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  1. Copy number variation (CNV) is a key genetic characteristic for cancer diagnostics and can be used as a biomarker for the selection of therapeutic treatments. Using data sets established in our previous study,...

    Authors: Daniall Masood, Luyao Ren, Cu Nguyen, Francesco G. Brundu, Lily Zheng, Yongmei Zhao, Erich Jaeger, Yong Li, Seong Won Cha, Aaron Halpern, Sean Truong, Michael Virata, Chunhua Yan, Qingrong Chen, Andy Pang, Reyes Alberto…
    Citation: Genome Biology 2024 25:163
  2. The functional coupling between alternative pre-mRNA splicing (AS) and the mRNA quality control mechanism called nonsense-mediated decay (NMD) can modulate transcript abundance. Previous studies have identifie...

    Authors: Anna Zhuravskaya, Karen Yap, Fursham Hamid and Eugene V. Makeyev
    Citation: Genome Biology 2024 25:162
  3. Neuroblastoma is a common pediatric cancer, where preclinical studies suggest that a mesenchymal-like gene expression program contributes to chemotherapy resistance. However, clinical outcomes remain poor, imp...

    Authors: Richard H. Chapple, Xueying Liu, Sivaraman Natarajan, Margaret I. M. Alexander, Yuna Kim, Anand G. Patel, Christy W. LaFlamme, Min Pan, William C. Wright, Hyeong-Min Lee, Yinwen Zhang, Meifen Lu, Selene C. Koo, Courtney Long, John Harper, Chandra Savage…
    Citation: Genome Biology 2024 25:161
  4. Methylation-based liquid biopsies show promises in detecting cancer using circulating cell-free DNA; however, current limitations impede clinical application. Most assays necessitate substantial DNA inputs, po...

    Authors: Xiao-Long Cui, Ji Nie, Houxiang Zhu, Krissana Kowitwanich, Alana V. Beadell, Diana C. West-Szymanski, Zhou Zhang, Urszula Dougherty, Akushika Kwesi, Zifeng Deng, Yan Li, Danqing Meng, Kevin Roggin, Teresa Barry, Ryan Owyang, Ben Fefferman…
    Citation: Genome Biology 2024 25:157
  5. Genetic changes that modify the function of transcriptional enhancers have been linked to the evolution of biological diversity across species. Multiple studies have focused on the role of nucleotide substitut...

    Authors: Acadia A. Kocher, Emily V. Dutrow, Severin Uebbing, Kristina M. Yim, María F. Rosales Larios, Marybeth Baumgartner, Timothy Nottoli and James P. Noonan
    Citation: Genome Biology 2024 25:156
  6. Genomic data holds huge potential for medical progress but requires strict safety measures due to its sensitive nature to comply with data protection laws. This conflict is especially pronounced in genome-wide...

    Authors: Alissa Brauneck, Louisa Schmalhorst, Stefan Weiss, Linda Baumbach, Uwe Völker, David Ellinghaus, Jan Baumbach and Gabriele Buchholtz
    Citation: Genome Biology 2024 25:154

    The Author Correction to this article has been published in Genome Biology 2024 25:160

  7. Protein folding has become a tractable problem with the significant advances in deep learning-driven protein structure prediction. Here we propose FoldPAthreader, a protein folding pathway prediction method th...

    Authors: Kailong Zhao, Pengxin Zhao, Suhui Wang, Yuhao Xia and Guijun Zhang
    Citation: Genome Biology 2024 25:152
  8. Deconvolution methods infer quantitative cell type estimates from bulk measurement of mixed samples including blood and tissue. DNA methylation sequencing measures multiple CpGs per read, but few existing deco...

    Authors: Irene Unterman, Dana Avrahami, Efrat Katsman, Triche Tim Jr., Benjamin Glaser and Benjamin P. Berman
    Citation: Genome Biology 2024 25:151
  9. Cancer is a complex disease composing systemic alterations in multiple scales. In this study, we develop the Tumor Multi-Omics pre-trained Network (TMO-Net) that integrates multi-omics pan-cancer datasets for ...

    Authors: Feng-ao Wang, Zhenfeng Zhuang, Feng Gao, Ruikun He, Shaoting Zhang, Liansheng Wang, Junwei Liu and Yixue Li
    Citation: Genome Biology 2024 25:149
  10. Sheep and goats have undergone domestication and improvement to produce similar phenotypes, which have been greatly impacted by structural variants (SVs). Here, we report a high-quality chromosome-level refere...

