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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. Current evidence suggests that cis-regulatory elements controlling gene expression may be the predominant target of natural selection in humans and other species. Detecting selection acting on these elements is c...

    Authors: Kade P. Pettie, Maxwell Mumbach, Amanda J. Lea, Julien Ayroles, Howard Y. Chang, Maya Kasowski and Hunter B. Fraser
    Citation: Genome Biology 2024 25:21
  11. CRISPR screens with single-cell transcriptomic readouts are a valuable tool to understand the effect of genetic perturbations including single nucleotide variants (SNVs) associated with diseases. Interpretatio...

    Authors: Sarah E. Cooper, Matthew A. Coelho, Magdalena E. Strauss, Aleksander M. Gontarczyk, Qianxin Wu, Mathew J. Garnett, John C. Marioni and Andrew R. Bassett
    Citation: Genome Biology 2024 25:20
  12. Neural tube defects (NTDs) are caused by genetic and environmental factors. ARMC5 is part of a novel ubiquitin ligase specific for POLR2A, the largest subunit of RNA polymerase II (Pol II).

    Authors: Hongyu Luo, Linjiang Lao, Kit Sing Au, Hope Northrup, Xiao He, Diane Forget, Marie-Soleil Gauthier, Benoit Coulombe, Isabelle Bourdeau, Wei Shi, Lucia Gagliardi, Maria Candida Barisson Villares Fragoso, Junzheng Peng and Jiangping Wu
    Citation: Genome Biology 2024 25:19
  13. Deletion of haploinsufficient genes or duplication of triplosensitive ones results in phenotypic effects in a concentration-dependent manner, and the mechanisms underlying these dosage-sensitive effects remain...

    Authors: Liang Yang, Jiali Lyu, Xi Li, Gaigai Guo, Xueya Zhou, Taoyu Chen, Yi Lin and Tingting Li
    Citation: Genome Biology 2024 25:17
  14. The oncogenic protein HOXA9 plays a critical role in leukemia transformation and maintenance, and its aberrant expression is a hallmark of most aggressive acute leukemia. Although inhibiting the upstream regul...

    Authors: Mengli Zhang, Judith Hyle, Xiaowen Chen, Ye Xin, Yingcai Jin, Jianxiang Zhang, Xue Yang, Xinfeng Chen, Shaela Wright, Zhenling Liu, Wojciech Rosikiewicz, Beisi Xu, Liusheng He, Hong Liu, Nana Ping, Depei Wu…
    Citation: Genome Biology 2024 25:16
  15. The three-dimensional genome organization influences diverse nuclear processes. Here we present Chromatin Interaction Predictor (ChIPr), a suite of regression models based on deep neural networks, random fores...

    Authors: Ahmed Abbas, Khyati Chandratre, Yunpeng Gao, Jiapei Yuan, Michael Q. Zhang and Ram S. Mani
    Citation: Genome Biology 2024 25:15
  16. Existing methods for analysis of spatial transcriptomic data focus on delineating the global gene expression variations of cell types across the tissue, rather than local gene expression changes driven by cell...

    Authors: Kaishu Mason, Anuja Sathe, Paul R. Hess, Jiazhen Rong, Chi-Yun Wu, Emma Furth, Katalin Susztak, Jonathan Levinsohn, Hanlee P. Ji and Nancy Zhang
    Citation: Genome Biology 2024 25:14
  17. CRISPR interference (CRISPRi) is the leading technique to silence gene expression in bacteria; however, design rules remain poorly defined. We develop a best-in-class prediction algorithm for guide silencing e...

    Authors: Yanying Yu, Sandra Gawlitt, Lisa Barros de Andrade e Sousa, Erinc Merdivan, Marie Piraud, Chase L. Beisel and Lars Barquist
    Citation: Genome Biology 2024 25:13
  18. Transcription factors bind DNA in specific sequence contexts. In addition to distinguishing one nucleobase from another, some transcription factors can distinguish between unmodified and modified bases. Curren...

