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  1. Deep learning has proven to be a powerful technique for transcription factor (TF) binding prediction but requires large training datasets. Transfer learning can reduce the amount of data required for deep lear...

    Authors: Gherman Novakovsky, Manu Saraswat, Oriol Fornes, Sara Mostafavi and Wyeth W. Wasserman

    Citation: Genome Biology 2021 22:280

    Content type: Research

    Published on:

  2. Mammalian development is associated with extensive changes in gene expression, chromatin accessibility, and nuclear structure. Here, we follow such changes associated with mouse embryonic stem cell differentia...

    Authors: Giancarlo Bonora, Vijay Ramani, Ritambhara Singh, He Fang, Dana L. Jackson, Sanjay Srivatsan, Ruolan Qiu, Choli Lee, Cole Trapnell, Jay Shendure, Zhijun Duan, Xinxian Deng, William S. Noble and Christine M. Disteche

    Citation: Genome Biology 2021 22:279

    Content type: Research

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  3. Here we describe a new integrative approach for accurate annotation and quantification of circRNAs named Short Read circRNA Pipeline (SRCP). Our strategy involves two steps: annotation of validated circRNAs fo...

    Authors: Avigayel Rabin, Michela Zaffagni, Reut Ashwal-Fluss, Ines Lucia Patop, Aarti Jajoo, Shlomo Shenzis, Liran Carmel and Sebastian Kadener

    Citation: Genome Biology 2021 22:277

    Content type: Method

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  4. The bacillus Calmette-Guérin (BCG) vaccine protects against tuberculosis and heterologous infections but elicits high inter-individual variation in specific and nonspecific, or trained, immune responses. While...

    Authors: Martin Stražar, Vera P. Mourits, Valerie A. C. M. Koeken, L. Charlotte J. de Bree, Simone J. C. F. M. Moorlag, Leo A. B. Joosten, Reinout van Crevel, Hera Vlamakis, Mihai G. Netea and Ramnik J. Xavier

    Citation: Genome Biology 2021 22:275

    Content type: Research

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  5. Illumina DNA methylation microarrays enable epigenome-wide analysis vastly used for the discovery of novel DNA methylation variation in health and disease. However, the microarrays’ probe design cannot fully c...

    Authors: Benjamin Planterose Jiménez, Manfred Kayser and Athina Vidaki

    Citation: Genome Biology 2021 22:274

    Content type: Research

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  6. Spatiotemporal changes in the chromatin accessibility landscape are essential to cell differentiation, development, health, and disease. The quest of identifying regulatory elements in open chromatin regions a...

    Authors: Pâmela A. Alexandre, Marina Naval-Sánchez, Moira Menzies, Loan T. Nguyen, Laercio R. Porto-Neto, Marina R. S. Fortes and Antonio Reverter

    Citation: Genome Biology 2021 22:273

    Content type: Research

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  7. Authors: Zhonghua Du, Xue Wen, Yichen Wang, Lin Jia, Shilin Zhang, Yudi Liu, Lei Zhou, Hui Li, Wang Yang, Cong Wang, Jingcheng Chen, Yajing Hao, Daniela Salgado Figueroa, Huiling Chen, Dan Li, Naifei Chen…

    Citation: Genome Biology 2021 22:272

    Content type: Author Correction

    Published on:

    The original article was published in Genome Biology 2021 22:233

  8. LightGBM is an ensemble model of decision trees for classification and regression prediction. We demonstrate its utility in genomic selection-assisted breeding with a large dataset of inbred and hybrid maize l...

    Authors: Jun Yan, Yuetong Xu, Qian Cheng, Shuqin Jiang, Qian Wang, Yingjie Xiao, Chuang Ma, Jianbing Yan and Xiangfeng Wang

    Citation: Genome Biology 2021 22:271

    Content type: Method

    Published on:

  9. Sequence Read Archive submissions to the National Center for Biotechnology Information often lack useful metadata, which limits the utility of these submissions. We describe the Sequence Taxonomic Analysis Too...

