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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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

  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. Single-cell technologies offer insights into molecular feature distributions, but comparing them poses challenges. We propose a kernel-testing framework for non-linear cell-wise distribution comparison, analyz...

    Authors: A. Ozier-Lafontaine, C. Fourneaux, G. Durif, P. Arsenteva, C. Vallot, O. Gandrillon, S. Gonin-Giraud, B. Michel and F. Picard
    Citation: Genome Biology 2024 25:114
  19. Untranslated regions (UTRs) are important mediators of post-transcriptional regulation. The length of UTRs and the composition of regulatory elements within them are known to vary substantially across genes, b...

    Authors: Nechama Wieder, Elston N. D’Souza, Alexandra C. Martin-Geary, Frederik H. Lassen, Jonathan Talbot-Martin, Maria Fernandes, Sonia P. Chothani, Owen J. L. Rackham, Sebastian Schafer, Julie L. Aspden, Daniel G. MacArthur, Robert W. Davies and Nicola Whiffin
    Citation: Genome Biology 2024 25:111
  20. Metazoans inherited genes from unicellular ancestors that perform essential biological processes such as cell division, metabolism, and protein translation. Multicellularity requires careful control and coordi...

    Authors: Anna S. Trigos, Felicia Bongiovanni, Yangyi Zhang, Maia Zethoven, Richard Tothill, Richard Pearson, Anthony T. Papenfuss and David L. Goode
    Citation: Genome Biology 2024 25:110
  21. Single-cell multiplexing techniques (cell hashing and genetic multiplexing) combine multiple samples, optimizing sample processing and reducing costs. Cell hashing conjugates antibody-tags or chemical-oligonuc...

    Authors: Fabiola Curion, Xichen Wu, Lukas Heumos, Mylene Mariana Gonzales André, Lennard Halle, Matiss Ozols, Melissa Grant-Peters, Charlotte Rich-Griffin, Hing-Yuen Yeung, Calliope A. Dendrou, Herbert B. Schiller and Fabian J. Theis
    Citation: Genome Biology 2024 25:109
  22. Prime editing enables precise base substitutions, insertions, and deletions at targeted sites without the involvement of double-strand DNA breaks or exogenous donor DNA templates. However, the large size of pr...

    Authors: Shuangshuang Mu, Huangyao Chen, Qianru Li, Shixue Gou, Xiaoyi Liu, Junwei Wang, Wei Zheng, Menglong Chen, Qin Jin, Liangxue Lai, Kepin Wang and Hui Shi
    Citation: Genome Biology 2024 25:108
  23. Long-read sequencing data, particularly those derived from the Oxford Nanopore sequencing platform, tend to exhibit high error rates. Here, we present NextDenovo, an efficient error correction and assembly too...

    Authors: Jiang Hu, Zhuo Wang, Zongyi Sun, Benxia Hu, Adeola Oluwakemi Ayoola, Fan Liang, Jingjing Li, José R. Sandoval, David N. Cooper, Kai Ye, Jue Ruan, Chuan-Le Xiao, Depeng Wang, Dong-Dong Wu and Sheng Wang
    Citation: Genome Biology 2024 25:107
  24. The proliferation antigen Ki-67 has been widely used in clinical settings for cancer staging for many years, but investigations on its biological functions have lagged. Recently, Ki-67 has been shown to regula...

    Authors: Konstantinos Stamatiou, Florentin Huguet, Lukas V. Serapinas, Christos Spanos, Juri Rappsilber and Paola Vagnarelli
    Citation: Genome Biology 2024 25:105
  25. Single-cell sequencing datasets are key in biology and medicine for unraveling insights into heterogeneous cell populations with unprecedented resolution. Here, we construct a single-cell multi-omics map of hu...

    Authors: Lu Pan, Paolo Parini, Roman Tremmel, Joseph Loscalzo, Volker M. Lauschke, Bradley A. Maron, Paola Paci, Ingemar Ernberg, Nguan Soon Tan, Zehuan Liao, Weiyao Yin, Sundararaman Rengarajan and Xuexin Li
    Citation: Genome Biology 2024 25:104
  26. Splicing factors are vital for the regulation of RNA splicing, but some have also been implicated in regulating transcription. The underlying molecular mechanisms of their involvement in transcriptional proces...

    Authors: Xian Du, Wenying Qin, Chunyu Yang, Lin Dai, Mingkui San, Yingdan Xia, Siyu Zhou, Mengyang Wang, Shuang Wu, Shaorui Zhang, Huiting Zhou, Fangshu Li, Fang He, Jingfeng Tang, Jia-Yu Chen, Yu Zhou…
    Citation: Genome Biology 2024 25:102
  27. Multiplexed assays of variant effect (MAVEs) have emerged as a powerful approach for interrogating thousands of genetic variants in a single experiment. The flexibility and widespread adoption of these techniq...

