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Journal articles on the topic 'Genomic compartment'

Author: Grafiati

Published: 9 October 2021

Last updated: 30 July 2025

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1

Szczepińska, Teresa, Ayatullah Faruk Mollah, and Dariusz Plewczynski. "Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows." International Journal of Molecular Sciences 22, no. 21 (2021): 11591. http://dx.doi.org/10.3390/ijms222111591.

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The nature of genome organization into two basic structural compartments is as yet undiscovered. However, it has been indicated to be a mechanism of gene expression regulation. Using the classification approach, we ranked genomic marks that hint at compartmentalization. We considered a broad range of marks, including GC content, histone modifications, DNA binding proteins, open chromatin, transcription and genome regulatory segmentation in GM12878 cells. Genomic marks were defined over CTCF or RNAPII loops, which are basic elements of genome 3D structure, and over 100 kb genomic windows. Exper

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Bock, Jason B., Hugo T. Matern, Andrew A. Peden, and Richard H. Scheller. "A genomic perspective on membrane compartment organization." Nature 409, no. 6822 (2001): 839–41. http://dx.doi.org/10.1038/35057024.

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Bernardi, Giorgio. "The “Genomic Code”: DNA Pervasively Moulds Chromatin Structures Leaving no Room for “Junk”." Life 11, no. 4 (2021): 342. http://dx.doi.org/10.3390/life11040342.

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The chromatin of the human genome was analyzed at three DNA size levels. At the first, compartment level, two “gene spaces” were found many years ago: A GC-rich, gene-rich “genome core” and a GC-poor, gene-poor “genome desert”, the former corresponding to open chromatin centrally located in the interphase nucleus, the latter to closed chromatin located peripherally. This bimodality was later confirmed and extended by the discoveries (1) of LADs, the Lamina-Associated Domains, and InterLADs; (2) of two “spatial compartments”, A and B, identified on the basis of chromatin interactions; and (3) o

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Bian, Qian, Erika C. Anderson, Qiming Yang, and Barbara J. Meyer. "Histone H3K9 methylation promotes formation of genome compartments inCaenorhabditis elegansvia chromosome compaction and perinuclear anchoring." Proceedings of the National Academy of Sciences 117, no. 21 (2020): 11459–70. http://dx.doi.org/10.1073/pnas.2002068117.

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Genomic regions preferentially associate with regions of similar transcriptional activity, partitioning genomes into active and inactive compartments within the nucleus. Here we explore mechanisms controlling genome compartment organization inCaenorhabditis elegansand investigate roles for compartments in regulating gene expression. Distal arms ofC. eleganschromosomes, which are enriched for heterochromatic histone modifications H3K9me1/me2/me3, interact with each other bothin cisandin trans,while interacting less frequently with central regions, leading to genome compartmentalization. Arms ar

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López-Moyado, Isaac F., Ageliki Tsagaratou, Hiroshi Yuita, et al. "Paradoxical association of TET loss of function with genome-wide DNA hypomethylation." Proceedings of the National Academy of Sciences 116, no. 34 (2019): 16933–42. http://dx.doi.org/10.1073/pnas.1903059116.

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Cancer genomes are characterized by focal increases in DNA methylation, co-occurring with widespread hypomethylation. Here, we show that TET loss of function results in a similar genomic footprint. Both 5hmC in wild-type (WT) genomes and DNA hypermethylation in TET-deficient genomes are largely confined to the active euchromatic compartment, consistent with the known functions of TET proteins in DNA demethylation and the known distribution of 5hmC at transcribed genes and active enhancers. In contrast, an unexpected DNA hypomethylation noted in multiple TET-deficient genomes is primarily obser

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Hay, El Hamidi, and Romdhane Rekaya. "A multi-compartment model for genomic selection in multi-breed populations." Livestock Science 177 (July 2015): 1–7. http://dx.doi.org/10.1016/j.livsci.2015.03.027.

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Antony-Debré, Iléana, Vladimir T. Manchev, Nathalie Balayn, et al. "Level of RUNX1 activity is critical for leukemic predisposition but not for thrombocytopenia." Blood 125, no. 6 (2015): 930–40. http://dx.doi.org/10.1182/blood-2014-06-585513.

