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  1. A key step for comparative genomics is to group open reading frames into functionally and evolutionarily meaningful gene clusters. Gene clustering is complicated by intraspecific duplications and horizontal ge...

    Authors: Saioa Manzano-Morales, Yang Liu, Sara González-Bodí, Jaime Huerta-Cepas and Jaime Iranzo
    Citation: Genome Biology 2023 24:250
  2. The high mutation rate throughout the entire melanoma genome presents a major challenge in stratifying true driver events from the background mutations. Numerous recurrent non-coding alterations, such as those...

    Authors: Zhao Wang, Menghan Luo, Qian Liang, Ke Zhao, Yuelin Hu, Wei Wang, Xiangling Feng, Bolang Hu, Jianjin Teng, Tianyi You, Ran Li, Zhengkai Bao, Wenhao Pan, Tielong Yang, Chao Zhang, Ting Li…
    Citation: Genome Biology 2023 24:248
  3. RNA velocity analysis of single cells offers the potential to predict temporal dynamics from gene expression. In many systems, RNA velocity has been observed to produce a vector field that qualitatively reflec...

    Authors: Shijie C. Zheng, Genevieve Stein-O’Brien, Leandros Boukas, Loyal A. Goff and Kasper D. Hansen
    Citation: Genome Biology 2023 24:246
  4. The Quartet Data Portal facilitates community access to well-characterized reference materials, reference datasets, and related resources established based on a family of four individuals with identical twins ...

    Authors: Jingcheng Yang, Yaqing Liu, Jun Shang, Qiaochu Chen, Qingwang Chen, Luyao Ren, Naixin Zhang, Ying Yu, Zhihui Li, Yueqiang Song, Shengpeng Yang, Andreas Scherer, Weida Tong, Huixiao Hong, Wenming Xiao, Leming Shi…
    Citation: Genome Biology 2023 24:245
  5. The endogenous adenosine deaminases acting on RNA (ADAR) have been harnessed to facilitate precise adenosine-to-inosine editing on RNAs. However, the practicability of this approach for therapeutic purposes is...

    Authors: Zongyi Yi, Yanxia Zhao, Zexuan Yi, Yongjian Zhang, Gangbin Tang, Xiaoxue Zhang, Huixian Tang, Wei Zhang, Ying Zhao, Huayuan Xu, Yuyang Nie, Xueqing Sun, Lijun Xing, Lian Dai, Pengfei Yuan and Wensheng Wei
    Citation: Genome Biology 2023 24:243
  6. Analysis of microbial data from archaeological samples is a growing field with great potential for understanding ancient environments, lifestyles, and diseases. However, high error rates have been a challenge ...

    Authors: Zoé Pochon, Nora Bergfeldt, Emrah Kırdök, Mário Vicente, Thijessen Naidoo, Tom van der Valk, N. Ezgi Altınışık, Maja Krzewińska, Love Dalén, Anders Götherström, Claudio Mirabello, Per Unneberg and Nikolay Oskolkov
    Citation: Genome Biology 2023 24:242
  7. Properly integrating spatially resolved transcriptomics (SRT) generated from different batches into a unified gene-spatial coordinate system could enable the construction of a comprehensive spatial transcripto...

    Authors: Tiantian Guo, Zhiyuan Yuan, Yan Pan, Jiakang Wang, Fengling Chen, Michael Q. Zhang and Xiangyu Li
    Citation: Genome Biology 2023 24:241
  8. Single-cell gene expression profiling provides unique opportunities to understand tumor heterogeneity and the tumor microenvironment. Because of cost and feasibility, profiling bulk tumors remains the primary ...

    Authors: Ariel A. Hippen, Dalia K. Omran, Lukas M. Weber, Euihye Jung, Ronny Drapkin, Jennifer A. Doherty, Stephanie C. Hicks and Casey S. Greene
    Citation: Genome Biology 2023 24:239
  9. Single-cell RNA-sequencing (scRNA-seq) technologies enable the capture of gene expression heterogeneity and consequently facilitate the study of cell-to-cell variability at the cell type level. Although differ...

    Authors: Huiwen Zheng, Jan Vijg, Atefeh Taherian Fard and Jessica Cara Mar
    Citation: Genome Biology 2023 24:238
  10. Technologies to study localized host–pathogen interactions are urgently needed. Here, we present a spatial transcriptomics approach to simultaneously capture host and pathogen transcriptome-wide spatial gene e...

    Authors: Hailey Sounart, Enikő Lázár, Yuvarani Masarapu, Jian Wu, Tibor Várkonyi, Tibor Glasz, András Kiss, Erik Borgström, Andrew Hill, Sefanit Rezene, Soham Gupta, Aleksandra Jurek, Anezka Niesnerová, Henrik Druid, Olaf Bergmann and Stefania Giacomello
    Citation: Genome Biology 2023 24:237
  11. Parts-based representations, such as non-negative matrix factorization and topic modeling, have been used to identify structure from single-cell sequencing data sets, in particular structure that is not as wel...

    Authors: Peter Carbonetto, Kaixuan Luo, Abhishek Sarkar, Anthony Hung, Karl Tayeb, Sebastian Pott and Matthew Stephens
    Citation: Genome Biology 2023 24:236
  12. When analyzing data from in situ RNA detection technologies, cell segmentation is an essential step in identifying cell boundaries, assigning RNA reads to cells, and studying the gene expression and morphologi...

    Authors: Yuxing Wang, Wenguan Wang, Dongfang Liu, Wenpin Hou, Tianfei Zhou and Zhicheng Ji
    Citation: Genome Biology 2023 24:235
  13. Xenobiotics are primarily metabolized by hepatocytes in the liver, and primary human hepatocytes are the gold standard model for the assessment of drug efficacy, safety, and toxicity in the early phases of dru...

    Authors: Eva Sanchez-Quant, Maria Lucia Richter, Maria Colomé-Tatché and Celia Pilar Martinez-Jimenez
    Citation: Genome Biology 2023 24:234
  14. We define and identify a new class of control genes for next-generation sequencing called total RNA expression genes (TREGs), which correlate with total RNA abundance in cell types of different sizes and trans...

    Authors: Louise A. Huuki-Myers, Kelsey D. Montgomery, Sang Ho Kwon, Stephanie C. Page, Stephanie C. Hicks, Kristen R. Maynard and Leonardo Collado-Torres
    Citation: Genome Biology 2023 24:233
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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

  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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
  44. 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
  45. 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

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