    Authors: Kenneth S. Katz, Oleg Shutov, Richard Lapoint, Michael Kimelman, J. Rodney Brister and Christopher O’Sullivan

    Citation: Genome Biology 2021 22:270

    Content type: Method

    Published on:

  10. Super-enhancers are clusters of enhancer elements that play critical roles in the maintenance of cell identity. Current investigations on super-enhancers are centered on the established ones in static cell typ...

    Authors: Yan Kai, Bin E. Li, Ming Zhu, Grace Y. Li, Fei Chen, Yingli Han, Hye Ji Cha, Stuart H. Orkin, Wenqing Cai, Jialiang Huang and Guo-Cheng Yuan

    Citation: Genome Biology 2021 22:269

    Content type: Research

    Published on:

  11. We present pandora, a novel pan-genome graph structure and algorithms for identifying variants across the full bacterial pan-genome. As much bacterial adaptability hinges on the accessory genome, methods which an...

    Authors: Rachel M. Colquhoun, Michael B. Hall, Leandro Lima, Leah W. Roberts, Kerri M. Malone, Martin Hunt, Brice Letcher, Jane Hawkey, Sophie George, Louise Pankhurst and Zamin Iqbal

    Citation: Genome Biology 2021 22:267

    Content type: Method

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  12. While long-read sequencing allows for the complete assembly of bacterial genomes, long-read assemblies contain a variety of errors. Here, we present Trycycler, a tool which produces a consensus assembly from m...

    Authors: Ryan R. Wick, Louise M. Judd, Louise T. Cerdeira, Jane Hawkey, Guillaume Méric, Ben Vezina, Kelly L. Wyres and Kathryn E. Holt

    Citation: Genome Biology 2021 22:266

    Content type: Software

    Published on:

  13. Variation in gene expression underlies interindividual variability in relevant traits including immune response. However, the genetic variation responsible for these gene expression changes remains largely unk...

    Authors: Anna Ullastres, Miriam Merenciano and Josefa González

    Citation: Genome Biology 2021 22:265

    Content type: Research

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  14. Cell type identification is one of the most important questions in single-cell RNA sequencing (scRNA-seq) data analysis. With the accumulation of public scRNA-seq data, supervised cell type identification meth...

    Authors: Wenjing Ma, Kenong Su and Hao Wu

    Citation: Genome Biology 2021 22:264

    Content type: Research

    Published on:

  15. With the recent increase in RNA sequencing efforts using large cohorts of individuals, surveying allele-specific gene expression is becoming increasingly frequent. Here, we report that, despite not containing ...

    Authors: Gamze Gürsoy, Nancy Lu, Sarah Wagner and Mark Gerstein

    Citation: Genome Biology 2021 22:263

    Content type: Short Report

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  16. Local genetic correlation quantifies the genetic similarity of complex traits in specific genomic regions. However, accurate estimation of local genetic correlation remains challenging, due to linkage disequil...

    Authors: Yiliang Zhang, Qiongshi Lu, Yixuan Ye, Kunling Huang, Wei Liu, Yuchang Wu, Xiaoyuan Zhong, Boyang Li, Zhaolong Yu, Brittany G. Travers, Donna M. Werling, James J. Li and Hongyu Zhao

    Citation: Genome Biology 2021 22:262

    Content type: Method

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  17. Long-read sequencing enables variant detection in genomic regions that are considered difficult-to-map by short-read sequencing. To fully exploit the benefits of longer reads, here we present a deep learning m...

    Authors: Mian Umair Ahsan, Qian Liu, Li Fang and Kai Wang

    Citation: Genome Biology 2021 22:261

    Content type: Method

    Published on:

  18. Drought is a major environmental disaster that causes crop yield loss worldwide. Metabolites are involved in various environmental stress responses of plants. However, the genetic control of metabolomes underl...

