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  1. Recent advances in microscopy have enabled studying chromosome organization at the single-molecule level, yet little is known about inherited chromosome organization. Here we adapt single-molecule chromosome t...

    Authors: Silvia Gutnik, Jia Emil You, Ahilya N. Sawh, Aude Andriollo and Susan E. Mango
    Citation: Genome Biology 2024 25:71
  2. Extensive research has been conducted on fruit development in crops, but the metabolic regulatory networks underlying perennial fruit trees remain poorly understood. To address this knowledge gap, we conduct a...

    Authors: Chao Gu, Mao-Song Pei, Zhi-Hua Guo, Lei Wu, Kai-Jie Qi, Xue-Ping Wang, Hong Liu, Zhongchi Liu, Zhaobo Lang and Shaoling Zhang
    Citation: Genome Biology 2024 25:70
  3. Long-read sequencing can enable the detection of base modifications, such as CpG methylation, in single molecules of DNA. The most commonly used methods for long-read sequencing are nanopore developed by Oxfor...

    Authors: Brynja D. Sigurpalsdottir, Olafur A. Stefansson, Guillaume Holley, Doruk Beyter, Florian Zink, Marteinn Þ. Hardarson, Sverrir Þ. Sverrisson, Nina Kristinsdottir, Droplaug N. Magnusdottir, Olafur Þ. Magnusson, Daniel F. Gudbjartsson, Bjarni V. Halldorsson and Kari Stefansson
    Citation: Genome Biology 2024 25:69
  4. In rheumatoid arthritis (RA), the activation of T and B cell clones specific for self-antigens leads to the chronic inflammation of the synovium. Here, we perform an in-depth quantitative analysis of the seven...

    Authors: Adrià Aterido, María López-Lasanta, Francisco Blanco, Antonio Juan-Mas, María Luz García-Vivar, Alba Erra, Carolina Pérez-García, Simón Ángel Sánchez-Fernández, Raimon Sanmartí, Antonio Fernández-Nebro, Mercedes Alperi-López, Jesús Tornero, Ana María Ortiz, Carlos Marras Fernández-Cid, Núria Palau, Wenjing Pan…
    Citation: Genome Biology 2024 25:68
  5. Bromo-adjacent homology-plant homeodomain domain containing protein 1 (BP1) is a reader of histone post-translational modifications in fungi. BP1 recognizes trimethylation of lysine 27 in histone H3 (H3K27me3)...

    Authors: Guangfei Tang, Haoxue Xia, Yufei Huang, Yuanwen Guo, Yun Chen, Zhonghua Ma and Wende Liu
    Citation: Genome Biology 2024 25:67
  6. Oncometabolites, often generated as a result of a gene mutation, show pro-oncogenic function when abnormally accumulated in cancer cells. Identification of such mutation-associated metabolites will facilitate ...

    Authors: GaRyoung Lee, Sang Mi Lee, Sungyoung Lee, Chang Wook Jeong, Hyojin Song, Sang Yup Lee, Hongseok Yun, Youngil Koh and Hyun Uk Kim
    Citation: Genome Biology 2024 25:66
  7. Tumors are able to acquire new capabilities, including traits such as drug resistance and metastasis that are associated with unfavorable clinical outcomes. Single-cell technologies have made it possible to st...

    Authors: Jae-Won Cho, Jingyi Cao and Martin Hemberg
    Citation: Genome Biology 2024 25:65
  8. The function of diverse ruminal microbes is tightly linked to rumen development and host physiology. The system of ruminal microbes is an excellent model to clarify the fundamental ecological relationships amo...

    Authors: Daming Sun, Gaorui Bian, Kai Zhang, Ning Liu, Yuyang Yin, Yuanlong Hou, Fei Xie, Weiyun Zhu, Shengyong Mao and Junhua Liu
    Citation: Genome Biology 2024 25:64
  9. Centromeres are critical for maintaining genomic stability in eukaryotes, and their turnover shapes genome architectures and drives karyotype evolution. However, the co-evolution of centromeres from different ...