    Authors: Ji Yang, Dong-Feng Wang, Jia-Hui Huang, Qiang-Hui Zhu, Ling-Yun Luo, Ran Lu, Xing-Long Xie, Hosein Salehian-Dehkordi, Ali Esmailizadeh, George E. Liu and Meng-Hua Li
    Citation: Genome Biology 2024 25:148
  11. Current clustering analysis of spatial transcriptomics data primarily relies on molecular information and fails to fully exploit the morphological features present in histology images, leading to compromised a...

    Authors: Xi Jiang, Shidan Wang, Lei Guo, Bencong Zhu, Zhuoyu Wen, Liwei Jia, Lin Xu, Guanghua Xiao and Qiwei Li
    Citation: Genome Biology 2024 25:147
  12. DNA methylation is an important epigenetic modification which has numerous roles in modulating genome function. Its levels are spatially correlated across the genome, typically high in repressed regions but lo...

    Authors: Martina Rimoldi, Ning Wang, Jilin Zhang, Diego Villar, Duncan T. Odom, Jussi Taipale, Paul Flicek and Maša Roller
    Citation: Genome Biology 2024 25:146
  13. Single-cell RNA sequencing (scRNA-seq) and spatially resolved transcriptomics (SRT) have led to groundbreaking advancements in life sciences. To develop bioinformatics tools for scRNA-seq and SRT data and perf...

    Authors: Hongrui Duo, Yinghong Li, Yang Lan, Jingxin Tao, Qingxia Yang, Yingxue Xiao, Jing Sun, Lei Li, Xiner Nie, Xiaoxi Zhang, Guizhao Liang, Mingwei Liu, Youjin Hao and Bo Li
    Citation: Genome Biology 2024 25:145
  14. Like its parent base 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) is a direct epigenetic modification of cytosines in the context of CpG dinucleotides. 5hmC is the most abundant oxidized form of 5mC,...

    Authors: Edahi Gonzalez-Avalos, Atsushi Onodera, Daniela Samaniego-Castruita, Anjana Rao and Ferhat Ay
    Citation: Genome Biology 2024 25:142
  15. Variation in X chromosome inactivation (XCI) in human-induced pluripotent stem cells (hiPSCs) can impact their ability to model biological sex biases. The gene-wise landscape of X chromosome gene dosage remain...

    Authors: Hande Topa, Clara Benoit-Pilven, Taru Tukiainen and Olli Pietiläinen
    Citation: Genome Biology 2024 25:144
  16. Targeted therapies exploiting vulnerabilities of cancer cells hold promise for improving patient outcome and reducing side-effects of chemotherapy. However, efficacy of precision therapies is limited in part b...

    Authors: Alena Malyukova, Mari Lahnalampi, Ton Falqués-Costa, Petri Pölönen, Mikko Sipola, Juha Mehtonen, Susanna Teppo, Karen Akopyan, Johanna Viiliainen, Olli Lohi, Anna K. Hagström-Andersson, Merja Heinäniemi and Olle Sangfelt
    Citation: Genome Biology 2024 25:143
  17. Reproductive isolation can result from adaptive processes (e.g., ecological speciation and mutation-order speciation) or stochastic processes such as “system drift” model. Ecological speciation predicts barrie...

    Authors: Sheng-Kai Hsu, Wei-Yun Lai, Johannes Novak, Felix Lehner, Ana Marija Jakšić, Elisabetta Versace and Christian Schlötterer
    Citation: Genome Biology 2024 25:141
  18. RNA-binding proteins (RBPs) regulate key aspects of RNA processing including alternative splicing, mRNA degradation and localization by physically binding RNA molecules. Current methods to map these interactio...

    Authors: Sophie Hawkins, Alexandre Mondaini, Seema C. Namboori, Grady G. Nguyen, Gene W. Yeo, Asif Javed and Akshay Bhinge
    Citation: Genome Biology 2024 25:140
  19. Weeds are attractive models for basic and applied research due to their impacts on agricultural systems and capacity to swiftly adapt in response to anthropogenic selection pressures. Currently, a lack of geno...

