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  1. The endoplasmic reticulum (ER) is a membranous organelle that maintains proteostasis and cellular homeostasis, controlling the fine balance between health and disease. Dysregulation of the ER stress response h...

    Authors: Xiaobo Ke, Kwontae You, Matthieu Pichaud, Henry J. Haiser, Daniel B. Graham, Hera Vlamakis, Jeffrey A. Porter and Ramnik J. Xavier
    Citation: Genome Biology 2021 22:292
  2. Alternative cleavage and polyadenylation (APA), an RNA processing event, occurs in over 70% of human protein-coding genes. APA results in mRNA transcripts with distinct 3′ ends. Most APA occurs within 3′ UTRs,...

    Authors: Ankeeta Shah, Briana E. Mittleman, Yoav Gilad and Yang I. Li
    Citation: Genome Biology 2021 22:291
  3. Cellular RNA-binding proteins (RBPs) have multiple roles in post-transcriptional control, and some are shown to bind DNA. However, the global localization and the general chromatin-binding ability of RBPs are ...

    Authors: Yue Ren, Yue Huo, Weiqian Li, Manman He, Siqi Liu, Jiabin Yang, Hongmei Zhao, Lingjie Xu, Yuehong Guo, Yanmin Si, Hualu Zhao, Shuan Rao, Jing Wang, Yanni Ma, Xiaoshuang Wang, Jia Yu…
    Citation: Genome Biology 2021 22:290
  4. Pancreatic ductal adenocarcinoma initiation is most frequently caused by Kras mutations.

    Authors: Angela J. Mathison, Romica Kerketta, Thiago Milech de Assuncao, Elise Leverence, Atefeh Zeighami, Guillermo Urrutia, Timothy J. Stodola, Marina Pasca di Magliano, Juan L. Iovanna, Michael T. Zimmermann, Gwen Lomberk and Raul Urrutia
    Citation: Genome Biology 2021 22:289
  5. High-throughput biological data analysis commonly involves identifying features such as genes, genomic regions, and proteins, whose values differ between two conditions, from numerous features measured simulta...

    Authors: Xinzhou Ge, Yiling Elaine Chen, Dongyuan Song, MeiLu McDermott, Kyla Woyshner, Antigoni Manousopoulou, Ning Wang, Wei Li, Leo D. Wang and Jingyi Jessica Li
    Citation: Genome Biology 2021 22:288
  6. The diversity of genomic alterations in cancer poses challenges to fully understanding the etiologies of the disease. Recent interest in infrequent mutations, in genes that reside in the “long tail” of the mut...

    Authors: Hussein Mohsen, Vignesh Gunasekharan, Tao Qing, Montrell Seay, Yulia Surovtseva, Sahand Negahban, Zoltan Szallasi, Lajos Pusztai and Mark B. Gerstein
    Citation: Genome Biology 2021 22:287
  7. The rise in throughput and quality of long-read sequencing should allow unambiguous identification of full-length transcript isoforms. However, its application to single-cell RNA-seq has been limited by throug...

    Authors: Elisabeth Rebboah, Fairlie Reese, Katherine Williams, Gabriela Balderrama-Gutierrez, Cassandra McGill, Diane Trout, Isaryhia Rodriguez, Heidi Liang, Barbara J. Wold and Ali Mortazavi
    Citation: Genome Biology 2021 22:286
  8. Regulation of protein output at the level of translation allows for a rapid adaptation to dynamic changes to the cell’s requirements. This precise control of gene expression is achieved by complex and interlin...

    Authors: Sarah L. Gillen, Chiara Giacomelli, Kelly Hodge, Sara Zanivan, Martin Bushell and Ania Wilczynska
    Citation: Genome Biology 2021 22:284
  9. Balancing the yield, quality and resistance to disease is a daunting challenge in crop breeding due to the negative relationship among these traits. Large-scale genomic landscape analysis of germplasm resource...

    Authors: Ning Xiao, Cunhong Pan, Yuhong Li, Yunyu Wu, Yue Cai, Yue Lu, Ruyi Wang, Ling Yu, Wei Shi, Houxiang Kang, Zhaobing Zhu, Niansheng Huang, Xiaoxiang Zhang, Zichun Chen, Jianju Liu, Zefeng Yang…
    Citation: Genome Biology 2021 22:283
  10. Zebrafish pigment cell differentiation provides an attractive model for studying cell fate progression as a neural crest progenitor engenders diverse cell types, including two morphologically distinct pigment ...

    Authors: Hyo Sik Jang, Yujie Chen, Jiaxin Ge, Alicia N. Wilkening, Yiran Hou, Hyung Joo Lee, You Rim Choi, Rebecca F. Lowdon, Xiaoyun Xing, Daofeng Li, Charles K. Kaufman, Stephen L. Johnson and Ting Wang
    Citation: Genome Biology 2021 22:282
  11. The adaptive CRISPR-Cas immune system stores sequences from past invaders as spacers in CRISPR arrays and thereby provides direct evidence that links invaders to hosts. Mapping CRISPR spacers has revealed many...

    Authors: Jochem N. A. Vink, Jan H. L. Baijens and Stan J. J. Brouns
    Citation: Genome Biology 2021 22:281
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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

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

  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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

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

  41. 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
  42. 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

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