    Authors: Chuanye Chen, Siying Wu, Yishuang Sun, Jingwei Zhou, Yiqian Chen, Jing Zhang, James A. Birchler, Fangpu Han, Ning Yang and Handong Su
    Citation: Genome Biology 2024 25:63
  10. Cancer cells often exhibit DNA copy number aberrations and can vary widely in their ploidy. Correct estimation of the ploidy of single-cell genomes is paramount for downstream analysis. Based only on single-ce...

    Authors: Michael P. Schneider, Amy E. Cullen, Justina Pangonyte, Jason Skelton, Harvey Major, Elke Van Oudenhove, Maria J. Garcia, Blas Chaves Urbano, Anna M. Piskorz, James D. Brenton, Geoff Macintyre and Florian Markowetz
    Citation: Genome Biology 2024 25:62
  11. Tartary buckwheat, Fagopyrum tataricum, is a pseudocereal crop with worldwide distribution and high nutritional value. However, the origin and domestication history of this crop remain to be elucidated.

    Authors: Yuqi He, Kaixuan Zhang, Yaliang Shi, Hao Lin, Xu Huang, Xiang Lu, Zhirong Wang, Wei Li, Xibo Feng, Taoxiong Shi, Qingfu Chen, Junzhen Wang, Yu Tang, Mark A. Chapman, Mateja Germ, Zlata Luthar…
    Citation: Genome Biology 2024 25:61
  12. Assembled genome sequences are being generated at an exponential rate. Here we present FCS-GX, part of NCBI’s Foreign Contamination Screen (FCS) tool suite, optimized to identify and remove contaminant sequenc...

    Authors: Alexander Astashyn, Eric S. Tvedte, Deacon Sweeney, Victor Sapojnikov, Nathan Bouk, Victor Joukov, Eyal Mozes, Pooja K. Strope, Pape M. Sylla, Lukas Wagner, Shelby L. Bidwell, Larissa C. Brown, Karen Clark, Emily W. Davis, Brian Smith-White, Wratko Hlavina…
    Citation: Genome Biology 2024 25:60
  13. CRISPR/Cas-derived base editor enables precise editing of target sites and has been widely used for basic research and crop genetic improvement. However, the editing efficiency of base editors at different tar...

    Authors: Guanying Wang, Fuqiu Wang, Zhongping Xu, Ying Wang, Can Zhang, Yi Zhou, Fengjiao Hui, Xiyan Yang, Xinhui Nie, Xianlong Zhang and Shuangxia Jin
    Citation: Genome Biology 2024 25:59
  14. Recent developments in auxin-inducible degron (AID) technology have increased its popularity for chemogenetic control of proteolysis. However, generation of human AID cell lines is challenging, especially in h...

    Authors: Shiqian Li, Yafei Wang, Miesje van der Stoel, Xin Zhou, Shrinidhi Madhusudan, Kristiina Kanerva, Van Dien Nguyen, Nazli Eskici, Vesa M. Olkkonen, You Zhou, Taneli Raivio and Elina Ikonen
    Citation: Genome Biology 2024 25:58
  15. A critical challenge of single-cell spatial transcriptomics (sc-ST) technologies is their panel size. Being based on fluorescence in situ hybridization, they are typically limited to panels of about a thousand...

    Authors: Mashrur Ahmed Yafi, Md. Hasibul Husain Hisham, Francisco Grisanti, James F. Martin, Atif Rahman and Md. Abul Hassan Samee
    Citation: Genome Biology 2024 25:57
  16. RNA secondary structure (RSS) can influence the regulation of transcription, RNA processing, and protein synthesis, among other processes. 3′ untranslated regions (3′ UTRs) of mRNA also hold the key for many a...

    Authors: Tianru Zhang, Changhao Li, Jiaying Zhu, Yanjun Li, Zhiye Wang, Chun-Yip Tong, Yu Xi, Yi Han, Hisashi Koiwa, Xu Peng and Xiuren Zhang
    Citation: Genome Biology 2024 25:54
  17. The FokI catalytic domain can be fused to various DNA binding architectures to improve the precision of genome editing tools. However, evaluation of off-target effects is essential for developing these tools. ...

