:210

  14. As one of the most common malignancies, esophageal cancer has two subtypes, squamous cell carcinoma and adenocarcinoma, arising from distinct cells-of-origin. Distinguishing cell-type-specific molecular featur...

    Authors: Yueyuan Zheng, Benjamin Ziman, Allen S. Ho, Uttam K. Sinha, Li-Yan Xu, En-Min Li, H Phillip Koeffler, Benjamin P. Berman and De-Chen Lin
    Citation: Genome Biology 2023 24:193
  15. Hundreds of functional genomic screens have been performed across a diverse set of cancer contexts, as part of efforts such as the Cancer Dependency Map, to identify gene dependencies—genes whose loss of funct...

    Authors: J. Michael Krill-Burger, Joshua M. Dempster, Ashir A. Borah, Brenton R. Paolella, David E. Root, Todd R. Golub, Jesse S. Boehm, William C. Hahn, James M. McFarland, Francisca Vazquez and Aviad Tsherniak
    Citation: Genome Biology 2023 24:192
  16. Cell-type composition is an important indicator of health. We present Guided Topic Model for deconvolution (GTM-decon) to automatically infer cell-type-specific gene topic distributions from single-cell RNA-se...

    Authors: Lakshmipuram Seshadri Swapna, Michael Huang and Yue Li
    Citation: Genome Biology 2023 24:190
  17. The binding of transcription factors at proximal promoters and distal enhancers is central to gene regulation. Identifying regulatory motifs and quantifying their impact on expression remains challenging. Usin...

    Authors: Jacob Hepkema, Nicholas Keone Lee, Benjamin J. Stewart, Siwat Ruangroengkulrith, Varodom Charoensawan, Menna R. Clatworthy and Martin Hemberg
    Citation: Genome Biology 2023 24:189
  18. MHC-I-associated peptides deriving from non-coding genomic regions and mutations can generate tumor-specific antigens, including neoantigens. Quantifying tumor-specific antigens’ RNA expression in malignant an...

    Authors: Maria Virginia Ruiz Cuevas, Marie-Pierre Hardy, Jean-David Larouche, Anca Apavaloaei, Eralda Kina, Krystel Vincent, Patrick Gendron, Jean-Philippe Laverdure, Chantal Durette, Pierre Thibault, Sébastien Lemieux, Claude Perreault and Grégory Ehx
    Citation: Genome Biology 2023 24:188
  19. The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 × data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and ...

    Authors: Jennifer R. S. Meadows, Jeffrey M. Kidd, Guo-Dong Wang, Heidi G. Parker, Peter Z. Schall, Matteo Bianchi, Matthew J. Christmas, Katia Bougiouri, Reuben M. Buckley, Christophe Hitte, Anthony K. Nguyen, Chao Wang, Vidhya Jagannathan, Julia E. Niskanen, Laurent A. F. Frantz, Meharji Arumilli…
    Citation: Genome Biology 2023 24:187

    The Author Correction to this article has been published in Genome Biology 2023 24:255

  20. Existing single nucleotide polymorphism (SNP) genotyping algorithms do not scale for species with thousands of sequenced strains, nor do they account for conspecific redundancy. Here we present a bioinformatic...

    Authors: Zhou Jason Shi, Stephen Nayfach and Katherine S. Pollard
    Citation: Genome Biology 2023 24:186
  21. Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is an increasingly popular technique to map genome-wide binding profiles of histone modifications, transcription factors, and co-factors. The ENCODE ...

    Authors: Anna Nordin, Gianluca Zambanini, Pierfrancesco Pagella and Claudio Cantù
    Citation: Genome Biology 2023 24:185
  22. Existing single-cell RNA sequencing (scRNA-seq) methods rely on reverse transcription (RT) and second-strand synthesis (SSS) to convert single-stranded RNA into double-stranded DNA prior to amplification, with...