    Authors: Coby Viner, Charles A. Ishak, James Johnson, Nicolas J. Walker, Hui Shi, Marcela K. Sjöberg-Herrera, Shu Yi Shen, Santana M. Lardo, David J. Adams, Anne C. Ferguson-Smith, Daniel D. De Carvalho, Sarah J. Hainer, Timothy L. Bailey and Michael M. Hoffman
    Citation: Genome Biology 2024 25:11
  19. The history of yeast Saccharomyces cerevisiae, aka brewer’s or baker’s yeast, is intertwined with our own. Initially domesticated 8,000 years ago to provide sustenance to our ancestors, for the past 150 years, ye...

    Authors: Hamid Kian Gaikani, Monika Stolar, Divya Kriti, Corey Nislow and Guri Giaever
    Citation: Genome Biology 2024 25:10
  20. To analyze the large volume of data generated by single-cell technologies and to identify cellular correlates of particular clinical or experimental outcomes, differential abundance analyses are often applied....

    Authors: Haidong Yi, Alec Plotkin and Natalie Stanley
    Citation: Genome Biology 2024 25:9
  21. Dramatic improvements in measuring genetic variation across agriculturally relevant populations (genomics) must be matched by improvements in identifying and measuring relevant trait variation in such populati...

    Authors: Christopher K. Tuggle, Jennifer L. Clarke, Brenda M. Murdoch, Eric Lyons, Nicole M. Scott, Bedrich Beneš, Jacqueline D. Campbell, Henri Chung, Courtney L. Daigle, Sruti Das Choudhury, Jack C. M. Dekkers, Joao R. R. Dórea, David S. Ertl, Max Feldman, Breno O. Fragomeni, Janet E. Fulton…
    Citation: Genome Biology 2024 25:8
  22. The cost-free increase in statistical power of using imputation to infer missing genotypes is undoubtedly appealing, but is it hazard-free? This case study of three type-2 diabetes (T2D) loci demonstrates that...

    Authors: Winston Lau, Aminah Ali, Hannah Maude, Toby Andrew, Dallas M. Swallow and Nikolas Maniatis
    Citation: Genome Biology 2024 25:7
  23. Authors: Jizeng Jia, Yilin Xie, Jingfei Cheng, Chuizheng Kong, Meiyue Wang, Lifeng Gao, Fei Zhao, Jingyu Guo, Kai Wang, Guangwei Li, Dangqun Cui, Tiezhu Hu, Guangyao Zhao, Daowen Wang, Zhengang Ru and Yijing Zhang
    Citation: Genome Biology 2024 25:5

    The original article was published in Genome Biology 2021 22:26

  24. Transposable elements (TEs) are important drivers of genome evolution. Nonetheless, TE annotation remains a complex and challenging task. As more genomes from phylogenetically diverse species are published, a ...

    Authors: Landen Gozashti and Hopi E. Hoekstra
    Citation: Genome Biology 2024 25:4

    The original article was published in Genome Biology 2019 20:275

    The Correspondence to this article has been published in Genome Biology 2024 25:6

  25. The majority of disease-associated variants identified through genome-wide association studies are located outside of protein-coding regions. Prioritizing candidate regulatory variants and gene targets to iden...

    Authors: Charles E. Breeze, Eric Haugen, María Gutierrez-Arcelus, Xiaozheng Yao, Andrew Teschendorff, Stephan Beck, Ian Dunham, John Stamatoyannopoulos, Nora Franceschini, Mitchell J. Machiela and Sonja I. Berndt
    Citation: Genome Biology 2024 25:3
  26. Formation of tissue-specific transcriptional programs underlies multicellular development, including dorsoventral (DV) patterning of the Drosophila embryo. This involves interactions between transcriptional enhan...

    Authors: George Hunt, Roshan Vaid, Sergei Pirogov, Alexander Pfab, Christoph Ziegenhain, Rickard Sandberg, Johan Reimegård and Mattias Mannervik
    Citation: Genome Biology 2024 25:2
  27. Capturing the genetic diversity of wild relatives is crucial for improving crops because wild species are valuable sources of agronomic traits that are essential to enhance the sustainability and adaptability ...