    Authors: Jacob Montgomery, Sarah Morran, Dana R. MacGregor, J. Scott McElroy, Paul Neve, Célia Neto, Martin M. Vila-Aiub, Maria Victoria Sandoval, Analia I. Menéndez, Julia M. Kreiner, Longjiang Fan, Ana L. Caicedo, Peter J. Maughan, Bianca Assis Barbosa Martins, Jagoda Mika, Alberto Collavo…
    Citation: Genome Biology 2024 25:139
  20. Deep mutational scanning (DMS) measures the effects of thousands of genetic variants in a protein simultaneously. The small sample size renders classical statistical methods ineffective. For example, p-values can...

    Authors: Jingyou Rao, Ruiqi Xin, Christian Macdonald, Matthew K. Howard, Gabriella O. Estevam, Sook Wah Yee, Mingsen Wang, James S. Fraser, Willow Coyote-Maestas and Harold Pimentel
    Citation: Genome Biology 2024 25:138
  21. In droplet-based single-cell and single-nucleus RNA-seq assays, systematic contamination of ambient RNA molecules biases the quantification of gene expression levels. Existing methods correct the contamination...

    Authors: Weijian Wang, Yihui Cen, Zezhen Lu, Yueqing Xu, Tianyi Sun, Ying Xiao, Wanlu Liu, Jingyi Jessica Li and Chaochen Wang
    Citation: Genome Biology 2024 25:136
  22. Dilated cardiomyopathy (DCM) is one of the most common causes of heart failure. Multiple identified mutations in nexilin (NEXN) have been suggested to be linked with severe DCM. However, the exact association ...

    Authors: Yanjiao Shao, Canzhao Liu, Hsin-Kai Liao, Ran Zhang, Baolei Yuan, Hanyan Yang, Ronghui Li, Siting Zhu, Xi Fang, Concepcion Rodriguez Esteban, Ju Chen and Juan Carlos Izpisua Belmonte
    Citation: Genome Biology 2024 25:135
  23. The marsupial specific RSX lncRNA is the functional analogue of the eutherian specific XIST, which coordinates X chromosome inactivation. We characterized the RSX interactome in a marsupial representative (the op...

    Authors: Kim L. McIntyre, Shafagh A. Waters, Ling Zhong, Gene Hart-Smith, Mark Raftery, Zahra A. Chew, Hardip R. Patel, Jennifer A. Marshall Graves and Paul D. Waters
    Citation: Genome Biology 2024 25:134
  24. High-efficiency prime editing (PE) is desirable for precise genome manipulation. The activity of mammalian PE systems can be largely improved by inhibiting DNA mismatch repair by coexpressing a dominant-negati...

    Authors: Xiaoshuang Liu, Dongfang Gu, Yiru Zhang, Yingli Jiang, Zhi Xiao, Rongfang Xu, Ruiying Qin, Juan Li and Pengcheng Wei
    Citation: Genome Biology 2024 25:131
  25. Bulk DNA sequencing of multiple samples from the same tumor is becoming common, yet most methods to infer copy-number aberrations (CNAs) from this data analyze individual samples independently. We introduce HA...

    Authors: Matthew A. Myers, Brian J. Arnold, Vineet Bansal, Metin Balaban, Katelyn M. Mullen, Simone Zaccaria and Benjamin J. Raphael
    Citation: Genome Biology 2024 25:130
  26. Authors: Jonathan P. Bradfeld, Rachel L. Kember, Anna Ulrich, Zhanna Balkhiyarova, Akram Alyass, Izzuddin M. Aris, Joshua A. Bell, K. Alaine Broadaway, Zhanghua Chen, Jin-Fang Chai, Neil M. Davies, Dietmar Fernandez-Orth, Mariona Bustamante, Ruby Fore, Amitavo Ganguli, Anni Heiskala…
    Citation: Genome Biology 2024 25:129

    The original article was published in Genome Biology 2024 25:22

  27. Cellular iron homeostasis is regulated by iron regulatory proteins (IRP1 and IRP2) that sense iron levels (and other metabolic cues) and modulate mRNA translation or stability via interaction with iron regulat...

    Authors: Hima Priyanka Nadimpalli, Georgia Katsioudi, Enes Salih Arpa, Lies Chikhaoui, Alaaddin Bulak Arpat, Angelica Liechti, Gaël Palais, Claudia Tessmer, Ilse Hofmann, Bruno Galy and David Gatfield
    Citation: Genome Biology 2024 25:128
  28. Gene regulatory network (GRN) models that are formulated as ordinary differential equations (ODEs) can accurately explain temporal gene expression patterns and promise to yield new insights into important cell...