    Authors: Jun Lyu and Chongyi Chen
    Citation: Genome Biology 2023 24:184
  23. Genetic variation in the human genome is a major determinant of individual disease risk, but the vast majority of missense variants have unknown etiological effects. Here, we present a robust learning framewor...

    Authors: Milind Jagota, Chengzhong Ye, Carlos Albors, Ruchir Rastogi, Antoine Koehl, Nilah Ioannidis and Yun S. Song
    Citation: Genome Biology 2023 24:182
  24. Although spatial organization of compartments and topologically associating domains at large scale is relatively well studied, the spatial organization of regulatory elements at fine scale is poorly understood...

    Authors: Li Deng, Qiangwei Zhou, Jie Zhou, Qing Zhang, Zhibo Jia, Guangfeng Zhu, Sheng Cheng, Lulu Cheng, Caijun Yin, Chao Yang, Jinxiong Shen, Junwei Nie, Jian-Kang Zhu, Guoliang Li and Lun Zhao
    Citation: Genome Biology 2023 24:181
  25. We present RBPNet, a novel deep learning method, which predicts CLIP-seq crosslink count distribution from RNA sequence at single-nucleotide resolution. By training on up to a million regions, RBPNet achieves ...

    Authors: Marc Horlacher, Nils Wagner, Lambert Moyon, Klara Kuret, Nicolas Goedert, Marco Salvatore, Jernej Ule, Julien Gagneur, Ole Winther and Annalisa Marsico
    Citation: Genome Biology 2023 24:180
  26. Asian rice is one of the world’s most widely cultivated crops. Large-scale resequencing analyses have been undertaken to explore the domestication and de-domestication genomic history of Asian rice, but the ev...

    Authors: Dongya Wu, Lingjuan Xie, Yanqing Sun, Yujie Huang, Lei Jia, Chenfeng Dong, Enhui Shen, Chu-Yu Ye, Qian Qian and Longjiang Fan
    Citation: Genome Biology 2023 24:179
  27. Differential gene expression in bulk transcriptomics data can reflect change of transcript abundance within a cell type and/or change in the proportions of cell types. Expression deconvolution methods can help...

    Authors: Saba Ghaffari, Kelly J. Bouchonville, Ehsan Saleh, Remington E. Schmidt, Steven M. Offer and Saurabh Sinha
    Citation: Genome Biology 2023 24:178
  28. RNA profiling technologies at single-cell resolutions, including single-cell and single-nuclei RNA sequencing (scRNA-seq and snRNA-seq, scnRNA-seq for short), can help characterize the composition of tissues a...

    Authors: Francisco Avila Cobos, Mohammad Javad Najaf Panah, Jessica Epps, Xiaochen Long, Tsz-Kwong Man, Hua-Sheng Chiu, Elad Chomsky, Evgeny Kiner, Michael J. Krueger, Diego di Bernardo, Luis Voloch, Jan Molenaar, Sander R. van Hooff, Frank Westermann, Selina Jansky, Michele L. Redell…
    Citation: Genome Biology 2023 24:177
  29. Pinpointing genetic impacts on DNA methylation can improve our understanding of pathways that underlie gene regulation and disease risk.

    Authors: Sergio Villicaña, Juan Castillo-Fernandez, Eilis Hannon, Colette Christiansen, Pei-Chien Tsai, Jane Maddock, Diana Kuh, Matthew Suderman, Christine Power, Caroline Relton, George Ploubidis, Andrew Wong, Rebecca Hardy, Alissa Goodman, Ken K. Ong and Jordana T. Bell
    Citation: Genome Biology 2023 24:176
  30. We propose a statistical framework ISLET to infer individual-specific and cell-type-specific transcriptome reference panels. ISLET models the repeatedly measured bulk gene expression data, to optimize the usag...

    Authors: Hao Feng, Guanqun Meng, Tong Lin, Hemang Parikh, Yue Pan, Ziyi Li, Jeffrey Krischer and Qian Li
    Citation: Genome Biology 2023 24:174
  31. The appearance of Slavs in East-Central Europe has been the subject of an over 200-year debate driven by two conflicting hypotheses. The first assumes that Slavs came to the territory of contemporary Poland no...

