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  1. Chromatin states and enhancers associate gene expression, cell identity and disease. Here, we systematically delineate the acute innate immune response to endotoxin in terms of human macrophage enhancer activi...

    Authors: Ping Zhang, Harindra E. Amarasinghe, Justin P. Whalley, Chwen Tay, Hai Fang, Gabriele Migliorini, Andrew C. Brown, Alice Allcock, Giuseppe Scozzafava, Phalguni Rath, Benjamin Davies and Julian C. Knight
    Citation: Genome Biology 2022 23:136
  2. The COVID-19 pandemic has emphasized the importance of accurate detection of known and emerging pathogens. However, robust characterization of pathogenic sequences remains an open challenge. To address this ne...

    Authors: Advait Balaji, Bryce Kille, Anthony D. Kappell, Gene D. Godbold, Madeline Diep, R. A. Leo Elworth, Zhiqin Qian, Dreycey Albin, Daniel J. Nasko, Nidhi Shah, Mihai Pop, Santiago Segarra, Krista L. Ternus and Todd J. Treangen
    Citation: Genome Biology 2022 23:133
  3. Proteogenomics aims to identify variant or unknown proteins in bottom-up proteomics, by searching transcriptome- or genome-derived custom protein databases. However, empirical observations reveal that these la...

    Authors: Laura Fancello and Thomas Burger
    Citation: Genome Biology 2022 23:132
  4. Genetic studies of human traits have revolutionized our understanding of the variation between individuals, and yet, the genetics of most traits is still poorly understood. In this review, we highlight the maj...

    Authors: Nadav Brandes, Omer Weissbrod and Michal Linial
    Citation: Genome Biology 2022 23:131
  5. A challenge in bulk gene differential expression analysis is to differentiate changes due to cell type-specific gene expression and cell type proportions. SCADIE is an iterative algorithm that simultaneously e...

    Authors: Daiwei Tang, Seyoung Park and Hongyu Zhao
    Citation: Genome Biology 2022 23:129
  6. Copy number alterations constitute important phenomena in tumor evolution. Whole genome single-cell sequencing gives insight into copy number profiles of individual cells, but is highly noisy. Here, we propose...

    Authors: Magda Markowska, Tomasz Cąkała, BłaŻej Miasojedow, Bogac Aybey, Dilafruz Juraeva, Johanna Mazur, Edith Ross, Eike Staub and Ewa Szczurek
    Citation: Genome Biology 2022 23:128
  7. Multiple sclerosis (MS) is an autoimmune condition of the central nervous system with a well-characterized genetic background. Prior analyses of MS genetics have identified broad enrichments across peripheral ...

    Authors: Michael H. Guo, Prashanth Sama, Brenna A. LaBarre, Hrishikesh Lokhande, John Balibalos, Ci Chu, Xiaomi Du, Pouya Kheradpour, Charles C. Kim, Taylor Oniskey, Thomas Snyder, Damien Z. Soghoian, Howard L. Weiner, Tanuja Chitnis and Nikolaos A. Patsopoulos
    Citation: Genome Biology 2022 23:127
  8. SARS-CoV-2 infection results in a broad spectrum of COVID-19 disease, from mild or no symptoms to hospitalization and death. COVID-19 disease severity has been associated with some pre-existing conditions and ...

    Authors: Matthew C. Pahl, Carole Le Coz, Chun Su, Prabhat Sharma, Rajan M. Thomas, James A. Pippin, Emylette Cruz Cabrera, Matthew E. Johnson, Michelle E. Leonard, Sumei Lu, Alessandra Chesi, Kathleen E. Sullivan, Neil Romberg, Struan F. A. Grant and Andrew D. Wells
    Citation: Genome Biology 2022 23:125
  9. Tumors are complex tissues of cancerous cells surrounded by a heterogeneous cellular microenvironment with which they interact. Single-cell sequencing enables molecular characterization of single cells within ...

    Authors: Jan Dohmen, Artem Baranovskii, Jonathan Ronen, Bora Uyar, Vedran Franke and Altuna Akalin
    Citation: Genome Biology 2022 23:123
  10. DNA methylation plays vital roles in both prokaryotes and eukaryotes. There are three forms of DNA methylation in prokaryotes: N6-methyladenine (6mA), N4-methylcytosine (4mC), and 5-methylcytosine (5mC). Although...