    Authors: Fei Zhang, Jinfeng Wu, Nir Sade, Si Wu, Aiman Egbaria, Alisdair R. Fernie, Jianbing Yan, Feng Qin, Wei Chen, Yariv Brotman and Mingqiu Dai

    Citation: Genome Biology 2021 22:260

    Content type: Research

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  19. Polygenic risk scores (PRSs) have wide applications in human genetics research, but often include tuning parameters which are difficult to optimize in practice due to limited access to individual-level data. H...

    Authors: Zijie Zhao, Yanyao Yi, Jie Song, Yuchang Wu, Xiaoyuan Zhong, Yupei Lin, Timothy J. Hohman, Jason Fletcher and Qiongshi Lu

    Citation: Genome Biology 2021 22:257

    Content type: Method

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  20. We develop the Oncogene Concatenated Enriched Amplicon Nanopore Sequencing (OCEANS) method, in which variants with low variant allele frequency (VAFs) are amplified and subsequently concatenated for Nanopore S...

    Authors: Deepak Thirunavukarasu, Lauren Y. Cheng, Ping Song, Sherry X. Chen, Mitesh J. Borad, Lawrence Kwong, Phillip James, Daniel J. Turner and David Yu Zhang

    Citation: Genome Biology 2021 22:227

    Content type: Method

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  21. Currently, different sequencing platforms are used to generate plant genomes and no workflow has been properly developed to optimize time, cost, and assembly quality. We present LeafGo, a complete de novo plan...

    Authors: Patrick Driguez, Salim Bougouffa, Karen Carty, Alexander Putra, Kamel Jabbari, Muppala Reddy, Richard Soppe, Ming Sin Cheung, Yoshinori Fukasawa and Luca Ermini

    Citation: Genome Biology 2021 22:256

    Content type: Method

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  22. Introgressive hybridization can reassort genetic variants into beneficial combinations, permitting adaptation to new ecological niches. To evaluate evolutionary patterns and dynamics that contribute to introgr...

    Authors: Abraham Morales-Cruz, Jonas A. Aguirre-Liguori, Yongfeng Zhou, Andrea Minio, Summaira Riaz, Andrew M. Walker, Dario Cantu and Brandon S. Gaut

    Citation: Genome Biology 2021 22:254

    Content type: Research

    Published on:

  23. Polycomb repressive complex 1 (PRC1) and PRC2 are chromatin regulators maintaining transcriptional repression. The deposition of H3 lysine 27 tri-methylation (H3K27me3) by PRC2 is known to be required for tran...

    Authors: Shujing Liu, Minerva S. Trejo-Arellano, Yichun Qiu, D. Magnus Eklund, Claudia Köhler and Lars Hennig

    Citation: Genome Biology 2021 22:253

    Content type: Research

    Published on:

  24. Detecting multiplets in single nucleus (sn)ATAC-seq data is challenging due to data sparsity and limited dynamic range. AMULET (ATAC-seq MULtiplet Estimation Tool) enumerates regions with greater than two uniq...

    Authors: Asa Thibodeau, Alper Eroglu, Christopher S. McGinnis, Nathan Lawlor, Djamel Nehar-Belaid, Romy Kursawe, Radu Marches, Daniel N. Conrad, George A. Kuchel, Zev J. Gartner, Jacques Banchereau, Michael L. Stitzel, A. Ercument Cicek and Duygu Ucar

    Citation: Genome Biology 2021 22:252

    Content type: Method

    Published on:

  25. We develop a novel computational method, NucHMM, to identify functional nucleosome states associated with cell type-specific combinatorial histone marks and nucleosome organization features such as phasing, sp...

    Authors: Kun Fang, Tianbao Li, Yufei Huang and Victor X. Jin

    Citation: Genome Biology 2021 22:250

    Content type: Method

    Published on:

  26. Aligning sequencing reads onto a reference is an essential step of the majority of genomic analysis pipelines. Computational algorithms for read alignment have evolved in accordance with technological advances...