    Authors: Noé Cochetel, Andrea Minio, Andrea Guarracino, Jadran F. Garcia, Rosa Figueroa-Balderas, Mélanie Massonnet, Takao Kasuga, Jason P. Londo, Erik Garrison, Brandon S. Gaut and Dario Cantu
    Citation: Genome Biology 2023 24:290
  28. Many deep learning-based methods have been proposed to handle complex single-cell data. Deep learning approaches may also prove useful to jointly analyze single-cell RNA sequencing (scRNA-seq) and single-cell ...

    Authors: Biqing Zhu, Yuge Wang, Li-Ting Ku, David van Dijk, Le Zhang, David A. Hafler and Hongyu Zhao
    Citation: Genome Biology 2023 24:292
  29. Spatial omics technologies can help identify spatially organized biological processes, but existing computational approaches often overlook structural dependencies in the data. Here, we introduce Smoother, a u...

    Authors: Jiayu Su, Jean-Baptiste Reynier, Xi Fu, Guojie Zhong, Jiahao Jiang, Rydberg Supo Escalante, Yiping Wang, Luis Aparicio, Benjamin Izar, David A. Knowles and Raul Rabadan
    Citation: Genome Biology 2023 24:291
  30. Metabolites play critical roles in regulating nutritional qualities of plants, thereby influencing their consumption and human health. However, the genetic basis underlying the metabolite-based nutrient qualit...

    Authors: Zehong Ding, Lili Fu, Bin Wang, Jianqiu Ye, Wenjun Ou, Yan Yan, Meiying Li, Liwang Zeng, Xuekui Dong, Weiwei Tie, Xiaoxue Ye, Jinghao Yang, Zhengnan Xie, Yu Wang, Jianchun Guo, Songbi Chen…
    Citation: Genome Biology 2023 24:289
  31. Deconvolution of cell mixtures in “bulk” transcriptomic samples from homogenate human tissue is important for understanding disease pathologies. However, several experimental and computational challenges imped...

    Authors: Sean K. Maden, Sang Ho Kwon, Louise A. Huuki-Myers, Leonardo Collado-Torres, Stephanie C. Hicks and Kristen R. Maynard
    Citation: Genome Biology 2023 24:288
  32. The coordinated transcriptional regulation of activated T-cells is based on a complex dynamic behavior of signaling networks. Given an external stimulus, T-cell gene expression is characterized by impulse and ...

    Authors: Michael Rade, Sebastian Böhlen, Vanessa Neuhaus, Dennis Löffler, Conny Blumert, Maximilian Merz, Ulrike Köhl, Susann Dehmel, Katherina Sewald and Kristin Reiche
    Citation: Genome Biology 2023 24:287
  33. Expression quantitative trait locus (eQTL) analysis has emerged as an important tool in elucidating the link between genetic variants and gene expression, thereby bridging the gap between risk SNPs and associa...

    Authors: Yong Zeng, Rahi Jain, Magnus Lam, Musaddeque Ahmed, Haiyang Guo, Wenjie Xu, Yuan Zhong, Gong-Hong Wei, Wei Xu and Housheng Hansen He
    Citation: Genome Biology 2023 24:285
  34. Point mutations in histone variant H3.3 (H3.3K27M, H3.3G34R) and the H3.3-specific ATRX/DAXX chaperone complex are frequent events in pediatric gliomas. These H3.3 point mutations affect many chromatin modific...

    Authors: Hsiao P. J. Voon, Linda Hii, Andrew Garvie, Maheshi Udugama, Brian Krug, Caterina Russo, Anderly C. Chüeh, Roger J. Daly, Alison Morey, Toby D. M. Bell, Stephen J. Turner, Joseph Rosenbluh, Paul Daniel, Ron Firestein, Jeffrey R. Mann, Philippe Collas…
    Citation: Genome Biology 2023 24:284
  35. Strain-level diversity is widespread among bacterial species and can expand the functional potential of natural microbial communities. However, to what extent communities undergo consistent shifts in strain co...