    Authors: Xuwen Li, Shiyuan Guo, Yan Cui, Zijian Zhang, Xinlong Luo, Margarita T. Angelova, Laura F. Landweber, Yinsheng Wang and Tao P. Wu
    Citation: Genome Biology 2022 23:122
  11. The plasticity along the epithelial-mesenchymal transition (EMT) spectrum has been shown to be regulated by various epigenetic repertoires. Emerging evidence of local chromatin conformation changes suggests th...

    Authors: Qing You Pang, Tuan Zea Tan, Vignesh Sundararajan, Yi-Chia Chiu, Edward Yu Wing Chee, Vin Yee Chung, Mahesh A. Choolani and Ruby Yun-Ju Huang
    Citation: Genome Biology 2022 23:121
  12. Cancer is a set of diseases characterized by unchecked cell proliferation and invasion of surrounding tissues. The many genes that have been genetically associated with cancer or shown to directly contribute t...

    Authors: Anupama Jha, Mathieu Quesnel-Vallières, David Wang, Andrei Thomas-Tikhonenko, Kristen W Lynch and Yoseph Barash
    Citation: Genome Biology 2022 23:117
  13. Pleiotropy describes the phenomenon in which a gene affects multiple phenotypes. The extent of pleiotropy is still disputed, mainly because of issues of inadequate power of analyses. A further challenge is tha...

    Authors: Eirini Christodoulaki, Viola Nolte, Wei-Yun Lai and Christian Schlötterer
    Citation: Genome Biology 2022 23:116
  14. Several high-throughput antibody-free methods for RNA modification detection from sequencing data have been developed. We present JACUSA2 as a versatile software solution and comprehensive analysis framework f...

    Authors: Michael Piechotta, Isabel S. Naarmann-de Vries, Qi Wang, Janine Altmüller and Christoph Dieterich
    Citation: Genome Biology 2022 23:115
  15. Technological development has enabled the profiling of gene expression and chromatin accessibility from the same cell. We develop scREG, a dimension reduction methodology, based on the concept of cis-regulatory p...

    Authors: Zhana Duren, Fengge Chang, Fnu Naqing, Jingxue Xin, Qiao Liu and Wing Hung Wong
    Citation: Genome Biology 2022 23:114
  16. Colorectal cancer (CRC) consensus molecular subtypes (CMS) have different immunological, stromal cell, and clinicopathological characteristics. Single-cell characterization of CMS subtype tumor microenvironmen...

    Authors: Ateeq M. Khaliq, Cihat Erdogan, Zeyneb Kurt, Sultan Sevgi Turgut, Miles W. Grunvald, Tim Rand, Sonal Khare, Jeffrey A. Borgia, Dana M. Hayden, Sam G. Pappas, Henry R. Govekar, Audrey E. Kam, Jochen Reiser, Kiran Turaga, Milan Radovich, Yong Zang…
    Citation: Genome Biology 2022 23:113
  17. Integration of single-cell multiomics profiles generated by different single-cell technologies from the same biological sample is still challenging. Previous approaches based on shared features have only provi...

    Authors: Jinzhuang Dou, Shaoheng Liang, Vakul Mohanty, Qi Miao, Yuefan Huang, Qingnan Liang, Xuesen Cheng, Sangbae Kim, Jongsu Choi, Yumei Li, Li Li, May Daher, Rafet Basar, Katayoun Rezvani, Rui Chen and Ken Chen
    Citation: Genome Biology 2022 23:112
  18. Recent proteogenomic studies revealed extensive translation outside of annotated protein coding regions, such as non-coding RNAs and untranslated regions of mRNAs. This non-canonical translation is largely due...

    Authors: Dmitry E. Andreev, Gary Loughran, Alla D. Fedorova, Maria S. Mikhaylova, Ivan N. Shatsky and Pavel V. Baranov
    Citation: Genome Biology 2022 23:111
  19. The precise spatiotemporal gene expression is orchestrated by enhancers that lack general sequence features and thus are difficult to be computationally identified. By nascent RNA sequencing combined with epig...