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Key Points A half loss of RUNX1 activity leads to defects in primitive erythropoiesis, megakaryopoiesis, and proplatelet formation. An almost complete loss of RUNX1 activity leads to the amplification of the granulomonocytic compartment with increased genomic instability.

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Pulkina, A. A., M. V. Sergeeva, A. Krokhin, M. A. Stukova, and A. Egorov. "Evidence for the extracellular delivery of influenza NS1 protein." Microbiology Independent Research Journal (MIR Journal) 8, no. 1 (2021): 27–37. http://dx.doi.org/10.18527/2500-2236-2021-8-1-27-37.

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We constructed a reporter influenza A/Puerto Rico/8/1934 virus expressing truncated 124aa N-terminal NS1 protein fused to a luciferase reporter sequence (NanoLuc) without signal peptide. The reproduction activity of the vector correlated well with the luminescent activity in the lysates of infected cell cultures or mouse respiratory organ suspensions. Surprisingly, we found that luciferase enzymatic activity was present not only in the intracellular compartments but also in cell culture supernatants as well as in the sera or bronchiolar lavages of infected mice. This fact allowed us to formula

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Pulkina, Anastasia, Maria Sergeeva, Artem Krokhin, Marina Stukova, and Andrej Egorov. "Evidence for the extracellular delivery of influenza NS1 protein." MIR J 8, no. 1 (2021): 27–37. https://doi.org/10.18527/2500-2236-2021-8-1-27-37.

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   We constructed a reporter influenza A/Puerto Rico/8/1934 virus expressing truncated 124aa N-terminal NS1 protein fused to a luciferase reporter sequence (NanoLuc) without signal peptide. The reproduction activity of the vector correlated well with the luminescent activity in the lysates of infected cell cultures or mouse respiratory organ suspensions. Surprisingly, we found that luciferase enzymatic activity was present not only in the intracellular compartments but also in cell culture supernatants as well as in the sera or bronchiolar lavages of infected mice. This fact allowed

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Junaid, Alim, Baljinder Singh, and Sabhyata Bhatia. "Evolutionary insights into 3D genome organization and epigenetic landscape ofVigna mungo." Life Science Alliance 7, no. 1 (2023): e202302074. http://dx.doi.org/10.26508/lsa.202302074.

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Eukaryotic genomes show an intricate three-dimensional (3D) organization within the nucleus that regulates multiple biological processes including gene expression. Contrary to animals, understanding of 3D genome organization in plants remains at a nascent stage. Here, we investigate the evolution of 3D chromatin architecture in legumes. By using cutting-edge PacBio, Illumina, and Hi-C contact reads, we report a gap-free, chromosome-scale reference genome assembly ofVigna mungo, an important minor legume cultivated in Southeast Asia. We spatially resolvedV. mungochromosomes into euchromatic, tr

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Novitsky, Vladimir, Curt G. Beckwith, Kristin Carpenter-Azevedo, et al. "Limited Short-Term Evolution of SARS-CoV-2 RNA-Dependent RNA Polymerase under Remdesivir Exposure in Upper Respiratory Compartments." Viruses 16, no. 10 (2024): 1511. http://dx.doi.org/10.3390/v16101511.

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Background: The extent of the SARS-CoV-2 short-term evolution under Remdesivir (RDV) exposure and whether it varies across different upper respiratory compartments are not fully understood. Methods: Patients hospitalized for COVID-19, with or without RDV therapy, were enrolled and completed up to three visits, in which they provided specimens from four respiratory compartments. Near full-length genome SARS-CoV-2 sequences were obtained from viral RNA, standard lineage and variant assignments were performed, and viral mutations in the RNA-dependent RNA polymerase (RdRp) region—the RDV target ge

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Berná, Luisa, María Laura Chiribao, Sebastián Pita, Fernando Alvarez-Valin, and Adriana Parodi-Talice. "Exploring the genomic landscape of the GP63 family in Trypanosoma cruzi: Evolutionary dynamics and functional peculiarities." PLOS Neglected Tropical Diseases 19, no. 3 (2025): e0012950. https://doi.org/10.1371/journal.pntd.0012950.

