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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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

  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. A specific 3-dimensional intrachromosomal architecture of core stem cell factor genes is required to reprogram a somatic cell into pluripotency. As little is known about the epigenetic readers that orchestrate...

    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 22:233

    The Author Correction to this article has been published in Genome Biology 2021 22:272

  21. 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
  22. 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
  23. Biomolecular condensates have been implicated in multiple cellular processes. However, the global role played by condensates in 3D chromatin organization remains unclear. At present, 1,6-hexanediol (1,6-HD) is...

    Authors: Xinyi Liu, Shaoshuai Jiang, Lin Ma, Jiale Qu, Longying Zhao, Xing Zhu and Junjun Ding
    Citation: Genome Biology 2021 22:230
  24. Liquid-liquid phase separation (LLPS) is an important organizing principle for biomolecular condensation and chromosome compartmentalization. However, while many proteins have been reported to undergo LLPS, qu...

    Authors: Minglei Shi, Kaiqiang You, Taoyu Chen, Chao Hou, Zhengyu Liang, Mingwei Liu, Jifeng Wang, Taotao Wei, Jun Qin, Yang Chen, Michael Q. Zhang and Tingting Li
    Citation: Genome Biology 2021 22:229
  25. Chromatin interactions play important roles in regulating gene expression. However, the availability of genome-wide chromatin interaction data is limited. We develop a computational method, chromatin interacti...

    Authors: Fan Cao, Yu Zhang, Yichao Cai, Sambhavi Animesh, Ying Zhang, Semih Can Akincilar, Yan Ping Loh, Xinya Li, Wee Joo Chng, Vinay Tergaonkar, Chee Keong Kwoh and Melissa J. Fullwood
    Citation: Genome Biology 2021 22:226
  26. Retrotransposons are genetic elements inducing mutations in all domains of life. Despite their detrimental effect, retrotransposons can become temporarily active during epigenetic reprogramming and cellular st...

    Authors: Antoine Porquier, Constance Tisserant, Francisco Salinas, Carla Glassl, Lucas Wange, Wolfgang Enard, Andreas Hauser, Matthias Hahn and Arne Weiberg
    Citation: Genome Biology 2021 22:225
  27. Tandem repeat (TR) expansion is the underlying cause of over 40 neurological disorders. Long-read sequencing offers an exciting avenue over conventional technologies for detecting TR expansions. Here, we prese...

    Authors: Readman Chiu, Indhu-Shree Rajan-Babu, Jan M. Friedman and Inanc Birol
    Citation: Genome Biology 2021 22:224
  28. Single-cell RNA-seq (scRNA-seq) profiles gene expression with high resolution. Here, we develop a stepwise computational method-called SCAPTURE to identify, evaluate, and quantify cleavage and polyadenylation ...

    Authors: Guo-Wei Li, Fang Nan, Guo-Hua Yuan, Chu-Xiao Liu, Xindong Liu, Ling-Ling Chen, Bin Tian and Li Yang
    Citation: Genome Biology 2021 22:221
  29. Six million Jews were killed by Nazi Germany and its collaborators during World War II. Archaeological excavations in the area of the death camp in Sobibór, Poland, revealed ten sets of human skeletal remains ...

    Authors: Marta Diepenbroek, Christina Amory, Harald Niederstätter, Bettina Zimmermann, Maria Szargut, Grażyna Zielińska, Arne Dür, Iwona Teul, Wojciech Mazurek, Krzysztof Persak, Andrzej Ossowski and Walther Parson
    Citation: Genome Biology 2021 22:200
  30. 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 22:220

    The Author Correction to this article has been published in Genome Biology 2021 22:246

  31. Precise splice junction calls are currently unavailable in scRNA-seq pipelines such as the 10x Chromium platform but are critical for understanding single-cell biology. Here, we introduce SICILIAN, a new metho...