    Authors: Mohammed Alser, Jeremy Rotman, Dhrithi Deshpande, Kodi Taraszka, Huwenbo Shi, Pelin Icer Baykal, Harry Taegyun Yang, Victor Xue, Sergey Knyazev, Benjamin D. Singer, Brunilda Balliu, David Koslicki, Pavel Skums, Alex Zelikovsky, Can Alkan, Onur Mutlu…

    Citation: Genome Biology 2021 22:249

    Content type: Review

    Published on:

  27. Single-cell RNA-seq datasets are often first analyzed independently without harnessing model fits from previous studies, and are then contextualized with public data sets, requiring time-consuming data wrangli...

    Authors: David S. Fischer, Leander Dony, Martin König, Abdul Moeed, Luke Zappia, Lukas Heumos, Sophie Tritschler, Olle Holmberg, Hananeh Aliee and Fabian J. Theis

    Citation: Genome Biology 2021 22:248

    Content type: Software

    Published on:

  28. Genome-wide association studies have reported more than 100 risk loci for rheumatoid arthritis (RA). These loci are shown to be enriched in immune cell-specific enhancers, but the analysis so far has excluded ...

    Authors: Xiangyu Ge, Mojca Frank-Bertoncelj, Kerstin Klein, Amanda McGovern, Tadeja Kuret, Miranda Houtman, Blaž Burja, Raphael Micheroli, Chenfu Shi, Miriam Marks, Andrew Filer, Christopher D. Buckley, Gisela Orozco, Oliver Distler, Andrew P. Morris, Paul Martin…

    Citation: Genome Biology 2021 22:247

    Content type: Research

    Published on:

  29. Authors: Kim-Anh Lê Cao, Al J. Abadi, Emily F. Davis-Marcisak, Lauren Hsu, Arshi Arora, Alexis Coullomb, Atul Deshpande, Yuzhou Feng, Pratheepa Jeganathan, Melanie Loth, Chen Meng, Wancen Mu, Vera Pancaldi, Kris Sankaran, Dario Righelli, Amrit Singh…

    Citation: Genome Biology 2021 22:246

    Content type: Author Correction

    Published on:

    The original article was published in Genome Biology 2021 22:220

  30. Nullomers and nullpeptides are short DNA or amino acid sequences that are absent from a genome or proteome, respectively. One potential cause for their absence could be their having a detrimental impact on an ...

    Authors: Ilias Georgakopoulos-Soares, Ofer Yizhar-Barnea, Ioannis Mouratidis, Martin Hemberg and Nadav Ahituv

    Citation: Genome Biology 2021 22:245

    Content type: Research

    Published on:

  31. The transcription factor CTCF appears indispensable in defining topologically associated domain boundaries and maintaining chromatin loop structures within these domains, supported by numerous functional studi...

    Authors: Beisi Xu, Hong Wang, Shaela Wright, Judith Hyle, Yang Zhang, Ying Shao, Mingming Niu, Yiping Fan, Wojciech Rosikiewicz, Mohamed Nadhir Djekidel, Junmin Peng, Rui Lu and Chunliang Li

    Citation: Genome Biology 2021 22:244

    Content type: Research

    Published on:

  32. To date, the locus with the most robust human genetic association to COVID-19 severity is 3p21.31. Here, we integrate genome-scale CRISPR loss-of-function screens and eQTLs in diverse cell types and tissues to...

    Authors: Silva Kasela, Zharko Daniloski, Sailalitha Bollepalli, Tristan X. Jordan, Benjamin R. tenOever, Neville E. Sanjana and Tuuli Lappalainen

    Citation: Genome Biology 2021 22:242

    Content type: Short Report

    Published on:

  33. Genome-wide association studies reveal many non-coding variants associated with complex traits. However, model organism studies largely remain as an untapped resource for unveiling the effector genes of non-co...