    Authors: Long Xie, Hu Feng, Zhifang Li, Di Li, Xiali Yang, Tanglong Yuan, Nana Yan, Chenfei He, Jitan Zheng, Zhenrui Zuo, Yaxuan Zheng, Yaqi Cao, Yangqing Lu, Xing Yao Xiong and Erwei Zuo
    Citation: Genome Biology 2024 25:51
  18. Nanopore sequencing generates noisy electrical signals that need to be converted into a standard string of DNA nucleotide bases using a computational step called basecalling. The performance of basecalling has...

    Authors: Gagandeep Singh, Mohammed Alser, Kristof Denolf, Can Firtina, Alireza Khodamoradi, Meryem Banu Cavlak, Henk Corporaal and Onur Mutlu
    Citation: Genome Biology 2024 25:49
  19. N6-methyladenosine (m6A) is the most abundant mRNA modification, and controls mRNA stability. m6A distribution varies considerably between and within species. Yet, it is unclear to what extent this variability...

    Authors: Ran Shachar, David Dierks, Miguel Angel Garcia-Campos, Anna Uzonyi, Ursula Toth, Walter Rossmanith and Schraga Schwartz
    Citation: Genome Biology 2024 25:48
  20. Genome-wide ensemble sequencing methods improved our understanding of chromatin organization in eukaryotes but lack the ability to capture single-cell heterogeneity and spatial organization. To overcome these ...

    Authors: Xavier Devos, Jean-Bernard Fiche, Marion Bardou, Olivier Messina, Christophe Houbron, Julian Gurgo, Marie Schaeffer, Markus Götz, Thomas Walter, Florian Mueller and Marcelo Nollmann
    Citation: Genome Biology 2024 25:47
  21. Single-strand breaks are the major DNA damage in the genome and serve a crucial role in various biological processes. To reveal the significance of single-strand breaks, multiple sequencing-based single-strand...

    Authors: Sheng Xu, Junkang Wei, Siqi Sun, Jizhou Zhang, Ting-Fung Chan and Yu Li
    Citation: Genome Biology 2024 25:46
  22. Glioblastoma (GBM) brain tumors lacking IDH1 mutations (IDHwt) have the worst prognosis of all brain neoplasms. Patients receive surgery and chemoradiotherapy but tumors almost always fatally recur.

    Authors: Georgette Tanner, Rhiannon Barrow, Shoaib Ajaib, Muna Al-Jabri, Nazia Ahmed, Steven Pollock, Martina Finetti, Nora Rippaus, Alexander F. Bruns, Khaja Syed, James A. Poulter, Laura Matthews, Thomas Hughes, Erica Wilson, Colin Johnson, Frederick S. Varn…
    Citation: Genome Biology 2024 25:45
  23. The androgen receptor (AR) is a tumor suppressor in estrogen receptor (ER) positive breast cancer, a role sustained in some ER negative breast cancers. Key factors dictating AR genomic activity in a breast con...

    Authors: Leila Hosseinzadeh, Zoya Kikhtyak, Geraldine Laven-Law, Stephen M. Pederson, Caroline G. Puiu, Clive S. D’Santos, Elgene Lim, Jason S. Carroll, Wayne D. Tilley, Amy R. Dwyer and Theresa E. Hickey
    Citation: Genome Biology 2024 25:44
  24. Drug targets with genetic evidence are expected to increase clinical success by at least twofold. Yet, translating disease-associated genetic variants into functional knowledge remains a fundamental challenge ...

    Authors: Celia Alda-Catalinas, Ximena Ibarra-Soria, Christina Flouri, Jorge Esparza Gordillo, Diana Cousminer, Anna Hutchinson, Bin Sun, William Pembroke, Sebastian Ullrich, Adam Krejci, Adrian Cortes, Alison Acevedo, Sunir Malla, Carl Fishwick, Gerard Drewes and Radu Rapiteanu
    Citation: Genome Biology 2024 25:42
  25. Protein function annotation has been one of the longstanding issues in biological sciences, and various computational methods have been developed. However, the existing methods suffer from a serious long-tail ...

    Authors: Lingyan Zheng, Shuiyang Shi, Mingkun Lu, Pan Fang, Ziqi Pan, Hongning Zhang, Zhimeng Zhou, Hanyu Zhang, Minjie Mou, Shijie Huang, Lin Tao, Weiqi Xia, Honglin Li, Zhenyu Zeng, Shun Zhang, Yuzong Chen…
    Citation: Genome Biology 2024 25:41
  26. Pervasive usage of alternative promoters leads to the deregulation of gene expression in carcinogenesis and may drive the emergence of new genes in spermatogenesis. However, little is known regarding the mecha...