    Authors: Roozbeh Dehghannasiri, Julia Eve Olivieri, Ana Damljanovic and Julia Salzman
    Citation: Genome Biology 2021 22:219
  32. Human-to-human transmission of symbiotic, anaerobic bacteria is a fundamental evolutionary adaptation essential for membership of the human gut microbiota. However, despite its importance, the genomic and biol...

    Authors: Hilary P. Browne, Alexandre Almeida, Nitin Kumar, Kevin Vervier, Anne T. Adoum, Elisa Viciani, Nicholas J. R. Dawson, Samuel C. Forster, Claire Cormie, David Goulding and Trevor D. Lawley
    Citation: Genome Biology 2021 22:204
  33. Spatial interactions and insulation of chromatin regions are associated with transcriptional regulation. Domains of frequent chromatin contacts are proposed as functional units, favoring and delimiting gene re...

    Authors: Marie Zufferey, Yuanlong Liu, Daniele Tavernari, Marco Mina and Giovanni Ciriello
    Citation: Genome Biology 2021 22:218
  34. The phenotype of an individual can be affected not only by the individual’s own genotypes, known as direct genetic effects (DGE), but also by genotypes of interacting partners, indirect genetic effects (IGE). ...

    Authors: Amelie Baud, Francesco Paolo Casale, Amanda M. Barkley-Levenson, Nilgoun Farhadi, Charlotte Montillot, Binnaz Yalcin, Jerome Nicod, Abraham A. Palmer and Oliver Stegle
    Citation: Genome Biology 2021 22:216
  35. We introduce STrain Resolution ON assembly Graphs (STRONG), which identifies strains de novo, from multiple metagenome samples. STRONG performs coassembly, and binning into metagenome assembled genomes (MAGs),...

    Authors: Christopher Quince, Sergey Nurk, Sebastien Raguideau, Robert James, Orkun S. Soyer, J. Kimberly Summers, Antoine Limasset, A. Murat Eren, Rayan Chikhi and Aaron E. Darling
    Citation: Genome Biology 2021 22:214
  36. With viral infections, multiple related viral strains are often present due to coinfection or within-host evolution. We describe Haploflow, a deBruijn graph-based assembler for de novo genome assembly of viral...

    Authors: Adrian Fritz, Andreas Bremges, Zhi-Luo Deng, Till Robin Lesker, Jasper Götting, Tina Ganzenmueller, Alexander Sczyrba, Alexander Dilthey, Frank Klawonn and Alice Carolyn McHardy
    Citation: Genome Biology 2021 22:212
  37. Understanding the genetic architecture of temperature adaptation is key for characterizing and predicting the effect of climate change on natural populations. One particularly promising approach is Evolve and ...

    Authors: Kathrin A. Otte, Viola Nolte, François Mallard and Christian Schlötterer
    Citation: Genome Biology 2021 22:211
  38. Authors: Zhi-Qiang Chen, Yanjun Zan, Pascal Milesi, Linghua Zhou, Jun Chen, Lili Li, BinBin Cui, Shihui Niu, Johan Westin, Bo Karlsson, Maria Rosario García-Gil, Martin Lascoux and Harry X. Wu
    Citation: Genome Biology 2021 22:210

    The original article was published in Genome Biology 2021 22:179

  39. Akkermansia muciniphila is a human gut microbe with a key role in the physiology of the intestinal mucus layer and reported associations with decreased body mass and increased gut barrier function and health. Des...

    Authors: Nicolai Karcher, Eleonora Nigro, Michal Punčochář, Aitor Blanco-Míguez, Matteo Ciciani, Paolo Manghi, Moreno Zolfo, Fabio Cumbo, Serena Manara, Davide Golzato, Anna Cereseto, Manimozhiyan Arumugam, Thi Phuong Nam Bui, Hanne L. P. Tytgat, Mireia Valles-Colomer, Willem M. de Vos…
    Citation: Genome Biology 2021 22:209

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