    Authors: Chenyang Dong, Shane P. Simonett, Sunyoung Shin, Donnie S. Stapleton, Kathryn L. Schueler, Gary A. Churchill, Leina Lu, Xiaoxiao Liu, Fulai Jin, Yan Li, Alan D. Attie, Mark P. Keller and Sündüz Keleş

    Citation: Genome Biology 2021 22:241

    Content type: Method

    Published on:

  34. The human genome encodes over 14,000 pseudogenes that are evolutionary relics of protein-coding genes and commonly considered as nonfunctional. Emerging evidence suggests that some pseudogenes may exert import...

    Authors: Ming Sun, Yunfei Wang, Caishang Zheng, Yanjun Wei, Jiakai Hou, Peng Zhang, Wei He, Xiangdong Lv, Yao Ding, Han Liang, Chung-Chau Hon, Xi Chen, Han Xu and Yiwen Chen

    Citation: Genome Biology 2021 22:240

    Content type: Research

    Published on:

  35. Several bioinformatic tools have been developed for genome-wide identification of orthologous and paralogous genes. However, no corresponding tool allows the detection of exon homology relationships. Here, we ...

    Authors: Yamile Márquez, Federica Mantica, Luca Cozzuto, Demian Burguera, Antonio Hermoso-Pulido, Julia Ponomarenko, Scott W. Roy and Manuel Irimia

    Citation: Genome Biology 2021 22:239

    Content type: Software

    Published on:

  36. Functional genomics experiments, like ChIP-Seq or ATAC-Seq, produce results that are summarized as a region set. There is no way to objectively evaluate the effectiveness of region set similarity metrics. We p...

    Authors: Aaron Gu, Hyun Jae Cho and Nathan C. Sheffield

    Citation: Genome Biology 2021 22:238

    Content type: Short Report

    Published on:

  37. Structural variants (SVs) significantly drive genome diversity and environmental adaptation for diverse species. Unlike the prevalent small SVs (< kilobase-scale) in higher eukaryotes, large-size SVs rarely ex...

    Authors: Yumin Huang, Wei Huang, Zhuang Meng, Guilherme Tomaz Braz, Yunfei Li, Kai Wang, Hai Wang, Jinsheng Lai, Jiming Jiang, Zhaobin Dong and Weiwei Jin

    Citation: Genome Biology 2021 22:237

    Content type: Research

    Published on:

  38. After repairing double-strand breaks (DSBs) caused by CRISPR-Cas9 cleavage, genomic damage, such as large deletions, may have pathogenic consequences.

    Authors: Wei Wen, Zi-Jun Quan, Si-Ang Li, Zhi-Xue Yang, Ya-Wen Fu, Feng Zhang, Guo-Hua Li, Mei Zhao, Meng-Di Yin, Jing Xu, Jian-Ping Zhang, Tao Cheng and Xiao-Bing Zhang

    Citation: Genome Biology 2021 22:236

    Content type: Research

    Published on:

  39. Prime editing is a revolutionary genome-editing technology that can make a wide range of precise edits in DNA. However, designing highly efficient prime editors (PEs) remains challenging. We develop Easy-Prime...

    Authors: Yichao Li, Jingjing Chen, Shengdar Q. Tsai and Yong Cheng

    Citation: Genome Biology 2021 22:235

    Content type: Software

    Published on:

  40. Single-cell RNA sequencing (scRNA-seq) provides new opportunities to characterize cell populations, typically accomplished through some type of clustering analysis. Estimation of the optimal cluster number (K) is...

    Authors: Siyao Liu, Aatish Thennavan, Joseph P. Garay, J. S. Marron and Charles M. Perou

    Citation: Genome Biology 2021 22:232

    Content type: Method

    Published on:

  41. Efficiently scaling genomic variant search indexes to thousands of samples is computationally challenging due to the presence of multiple coordinate systems to avoid reference biases. We present VariantStore, ...

    Authors: Prashant Pandey, Yinjie Gao and Carl Kingsford

    Citation: Genome Biology 2021 22:231

    Content type: Method

    Published on:

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