    Authors: Melina Claussnitzer, Victoria N. Parikh, Alex H. Wagner, Jeremy A. Arbesfeld, Carol J. Bult, Helen V. Firth, Lara A. Muffley, Alex N. Nguyen Ba, Kevin Riehle, Frederick P. Roth, Daniel Tabet, Benedetta Bolognesi, Andrew M. Glazer and Alan F. Rubin
    Citation: Genome Biology 2024 25:100
  28. Spatial molecular data has transformed the study of disease microenvironments, though, larger datasets pose an analytics challenge prompting the direct adoption of single-cell RNA-sequencing tools including no...

    Authors: Dharmesh D. Bhuva, Chin Wee Tan, Agus Salim, Claire Marceaux, Marie A. Pickering, Jinjin Chen, Malvika Kharbanda, Xinyi Jin, Ning Liu, Kristen Feher, Givanna Putri, Wayne D. Tilley, Theresa E. Hickey, Marie-Liesse Asselin-Labat, Belinda Phipson and Melissa J. Davis
    Citation: Genome Biology 2024 25:99
  29. Amino acid substitutions can perturb protein activity in multiple ways. Understanding their mechanistic basis may pinpoint how residues contribute to protein function. Here, we characterize the mechanisms unde...

    Authors: Sarah Gersing, Thea K. Schulze, Matteo Cagiada, Amelie Stein, Frederick P. Roth, Kresten Lindorff-Larsen and Rasmus Hartmann-Petersen
    Citation: Genome Biology 2024 25:98
  30. As most viruses remain uncultivated, metagenomics is currently the main method for virus discovery. Detecting viruses in metagenomic data is not trivial. In the past few years, many bioinformatic virus identif...

    Authors: Ling-Yi Wu, Yasas Wijesekara, Gonçalo J. Piedade, Nikolaos Pappas, Corina P. D. Brussaard and Bas E. Dutilh
    Citation: Genome Biology 2024 25:97
  31. We present a non-parametric statistical method called TDEseq that takes full advantage of smoothing splines basis functions to account for the dependence of multiple time points in scRNA-seq studies, and uses ...

    Authors: Yue Fan, Lei Li and Shiquan Sun
    Citation: Genome Biology 2024 25:96
  32. Aneuploidy, an abnormal number of chromosomes within a cell, is a hallmark of cancer. Patterns of aneuploidy differ across cancers, yet are similar in cancers affecting closely related tissues. The selection p...

    Authors: Juman Jubran, Rachel Slutsky, Nir Rozenblum, Lior Rokach, Uri Ben-David and Esti Yeger-Lotem
    Citation: Genome Biology 2024 25:95
  33. Recent innovations in single-cell RNA-sequencing (scRNA-seq) provide the technology to investigate biological questions at cellular resolution. Pooling cells from multiple individuals has become a common strat...

    Authors: Drew Neavin, Anne Senabouth, Himanshi Arora, Jimmy Tsz Hang Lee, Aida Ripoll-Cladellas, Lude Franke, Shyam Prabhakar, Chun Jimmie Ye, Davis J. McCarthy, Marta Melé, Martin Hemberg and Joseph E. Powell
    Citation: Genome Biology 2024 25:94
  34. Unraveling bacterial gene function drives progress in various areas, such as food production, pharmacology, and ecology. While omics technologies capture high-dimensional phenotypic data, linking them to genom...

    Authors: Thomas Roder, Grégory Pimentel, Pascal Fuchsmann, Mireille Tena Stern, Ueli von Ah, Guy Vergères, Stephan Peischl, Ola Brynildsrud, Rémy Bruggmann and Cornelia Bär
    Citation: Genome Biology 2024 25:93
  35. Although sequencing technologies have boosted the measurement of the genomic diversity of plant crops, it remains challenging to accurately genotype millions of genetic variants, especially structural variatio...

    Authors: Ze-Zhen Du, Jia-Bao He and Wen-Biao Jiao
    Citation: Genome Biology 2024 25:91
  36. Single-cell ATAC-seq has emerged as a powerful approach for revealing candidate cis-regulatory elements genome-wide at cell-type resolution. However, current single-cell methods suffer from limited throughput ...

    Authors: Xuan Zhang, Alexandre P. Marand, Haidong Yan and Robert J. Schmitz
    Citation: Genome Biology 2024 25:90
  37. Inferring gene regulatory networks (GRNs) from single-cell data is challenging due to heuristic limitations. Existing methods also lack estimates of uncertainty. Here we present Probabilistic Matrix Factorizat...

    Authors: Claudia Skok Gibbs, Omar Mahmood, Richard Bonneau and Kyunghyun Cho
    Citation: Genome Biology 2024 25:88

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