    Authors: Yilin Xie, Yan Chen, Zijuan Li, Jiafu Zhu, Min Liu, Yijing Zhang and Zhicheng Dong
    Citation: Genome Biology 2022 23:109
  20. Despite recent improvements in basecalling accuracy, nanopore sequencing still has higher error rates on short-tandem repeats (STRs). Instead of using basecalled reads, we developed DeepRepeat which converts i...

    Authors: Li Fang, Qian Liu, Alex Mas Monteys, Pedro Gonzalez-Alegre, Beverly L. Davidson and Kai Wang
    Citation: Genome Biology 2022 23:108
  21. Authors: Panagiotis Galanos, George Pappas, Alexander Polyzos, Athanassios Kotsinas, Ioanna Svolaki, Nickolaos N. Giakoumakis, Christina Glytsou, Ioannis S. Pateras, Umakanta Swain, Vassilis L. Souliotis, Alexandros G. Georgakilas, Nicholas Geacintov, Luca Scorrano, Claudia Lukas, Jiri Lukas, Zvi Livneh…
    Citation: Genome Biology 2022 23:107

    The original article was published in Genome Biology 2018 19:37

  22. Patient-derived organoid culture is a powerful system for studying the molecular mechanisms of cancers, especially colorectal cancer (CRC), one of the most prevalent cancers worldwide. There are two main types...

    Authors: Rui Wang, Yunuo Mao, Wendong Wang, Xin Zhou, Wei Wang, Shuai Gao, Jingyun Li, Lu Wen, Wei Fu and Fuchou Tang
    Citation: Genome Biology 2022 23:106
  23. Revealing the gene targets of distal regulatory elements is challenging yet critical for interpreting regulome data. Experiment-derived enhancer-gene links are restricted to a small set of enhancers and/or cel...

    Authors: Tingting Qin, Christopher Lee, Shiting Li, Raymond G. Cavalcante, Peter Orchard, Heming Yao, Hanrui Zhang, Shuze Wang, Snehal Patil, Alan P. Boyle and Maureen A. Sartor
    Citation: Genome Biology 2022 23:105
  24. Recent progress in deep learning has greatly improved the prediction of RNA splicing from DNA sequence. Here, we present Pangolin, a deep learning model to predict splice site strength in multiple tissues. Pan...

    Authors: Tony Zeng and Yang I Li
    Citation: Genome Biology 2022 23:103
  25. Genome-wide association studies (GWAS) aim to correlate phenotypic changes with genotypic variation. Upon transcription, single nucleotide variants (SNVs) may alter mRNA structure, with potential impacts on tr...

    Authors: Ángel Ferrero-Serrano, Megan M. Sylvia, Peter C. Forstmeier, Andrew J. Olson, Doreen Ware, Philip C. Bevilacqua and Sarah M. Assmann
    Citation: Genome Biology 2022 23:101
  26. Reproducibility is a significant challenge in (epi)genomic research due to the complexity of experiments composed of traditional biochemistry and informatics. Recent advances have exacerbated this as high-thro...

    Authors: Danying Shao, Gretta D. Kellogg, Ali Nematbakhsh, Prashant K. Kuntala, Shaun Mahony, B. Franklin Pugh and William K. M. Lai
    Citation: Genome Biology 2022 23:99
  27. Multiplex assays of variant effect (MAVEs) are a family of methods that includes deep mutational scanning experiments on proteins and massively parallel reporter assays on gene regulatory sequences. Despite th...

    Authors: Ammar Tareen, Mahdi Kooshkbaghi, Anna Posfai, William T. Ireland, David M. McCandlish and Justin B. Kinney
    Citation: Genome Biology 2022 23:98
  28. The advancement of highly multiplexed spatial technologies requires scalable methods that can leverage spatial information. We present MISTy, a flexible, scalable, and explainable machine learning framework fo...

