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  1. The evolution of genomic regulatory regions plays a critical role in shaping the diversity of life. While this process is primarily sequence-dependent, the enormous complexity of biological systems complicates...

    Authors: Samuel Khodursky, Eric B. Zheng, Nicolas Svetec, Sylvia M. Durkin, Sigi Benjamin, Alice Gadau, Xia Wu and Li Zhao
    Citation: Genome Biology 2023 24:232
  2. Malaria remains one of the deadliest infectious diseases. Transcriptional regulation effects of noncoding variants in this unusual genome of malaria parasites remain elusive. We developed a sequence-based, ab ...

    Authors: Chengqi Wang, Yibo Dong, Chang Li, Jenna Oberstaller, Min Zhang, Justin Gibbons, Camilla Valente Pires, Mianli Xiao, Lei Zhu, Rays H. Y. Jiang, Kami Kim, Jun Miao, Thomas D. Otto, Liwang Cui, John H. Adams and Xiaoming Liu
    Citation: Genome Biology 2023 24:231
  3. The increasing availability of multidimensional phenotypic data in large cohorts of genotyped individuals requires efficient methods to identify genetic effects on multiple traits. Permutational multivariate a...

    Authors: Diego Garrido-Martín, Miquel Calvo, Ferran Reverter and Roderic Guigó
    Citation: Genome Biology 2023 24:230
  4. Existing methods to detect tumor signal in liquid biopsy have focused on the analysis of nuclear cell-free DNA (cfDNA). However, non-nuclear cfDNA and in particular mitochondrial DNA (mtDNA) has been understud...

    Authors: Ymke van der Pol, Norbert Moldovan, Jip Ramaker, Sanne Bootsma, Kristiaan J. Lenos, Louis Vermeulen, Shahneen Sandhu, Idris Bahce, D. Michiel Pegtel, Stephen Q. Wong, Sarah-Jane Dawson, Dineika Chandrananda and Florent Mouliere
    Citation: Genome Biology 2023 24:229
  5. Clustering molecular data into informative groups is a primary step in extracting robust conclusions from big data. However, due to foundational issues in how they are defined and detected, such clusters are n...

    Authors: Chris Gaiteri, David R. Connell, Faraz A. Sultan, Artemis Iatrou, Bernard Ng, Boleslaw K. Szymanski, Ada Zhang and Shinya Tasaki
    Citation: Genome Biology 2023 24:228
  6. In several eukaryotes, DNA methylation occurs within the coding regions of many genes, termed gene body methylation (GbM). Whereas the role of DNA methylation on the silencing of transposons and repetitive DNA...

    Authors: Clara J. Williams, Dawei Dai, Kevin A. Tran, J. Grey Monroe and Ben P. Williams
    Citation: Genome Biology 2023 24:227
  7. The gut microbiota plays a crucial role in regulating host metabolism and producing uremic toxins in patients with end-stage renal disease (ESRD). Our objective is to advance toward a holistic understanding of...

    Authors: Pan Zhang, Xifan Wang, Shenghui Li, Xuesen Cao, Jianzhou Zou, Yi Fang, Yiqin Shi, Fangfang Xiang, Bo Shen, Yixuan Li, Bing Fang, Yue Zhang, Ruochun Guo, Qingbo Lv, Liwen Zhang, Yufei Lu…
    Citation: Genome Biology 2023 24:226
  8. Application of the widely used droplet-based microfluidic technologies in single-cell sequencing often yields doublets, introducing bias to downstream analyses. Especially, doublet-detection methods for single...

    Authors: Wenhao Zhang, Rui Jiang, Shengquan Chen and Ying Wang
    Citation: Genome Biology 2023 24:225
  9. Despite clear evidence of nonlinear interactions in the molecular architecture of polygenic diseases, linear models have so far appeared optimal in genotype-to-phenotype modeling. A key bottleneck for such mod...

    Authors: Nora Verplaetse, Antoine Passemiers, Adam Arany, Yves Moreau and Daniele Raimondi
    Citation: Genome Biology 2023 24:224
  10. Crop pangenomes made from individual cultivar assemblies promise easy access to conserved genes, but genome content variability and inconsistent identifiers hamper their exploration. To address this, we define...

    Authors: Bruno Contreras-Moreira, Shradha Saraf, Guy Naamati, Ana M. Casas, Sandeep S. Amberkar, Paul Flicek, Andrew R. Jones and Sarah Dyer
    Citation: Genome Biology 2023 24:223
  11. DNA barcodes enable Oxford Nanopore sequencing to sequence multiple barcoded DNA samples on a single flow cell. DNA sequences with the same barcode need to be grouped together through demultiplexing. As the nu...

    Authors: Renmin Han, Junhai Qi, Yang Xue, Xiujuan Sun, Fa Zhang, Xin Gao and Guojun Li
    Citation: Genome Biology 2023 24:222
  12. Genomic benchmark datasets are essential to driving the field of genomics and bioinformatics. They provide a snapshot of the performances of sequencing technologies and analytical methods and highlight future ...