    Authors: Ireneusz Stolarek, Michal Zenczak, Luiza Handschuh, Anna Juras, Malgorzata Marcinkowska-Swojak, Anna Spinek, Artur Dębski, Marzena Matla, Hanna Kóčka-Krenz, Janusz Piontek and Marek Figlerowicz
    Citation: Genome Biology 2023 24:173
  32. Metachromatic leukodystrophy (MLD) is a lysosomal storage disorder caused by mutations in the arylsulfatase A gene (ARSA) and categorized into three subtypes according to age of onset. The functional effect of mo...

    Authors: Marena Trinidad, Xinying Hong, Steven Froelich, Jessica Daiker, James Sacco, Hong Phuc Nguyen, Madelynn Campagna, Dean Suhr, Teryn Suhr, Jonathan H. LeBowitz, Michael H. Gelb and Wyatt T. Clark
    Citation: Genome Biology 2023 24:172
  33. Although long-read RNA-seq is increasingly applied to characterize full-length transcripts it can also enable detection of nucleotide variants, such as genetic mutations or RNA editing sites, which is signific...

    Authors: Zhiheng Liu, Giovanni Quinones-Valdez, Ting Fu, Elaine Huang, Mudra Choudhury, Fairlie Reese, Ali Mortazavi and Xinshu Xiao
    Citation: Genome Biology 2023 24:171
  34. Structural variant (SV) calling belongs to the standard tools of modern bioinformatics for identifying and describing alterations in genomes. Initially, this work presents several complex genomic rearrangement...

    Authors: Markus Schmidt and Arne Kutzner
    Citation: Genome Biology 2023 24:170
  35. Sequence alignments are the foundations of life science research, but most innovation so far focuses on optimal alignments, while information derived from suboptimal solutions is ignored. We argue that one opt...

    Authors: Andreas Grigorjew, Artur Gynter, Fernando H. C. Dias, Benjamin Buchfink, Hajk-Georg Drost and Alexandru I. Tomescu
    Citation: Genome Biology 2023 24:168
  36. In this manuscript, we introduce and benchmark Mandalorion v4.1 for the identification and quantification of full-length transcriptome sequencing reads. It further improves upon the already strong performance ...

    Authors: Roger Volden, Kayla D. Schimke, Ashley Byrne, Danilo Dubocanin, Matthew Adams and Christopher Vollmers
    Citation: Genome Biology 2023 24:167
  37. The oocyte-to-embryo transition (OET) converts terminally differentiated gametes into a totipotent embryo and is critically controlled by maternal mRNAs and proteins, while the genome is silent until zygotic g...

    Authors: Hongmei Zhang, Shuyan Ji, Ke Zhang, Yuling Chen, Jia Ming, Feng Kong, Lijuan Wang, Shun Wang, Zhuoning Zou, Zhuqing Xiong, Kai Xu, Zili Lin, Bo Huang, Ling Liu, Qiang Fan, Suoqin Jin…
    Citation: Genome Biology 2023 24:166
  38. Detecting allelic imbalance at the isoform level requires accounting for inferential uncertainty, caused by multi-mapping of RNA-seq reads. Our proposed method, SEESAW, uses Salmon and Swish to offer analysis ...

    Authors: Euphy Y. Wu, Noor P. Singh, Kwangbom Choi, Mohsen Zakeri, Matthew Vincent, Gary A. Churchill, Cheryl L. Ackert-Bicknell, Rob Patro and Michael I. Love
    Citation: Genome Biology 2023 24:165
  39. DNA methylation signatures are usually based on multivariate approaches that require hundreds of sites for predictions. Here, we propose a computational framework named CimpleG for the detection of small CpG m...

    Authors: Tiago Maié, Marco Schmidt, Myriam Erz, Wolfgang Wagner and Ivan G. Costa
    Citation: Genome Biology 2023 24:161
  40. 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
  41. 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

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