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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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

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