    Authors: Gilles L. C. Baud, Aiswarya Prasad, Kirsten M. Ellegaard and Philipp Engel
    Citation: Genome Biology 2023 24:283
  36. Many elite genes have been identified from the available cotton genomic data, providing various genetic resources for gene-driven breeding. However, backbone cultivar-driven breeding is the most widely applied...

    Authors: Shang Liu, Dongyun Zuo, Hailiang Cheng, Man He, Qiaolian Wang, Limin Lv, Youping Zhang, Javaria Ashraf, Ji Liu and Guoli Song
    Citation: Genome Biology 2023 24:282
  37. GCLiPP is a global RNA interactome capture method that detects RNA-binding protein (RBP) occupancy transcriptome-wide. GCLiPP maps RBP-occupied sites at a higher resolution than phase separation-based techniqu...

    Authors: Wandi S. Zhu, Adam J. Litterman, Harshaan S. Sekhon, Robin Kageyama, Maya M. Arce, Kimberly E. Taylor, Wenxue Zhao, Lindsey A. Criswell, Noah Zaitlen, David J. Erle and K. Mark Ansel
    Citation: Genome Biology 2023 24:281
  38. The dikaryotic stage dominates most of the life cycle in basidiomycetes, and each cell carries two different haploid nuclei. Accurate phasing of these two nuclear genomes and their interactions have long been ...

    Authors: Youjin Deng, Lin Guo, Longji Lin, Yuefeng Li, Jinxiang Zhang, Yue Zhang, Bin Yuan, Lina Ke, Baogui Xie and Ray Ming
    Citation: Genome Biology 2023 24:280
  39. Identifying host factors is key to understanding RNA virus pathogenicity. Besides proteins, RNAs can interact with virus genomes to impact replication.

    Authors: Kuo-Chieh Liao, Xuping Xie, Anna Karin Beatrice Sundstrom, Xin Ni Lim, Kiat Kee Tan, Yu Zhang, Jing Zou, Amanda Makha Bifani, Hui Xian Poh, Jia Jia Chen, Wy Ching Ng, Su Ying Lim, Eng Eong Ooi, October M. Sessions, Yvonne Tay, Pei-Yong Shi…
    Citation: Genome Biology 2023 24:279
  40. Epigenetic scores (EpiScores) can provide biomarkers of lifestyle and disease risk. Projecting new datasets onto a reference panel is challenging due to separation of technical and biological variation with ar...

    Authors: Charlotte Merzbacher, Barry Ryan, Thibaut Goldsborough, Robert F. Hillary, Archie Campbell, Lee Murphy, Andrew M. McIntosh, David Liewald, Sarah E. Harris, Allan F. McRae, Simon R. Cox, Timothy I. Cannings, Catalina A. Vallejos, Daniel L. McCartney and Riccardo E. Marioni
    Citation: Genome Biology 2023 24:278
  41. MALDI-TOF MS-based microbial identification relies on reference spectral libraries, which limits the screening of diverse isolates, including uncultured lineages. We present a new strategy for broad-spectrum i...

    Authors: Yuji Sekiguchi, Kanae Teramoto, Dieter M. Tourlousse, Akiko Ohashi, Mayu Hamajima, Daisuke Miura, Yoshihiro Yamada, Shinichi Iwamoto and Koichi Tanaka
    Citation: Genome Biology 2023 24:257
  42. Recent state-of-the-art sequencing technologies enable the investigation of challenging regions in the human genome and expand the scope of variant benchmarking datasets. Herein, we sequence a Chinese Quartet,...

    Authors: Peng Jia, Lianhua Dong, Xiaofei Yang, Bo Wang, Stephen J. Bush, Tingjie Wang, Jiadong Lin, Songbo Wang, Xixi Zhao, Tun Xu, Yizhuo Che, Ningxin Dang, Luyao Ren, Yujing Zhang, Xia Wang, Fan Liang…
    Citation: Genome Biology 2023 24:277

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