    Authors: Elena M. Pugacheva, Dharmendra Nath Bhatt, Samuel Rivero-Hinojosa, Md Tajmul, Liron Fedida, Emma Price, Yon Ji, Dmitri Loukinov, Alexander V. Strunnikov, Bing Ren and Victor V. Lobanenkov
    Citation: Genome Biology 2024 25:40
  27. Expansions of tandem repeats (TRs) cause approximately 60 monogenic diseases. We expect that the discovery of additional pathogenic repeat expansions will narrow the diagnostic gap in many diseases. A growing ...

    Authors: Sarah Fazal, Matt C. Danzi, Isaac Xu, Shilpa Nadimpalli Kobren, Shamil Sunyaev, Chloe Reuter, Shruti Marwaha, Matthew Wheeler, Egor Dolzhenko, Francesca Lucas, Stefan Wuchty, Mustafa Tekin, Stephan Züchner and Vanessa Aguiar-Pulido
    Citation: Genome Biology 2024 25:39
  28. Copy number alterations (CNAs) are among the most important genetic events in cancer, but their detection from sequencing data is challenging because of unknown sample purity, tumor ploidy, and general intra-t...

    Authors: Alice Antonello, Riccardo Bergamin, Nicola Calonaci, Jacob Househam, Salvatore Milite, Marc J. Williams, Fabio Anselmi, Alberto d’Onofrio, Vasavi Sundaram, Alona Sosinsky, William C. H. Cross and Giulio Caravagna
    Citation: Genome Biology 2024 25:38
  29. Sample multiplexing enables pooled analysis during single-cell RNA sequencing workflows, thereby increasing throughput and reducing batch effects. A challenge for all multiplexing techniques is to link sample-...

    Authors: Qin Zhu, Daniel N. Conrad and Zev J. Gartner
    Citation: Genome Biology 2024 25:37
  30. Mosaic loss of Y chromosome (LOY) is the most common chromosomal alteration in aging men. Here, we use single-cell RNA and ATAC sequencing to show that LOY is present in the kidney and increases with age and c...

    Authors: Parker C. Wilson, Amit Verma, Yasuhiro Yoshimura, Yoshiharu Muto, Haikuo Li, Nicole P. Malvin, Eryn E. Dixon and Benjamin D. Humphreys
    Citation: Genome Biology 2024 25:36
  31. Targeted spatial transcriptomics hold particular promise in analyzing complex tissues. Most such methods, however, measure only a limited panel of transcripts, which need to be selected in advance to inform on...

    Authors: Yida Zhang, Viktor Petukhov, Evan Biederstedt, Richard Que, Kun Zhang and Peter V. Kharchenko
    Citation: Genome Biology 2024 25:35
  32. Various laboratory-developed metabolomic methods lead to big challenges in inter-laboratory comparability and effective integration of diverse datasets.

    Authors: Naixin Zhang, Qiaochu Chen, Peipei Zhang, Kejun Zhou, Yaqing Liu, Haiyan Wang, Shumeng Duan, Yongming Xie, Wenxiang Yu, Ziqing Kong, Luyao Ren, Wanwan Hou, Jingcheng Yang, Xiaoyun Gong, Lianhua Dong, Xiang Fang…
    Citation: Genome Biology 2024 25:34
  33. The removal of introns occurs through the splicing of a 5′ splice site (5′ss) with a 3′ splice site (3′ss). These two elements are recognized by distinct components of the spliceosome. However, introns in high...

    Authors: Chaorui Duan, Truman Mooney, Luke Buerer, Cory Bowers, Stephen Rong, Seong Won Kim, Alger M. Fredericks, Sean F. Monaghan and William G. Fairbrother
    Citation: Genome Biology 2024 25:33
  34. Methanomassiliicoccales are a recently identified order of methanogens that are diverse across global environments particularly the gastrointestinal tracts of animals; however, their metabolic capacities are d...