    Authors: Jovan Tanevski, Ricardo Omar Ramirez Flores, Attila Gabor, Denis Schapiro and Julio Saez-Rodriguez
    Citation: Genome Biology 2022 23:97
  29. Genome-wide association studies have identified 3p21.31 as the main risk locus for severe COVID-19, although underlying mechanisms remain elusive. We perform an epigenomic dissection of 3p21.31, identifying a ...

    Authors: Bernard S. Stikker, Grégoire Stik, Antoinette F. van Ouwerkerk, Lianne Trap, Salvatore Spicuglia, Rudi W. Hendriks and Ralph Stadhouders
    Citation: Genome Biology 2022 23:96
  30. Biases of DNA repair can shape the nucleotide landscape of genomes at evolutionary timescales. The molecular mechanisms of those biases are still poorly understood because it is difficult to isolate the contri...

    Authors: Victoria O. Pokusaeva, Aránzazu Rosado Diez, Lorena Espinar, Albert Torelló Pérez and Guillaume J. Filion
    Citation: Genome Biology 2022 23:93
  31. Prime editing can induce a desired base substitution, insertion, or deletion in a target gene using reverse transcriptase after nick formation by CRISPR nickase. In this study, we develop a technology that can...

    Authors: Yeounsun Oh, Wi-jae Lee, Junho K. Hur, Woo Jeung Song, Youngjeon Lee, Hanseop Kim, Lee Wha Gwon, Young-Hyun Kim, Young-Ho Park, Chan Hyoung Kim, Kyung-Seob Lim, Bong-Seok Song, Jae-Won Huh, Sun-Uk Kim, Bong-Hyun Jun, Cheulhee Jung…
    Citation: Genome Biology 2022 23:92
  32. Interactions of chromatin with the nuclear lamina via lamina-associated domains (LADs) confer structural stability to the genome. The dynamics of positioning of LADs during differentiation, and how LADs imping...

    Authors: Julia Madsen-Østerbye, Mohamed Abdelhalim, Marie-Odile Baudement and Philippe Collas
    Citation: Genome Biology 2022 23:91
  33. Cardiac differentiation of human-induced pluripotent stem (hiPS) cells consistently produces a mixed population of cardiomyocytes and non-cardiac cell types, even when using well-characterized protocols. We so...

    Authors: Connie L. Jiang, Yogesh Goyal, Naveen Jain, Qiaohong Wang, Rachel E. Truitt, Allison J. Coté, Benjamin Emert, Ian A. Mellis, Karun Kiani, Wenli Yang, Rajan Jain and Arjun Raj
    Citation: Genome Biology 2022 23:90
  34. Promoters are sites of transcription initiation that harbour a high concentration of phenotype-associated genetic variation. The evolutionary gain and loss of promoters between species (collectively, termed tu...

    Authors: Robert S. Young, Lana Talmane, Sophie Marion de Procé and Martin S. Taylor
    Citation: Genome Biology 2022 23:89
  35. Cost-efficient library generation by early barcoding has been central in propelling single-cell RNA sequencing. Here, we optimize and validate prime-seq, an early barcoding bulk RNA-seq method. We show that it...

    Authors: Aleksandar Janjic, Lucas E. Wange, Johannes W. Bagnoli, Johanna Geuder, Phong Nguyen, Daniel Richter, Beate Vieth, Binje Vick, Irmela Jeremias, Christoph Ziegenhain, Ines Hellmann and Wolfgang Enard
    Citation: Genome Biology 2022 23:88
  36. Vascular invasion with tumor thrombus frequently occurs in advanced renal cell carcinoma (RCC). Thrombectomy is one of the most challenging surgeries with high rate of perioperative morbidity and mortality. Ho...

    Authors: Yue Shi, Qi Zhang, Hai Bi, Min Lu, Yezhen Tan, Daojia Zou, Liyuan Ge, Zhigang Chen, Cheng Liu, Weimin Ci and Lulin Ma
    Citation: Genome Biology 2022 23:87
  37. Determining the evolutionary relationships between genes is fundamental to comparative biological research. Here, we present SHOOT. SHOOT searches a user query sequence against a database of phylogenetic trees...

    Authors: David Mark Emms and Steven Kelly
    Citation: Genome Biology 2022 23:85

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