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Members of the GP63 metalloprotease family play crucial roles in parasite-host interactions, immune evasion, and pathogenesis. Although it has been widely studied in Leishmania spp., less is known about its function and diversity in Trypanosoma cruzi. This study focuses on characterizing the complete repertoire of GP63 sequences in the T. cruzi genome, refining gene annotations, and exploring the evolutionary dynamics that shape the diversity of these proteins. Eleven GP63 groups were identified, which are sharply defined and have a higher intra- than inter-group sequence identity. These GP63

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Isenhart, Randi, Son C. Nguyen, Leah Rosin, et al. "The length and strength of compartmental interactions are modulated by condensin II activity." PLOS Genetics 21, no. 7 (2025): e1011724. https://doi.org/10.1371/journal.pgen.1011724.

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The spatial organization of the genome is crucial for its function and integrity. Although the ring-like SMC complex condensin II has a well-documented role in organizing mitotic chromosomes, its function in interphase chromatin structure has remained more enigmatic. Using a combination of Oligopaint fluorescence in situ hybridization (FISH) and Hi-C, we show that altering condensin II levels in diploid Drosophila cells significantly changes chromosome architecture at large length scales between chromatin compartments. Notably, condensin II overexpression disrupts the robust boundary between h

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Highsmith, Max, and Jianlin Cheng. "Four-Dimensional Chromosome Structure Prediction." International Journal of Molecular Sciences 22, no. 18 (2021): 9785. http://dx.doi.org/10.3390/ijms22189785.

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Chromatin conformation plays an important role in a variety of genomic processes, including genome replication, gene expression, and gene methylation. Hi-C data is frequently used to analyze structural features of chromatin, such as AB compartments, topologically associated domains, and 3D structural models. Recently, the genomics community has displayed growing interest in chromatin dynamics. Here, we present 4DMax, a novel method, which uses time-series Hi-C data to predict dynamic chromosome conformation. Using both synthetic data and real time-series Hi-C data from processes, such as induc

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Ribeiro-dos-Santos, André M., Megan S. Hogan, Raven D. Luther, Ran Brosh, and Matthew T. Maurano. "Genomic context sensitivity of insulator function." Genome Research 32, no. 3 (2022): 425–36. http://dx.doi.org/10.1101/gr.276449.121.

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The specificity of interactions between genomic regulatory elements and potential target genes is influenced by the binding of insulator proteins such as CTCF, which can act as potent enhancer blockers when interposed between an enhancer and a promoter in a reporter assay. But not all CTCF sites genome-wide function as insulator elements, depending on cellular and genomic context. To dissect the influence of genomic context on enhancer blocker activity, we integrated reporter constructs with promoter-only, promoter and enhancer, and enhancer blocker configurations at hundreds of thousands of g

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Wang, Hong, and S. M. Hanash. "Contributions of Proteome Profiling to the Molecular Analysis of Cancer." Technology in Cancer Research & Treatment 1, no. 4 (2002): 237–45. http://dx.doi.org/10.1177/153303460200100404.

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The proteome is the most functional compartment encoded for in the genome. Technologies for protein separation and quantitation, coupled with mass spectrometry for protein identification, have provided the means for proteome profiling of tumor cell lines and tissues that complement genomic and transcriptomic profiling. The application of established and novel proteomic technologies to the molecular analysis of cancer is reviewed.

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3RD INTERNATIONAL MULTIDISCIPLINARY CANCER RESEARCH CONGRESS, Keynote Speakers. "Keynote Speakers." Doğu Karadeniz Sağlık Bilimleri Dergisi 2, Kongre Özel Sayısı (2023): 1–4. http://dx.doi.org/10.59312/ebshealth.1382566.