    Authors: Fei Xie, Shengwei Zhao, Xiaoxiu Zhan, Yang Zhou, Yin Li, Weiyun Zhu, Phillip B. Pope, Graeme T. Attwood, Wei Jin and Shengyong Mao
    Citation: Genome Biology 2024 25:32
  35. Centromeres load kinetochore complexes onto chromosomes, which mediate spindle attachment and allow segregation during cell division. Although centromeres perform a conserved cellular function, their underlyin...

    Authors: Joiselle B. Fernandes, Matthew Naish, Qichao Lian, Robin Burns, Andrew J. Tock, Fernando A. Rabanal, Piotr Wlodzimierz, Anette Habring, Robert E. Nicholas, Detlef Weigel, Raphael Mercier and Ian R. Henderson
    Citation: Genome Biology 2024 25:30
  36. Expression quantitative trait loci (eQTL) offer insights into the regulatory mechanisms of trait-associated variants, but their effects often rely on contexts that are unknown or unmeasured. We introduce PICAL...

    Authors: Martijn Vochteloo, Patrick Deelen, Britt Vink, Ellen A. Tsai, Heiko Runz, Sergio Andreu-Sánchez, Jingyuan Fu, Alexandra Zhernakova, Harm-Jan Westra and Lude Franke
    Citation: Genome Biology 2024 25:29
  37. Genetic regulation of gene expression is a complex process, with genetic effects known to vary across cellular contexts such as cell types and environmental conditions. We developed SURGE, a method for unsuper...

    Authors: Benjamin J. Strober, Karl Tayeb, Joshua Popp, Guanghao Qi, M. Grace Gordon, Richard Perez, Chun Jimmie Ye and Alexis Battle
    Citation: Genome Biology 2024 25:28
  38. Existing RNA velocity estimation methods strongly rely on predefined dynamics and cell-agnostic constant transcriptional kinetic rates, assumptions often violated in complex and heterogeneous single-cell RNA s...

    Authors: Haotian Cui, Hassaan Maan, Maria C. Vladoiu, Jiao Zhang, Michael D. Taylor and Bo Wang
    Citation: Genome Biology 2024 25:27
  39. Potato is one of the world’s major staple crops, and like many important crop plants, it has a polyploid genome. Polyploid haplotype assembly poses a major computational challenge. We introduce a novel strateg...

    Authors: Rebecca Serra Mari, Sven Schrinner, Richard Finkers, Freya Maria Rosemarie Ziegler, Paul Arens, Maximilian H.-W. Schmidt, Björn Usadel, Gunnar W. Klau and Tobias Marschall
    Citation: Genome Biology 2024 25:26
  40. CRISPR genome editing approaches theoretically enable researchers to define the function of each human gene in specific cell types, but challenges remain to efficiently perform genetic perturbations in relevan...

    Authors: Seok-Jin Heo, Lauren D. Enriquez, Scot Federman, Amy Y. Chang, Rachel Mace, Kaivalya Shevade, Phuong Nguyen, Adam J. Litterman, Shawn Shafer, Laralynne Przybyla and Eric D. Chow
    Citation: Genome Biology 2024 25:25
  41. Modeling of gene regulatory networks (GRNs) is limited due to a lack of direct measurements of genome-wide transcription factor activity (TFA) making it difficult to separate covariance and regulatory interact...

    Authors: Andreas Tjärnberg, Maggie Beheler-Amass, Christopher A. Jackson, Lionel A. Christiaen, David Gresham and Richard Bonneau
    Citation: Genome Biology 2024 25:24
  42. Sequence-specific RNA-binding proteins (RBPs) play central roles in splicing decisions. Here, we describe a modular splicing architecture that leverages in vitro-derived RNA affinity models for 79 human RBPs a...

    Authors: Kavi Gupta, Chenxi Yang, Kayla McCue, Osbert Bastani, Phillip A. Sharp, Christopher B. Burge and Armando Solar-Lezama
    Citation: Genome Biology 2024 25:23
  43. Pubertal growth patterns correlate with future health outcomes. However, the genetic mechanisms mediating growth trajectories remain largely unknown. Here, we modeled longitudinal height growth with Super-Impo...

    Authors: Jonathan P. Bradfield, Rachel L. Kember, Anna Ulrich, Zhanna Balkiyarova, 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 25:22

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