    Authors: Intekhab Hossain, Viola Fanfani, Jonas Fischer, John Quackenbush and Rebekka Burkholz
    Citation: Genome Biology 2024 25:127
  29. DNA replication progression can be affected by the presence of physical barriers like the RNA polymerases, leading to replication stress and DNA damage. Nonetheless, we do not know how transcription influences...

    Authors: Patricia Rojas, Jianming Wang, Giovanni Guglielmi, Martina Mustè Sadurnì, Lucas Pavlou, Geoffrey Ho Duen Leung, Vijay Rajagopal, Fabian Spill and Marco Saponaro
    Citation: Genome Biology 2024 25:126
  30. Vision depends on the interplay between photoreceptor cells of the neural retina and the underlying retinal pigment epithelium (RPE). Most genes involved in inherited retinal diseases display specific spatiote...

    Authors: Eva D’haene, Víctor López-Soriano, Pedro Manuel Martínez-García, Soraya Kalayanamontri, Alfredo Dueñas Rey, Ana Sousa-Ortega, Silvia Naranjo, Stijn Van de Sompele, Lies Vantomme, Quinten Mahieu, Sarah Vergult, Ana Neto, José Luis Gómez-Skarmeta, Juan Ramón Martínez-Morales, Miriam Bauwens, Juan Jesús Tena…
    Citation: Genome Biology 2024 25:123
  31. Pluripotent states of embryonic stem cells (ESCs) with distinct transcriptional profiles affect ESC differentiative capacity and therapeutic potential. Although single-cell RNA sequencing has revealed addition...

    Authors: Niannian Li, Kairang Jin, Bin Liu, Mingzhu Yang, PanPan Shi, Dai Heng, Jichang Wang and Lin Liu
    Citation: Genome Biology 2024 25:122
  32. Genomic regions that remain poorly understood, often referred to as the dark genome, contain a variety of functionally relevant and biologically informative features. These include endogenous viral elements (E...

    Authors: Daniel Blanco-Melo, Matthew A. Campbell, Henan Zhu, Tristan P. W. Dennis, Sejal Modha, Spyros Lytras, Joseph Hughes, Anna Gatseva and Robert J. Gifford
    Citation: Genome Biology 2024 25:120
  33. The precision-recall curve (PRC) and the area under the precision-recall curve (AUPRC) are useful for quantifying classification performance. They are commonly used in situations with imbalanced classes, such ...

    Authors: Wenyu Chen, Chen Miao, Zhenghao Zhang, Cathy Sin-Hang Fung, Ran Wang, Yizhen Chen, Yan Qian, Lixin Cheng, Kevin Y. Yip, Stephen Kwok-Wing Tsui and Qin Cao
    Citation: Genome Biology 2024 25:118
  34. Preeclampsia, one of the most lethal pregnancy-related diseases, is associated with the disruption of uterine spiral artery remodeling during placentation. However, the early molecular events leading to preecl...

    Authors: Xiaoli Gong, Wei He, Wan Jin, Hongwei Ma, Gang Wang, Jiaxin Li, Yu Xiao, Yangyu Zhao, Qiong Chen, Huanhuan Guo, Jiexia Yang, Yiming Qi, Wei Dong, Meng Fu, Xiaojuan Li, Jiusi Liu…
    Citation: Genome Biology 2024 25:117
  35. Structural variations (SVs) have significant impacts on complex phenotypes by rearranging large amounts of DNA sequence.

    Authors: Liu Yang, Hongwei Yin, Lijing Bai, Wenye Yao, Tan Tao, Qianyi Zhao, Yahui Gao, Jinyan Teng, Zhiting Xu, Qing Lin, Shuqi Diao, Zhangyuan Pan, Dailu Guan, Bingjie Li, Huaijun Zhou, Zhongyin Zhou…
    Citation: Genome Biology 2024 25:116
  36. In dinoflagellates, a unique and extremely divergent genomic and nuclear organization has evolved. The highly unusual features of dinoflagellate nuclei and genomes include permanently condensed liquid crystall...

    Authors: Georgi K. Marinov, Xinyi Chen, Matthew P. Swaffer, Tingting Xiang, Arthur R. Grossman and William J. Greenleaf
    Citation: Genome Biology 2024 25:115

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