    Authors: Sina Majidian, Daniel Paiva Agustinho, Chen-Shan Chin, Fritz J. Sedlazeck and Medhat Mahmoud
    Citation: Genome Biology 2023 24:221
  13. We describe MCProj—an algorithm for analyzing query scRNA-seq data by projections over reference single-cell atlases. We represent the reference as a manifold of annotated metacell gene expression distribution...

    Authors: Oren Ben-Kiki, Akhiad Bercovich, Aviezer Lifshitz, Ofir Raz, Dror Brook and Amos Tanay
    Citation: Genome Biology 2023 24:220
  14. Interactive graphical genome browsers are essential tools in genomics, but they do not contain all the recent genome assemblies. We create Genome Archive (GenArk) collection of UCSC Genome Browsers from NCBI a...

    Authors: Hiram Clawson, Brian T. Lee, Brian J. Raney, Galt P. Barber, Jonathan Casper, Mark Diekhans, Clay Fischer, Jairo Navarro Gonzalez, Angie S. Hinrichs, Christopher M. Lee, Luis R. Nassar, Gerardo Perez, Brittney Wick, Daniel Schmelter, Matthew L. Speir, Joel Armstrong…
    Citation: Genome Biology 2023 24:217
  15. Oxidation Resistance 1 (OXR1) gene is a highly conserved gene of the TLDc domain-containing family. OXR1 is involved in fundamental biological and cellular processes, including DNA damage response, antioxidant pa...

    Authors: Xiaolin Lin, Wei Wang, Mingyi Yang, Nadirah Damseh, Mirta Mittelstedt Leal de Sousa, Fadi Jacob, Anna Lång, Elise Kristiansen, Marco Pannone, Miroslava Kissova, Runar Almaas, Anna Kuśnierczyk, Richard Siller, Maher Shahrour, Motee Al-Ashhab, Bassam Abu-Libdeh…
    Citation: Genome Biology 2023 24:216
  16. Dominance and other non-additive genetic effects arise from the interaction between alleles, and historically these phenomena play a major role in quantitative genetics. However, most genome-wide association s...

    Authors: Leilei Cui, Bin Yang, Shijun Xiao, Jun Gao, Amelie Baud, Delyth Graham, Martin McBride, Anna Dominiczak, Sebastian Schafer, Regina Lopez Aumatell, Carme Mont, Albert Fernandez Teruel, Norbert Hübner, Jonathan Flint, Richard Mott and Lusheng Huang
    Citation: Genome Biology 2023 24:215
  17. Recovering metagenome-assembled genomes (MAGs) from shotgun sequencing data is an increasingly common task in microbiome studies, as MAGs provide deeper insight into the functional potential of both culturable...

    Authors: Pauline Trinh, David S. Clausen and Amy D. Willis
    Citation: Genome Biology 2023 24:214
  18. In birds, sex is genetically determined; however, the molecular mechanism is not well-understood. The avian Z sex chromosome (chrZ) lacks whole chromosome inactivation, in contrast to the mammalian chrX. To in...

    Authors: Ruslan Deviatiiarov, Hiroki Nagai, Galym Ismagulov, Anastasia Stupina, Kazuhiro Wada, Shinji Ide, Noriyuki Toji, Heng Zhang, Woranop Sukparangsi, Sittipon Intarapat, Oleg Gusev and Guojun Sheng
    Citation: Genome Biology 2023 24:213
  19. Single-cell sequencing provides detailed insights into biological processes including cell differentiation and identity. While providing deep cell-specific information, the method suffers from technical constr...

    Authors: Fabian Hausmann, Can Ergen, Robin Khatri, Mohamed Marouf, Sonja Hänzelmann, Nicola Gagliani, Samuel Huber, Pierre Machart and Stefan Bonn
    Citation: Genome Biology 2023 24:212
  20. Structural variations (SVs) in individual genomes are major determinants of complex traits, including adaptability to environmental variables. The Mongolian and Hainan cattle breeds in East Asia are of taurine...

    Authors: Xiaoting Xia, Fengwei Zhang, Shuang Li, Xiaoyu Luo, Lixin Peng, Zheng Dong, Hubert Pausch, Alexander S. Leonard, Danang Crysnanto, Shikang Wang, Bin Tong, Johannes A. Lenstra, Jianlin Han, Fuyong Li, Tieshan Xu, Lihong Gu…
    Citation: Genome Biology 2023 24:211
  21. 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 24:210

    The original article was published in Genome Biology 2023 24:194

  22. Identifying spatially variable genes (SVGs) is a key step in the analysis of spatially resolved transcriptomics data. SVGs provide biological insights by defining transcriptomic differences within tissues, whi...

    Authors: Natalie Charitakis, Agus Salim, Adam T. Piers, Kevin I. Watt, Enzo R. Porrello, David A. Elliott and Mirana Ramialison
    Citation: Genome Biology 2023 24:209
  23. 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
  24. 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
  25. In Arabidopsis, RNA Polymerase II (Pol II) often pauses within a few hundred base pairs downstream of the polyadenylation site, reflecting efficient transcriptional termination, but how such pausing is regulat...

    Authors: Sixian Zhou, Fengli Zhao, Danling Zhu, Qiqi Zhang, Ziwei Dai and Zhe Wu
    Citation: Genome Biology 2023 24:206
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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

  36. 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

  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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

  43. 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
  44. 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
  45. 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

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