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Keynote Speakers Besim Ogretmen - Roles and Mechanisms of Sphingolipid Metabolism in the Regulation of Tumor Growth and Therapeutics: Implications in Personalized Cancer Chemotherapy and Tumor Immunology Chiara Raggi - Metabolic Aspects of Cholangiocarcinoma Stem-Compartment Candan Hızel Peery - Polygenic Risk Score (PRS) for Cancer - Can It Deliver on the Promise of Precision Oncology? Abdullah Kahraman - Comprehensive Genomic Profiling for Precision Oncology

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18

Giessler, Klara M., Kortine Kleinheinz, Daniel Huebschmann, et al. "Genetic subclone architecture of tumor clone-initiating cells in colorectal cancer." Journal of Experimental Medicine 214, no. 7 (2017): 2073–88. http://dx.doi.org/10.1084/jem.20162017.

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A hierarchically organized cell compartment drives colorectal cancer (CRC) progression. Genetic barcoding allows monitoring of the clonal output of tumorigenic cells without prospective isolation. In this study, we asked whether tumor clone-initiating cells (TcICs) were genetically heterogeneous and whether differences in self-renewal and activation reflected differential kinetics among individual subclones or functional hierarchies within subclones. Monitoring genomic subclone kinetics in three patient tumors and corresponding serial xenografts and spheroids by high-coverage whole-genome sequ

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Ryland, Georgina L., Lucy C. Fox, Xiangting Chen, et al. "Longitudinal Genomic Characterization Using Cell-Free DNA in Patients with Idiopathic Aplastic Anemia." Blood 136, Supplement 1 (2020): 5–6. http://dx.doi.org/10.1182/blood-2020-140912.

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The molecular profile of clonal hematopoiesis in patients (pts) with idiopathic aplastic anaemia (iAA) has been shown to predict response to immunosuppressive therapy (IST). Moreover, clonal evolution is associated with transformation of iAA to aggressive myeloid malignancies such as myelodysplastic syndrome (MDS) and acute myeloid leukaemia (AML). Detection of somatic mutations may help identify pts more likely to respond to IST and also those at increased risk of transformation however the predictive value of detecting mutations at a single timepoint is limited. Longitudinal detection of cha

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Fink, Ludger, Grazyna Kwapiszewska, Jochen Wilhelm, and Rainer M. Bohle. "Laser-microdissection for cell type- and compartment-specific analyses on genomic and proteomic level." Experimental and Toxicologic Pathology 57 (June 2006): 25–29. http://dx.doi.org/10.1016/j.etp.2006.02.010.

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21

Wang, Maojun, Jianying Li, Pengcheng Wang, et al. "Comparative Genome Analyses Highlight Transposon-Mediated Genome Expansion and the Evolutionary Architecture of 3D Genomic Folding in Cotton." Molecular Biology and Evolution 38, no. 9 (2021): 3621–36. http://dx.doi.org/10.1093/molbev/msab128.

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Abstract Transposable element (TE) amplification has been recognized as a driving force mediating genome size expansion and evolution, but the consequences for shaping 3D genomic architecture remains largely unknown in plants. Here, we report reference-grade genome assemblies for three species of cotton ranging 3-fold in genome size, namely Gossypium rotundifolium (K2), G. arboreum (A2), and G. raimondii (D5), using Oxford Nanopore Technologies. Comparative genome analyses document the details of lineage-specific TE amplification contributing to the large genome size differences (K2, 2.44 Gb;

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Conzemius, Rick, Haleh Ganjian, Dieter Blaas, and Renate Fuchs. "ICAM-1 Binding Rhinoviruses A89 and B14 Uncoat in Different Endosomal Compartments." Journal of Virology 90, no. 17 (2016): 7934–42. http://dx.doi.org/10.1128/jvi.00712-16.

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ABSTRACTHuman rhinovirus A89 (HRV-A89) and HRV-B14 bind to and are internalized by intercellular adhesion molecule 1 (ICAM-1); as demonstrated earlier, the RNA genome of HRV-B14 penetrates into the cytoplasm from endosomal compartments of the lysosomal pathway. Here, we show by immunofluorescence microscopy that HRV-A89 but not HRV-B14 colocalizes with transferrin in the endocytic recycling compartment (ERC). Applying drugs differentially interfering with endosomal recycling and with the pathway to lysosomes, we demonstrate that these two major-group HRVs productively uncoat in distinct endoso

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Zaunschirm, Mathias, Marc Pignitter, Antonio Kopic, et al. "Exposure of Human Gastric Cells to Oxidized Lipids Stimulates Pathways of Amino Acid Biosynthesis on a Genomic and Metabolomic Level." Molecules 24, no. 22 (2019): 4111. http://dx.doi.org/10.3390/molecules24224111.

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The Western diet is characterized by a high consumption of heat-treated fats and oils. During deep-frying processes, vegetable oils are subjected to high temperatures which result in the formation of lipid peroxidation products. Dietary intake of oxidized vegetable oils has been associated with various biological effects, whereas knowledge about the effects of structurally-characterized lipid peroxidation products and their possible absorption into the body is scarce. This study investigates the impact of linoleic acid, one of the most abundant polyunsaturated fatty acids in vegetable oils, an

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Samborskaia, Margarita D., Aleksandra Galitsyna, Ilya Pletenev, et al. "Cumulative contact frequency of a chromatin region is an intrinsic property linked to its function." PeerJ 8 (August 10, 2020): e9566. http://dx.doi.org/10.7717/peerj.9566.

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Regulation of gene transcription is a complex process controlled by many factors, including the conformation of chromatin in the nucleus. Insights into chromatin conformation on both local and global scales can be provided by the Hi-C (high-throughput chromosomes conformation capture) method. One of the drawbacks of Hi-C analysis and interpretation is the presence of systematic biases, such as different accessibility to enzymes, amplification, and mappability of DNA regions, which all result in different visibility of the regions. Iterative correction (IC) is one of the most popular techniques

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Philpott, Sean, Harold Burger, Christos Tsoukas, et al. "Human Immunodeficiency Virus Type 1 Genomic RNA Sequences in the Female Genital Tract and Blood: Compartmentalization and Intrapatient Recombination." Journal of Virology 79, no. 1 (2005): 353–63. http://dx.doi.org/10.1128/jvi.79.1.353-363.2005.

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ABSTRACT Investigation of human immunodeficiency virus type 1 (HIV-1) in the genital tract of women is crucial to the development of vaccines and therapies. Previous analyses of HIV-1 in various anatomic sites have documented compartmentalization, with viral sequences from each location that were distinct yet phylogenetically related. Full-length RNA genomes derived from different compartments in the same individual, however, have not yet been studied. Furthermore, although there is evidence that intrapatient recombination may occur frequently, recombinants comprising viruses from different si

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Caye, Aurélie, Kevin Rouault-Pierre, Marion Strullu, et al. "Despite mutation acquisition in hematopoietic stem cells, JMML-propagating cells are not always restricted to this compartment." Leukemia 34, no. 6 (2019): 1658–68. http://dx.doi.org/10.1038/s41375-019-0662-y.

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AbstractJuvenile myelomonocytic leukemia (JMML) is a rare aggressive myelodysplastic/myeloproliferative neoplasm of early childhood, initiated by RAS-activating mutations. Genomic analyses have recently described JMML mutational landscape; however, the nature of JMML-propagating cells (JMML-PCs) and the clonal architecture of the disease remained until now elusive. Combining genomic (exome, RNA-seq), Colony forming assay and xenograft studies, we detect the presence of JMML-PCs that faithfully reproduce JMML features including the complex/nonlinear organization of dominant/minor clones, both a

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Helaine, Charly, Aurélie E. Ferré, Marine M. Leblond, et al. "Angiopoietin-2 Combined with Radiochemotherapy Impedes Glioblastoma Recurrence by Acting in an Autocrine and Paracrine Manner: A Preclinical Study." Cancers 12, no. 12 (2020): 3585. http://dx.doi.org/10.3390/cancers12123585.

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(1) We wanted to assess the impact of Ang2 in RCT-induced changes in the environment of glioblastoma. (2) The effect of Ang2 overexpression in tumor cells was studied in the GL261 syngeneic immunocompetent model of GB in response to fractionated RCT. (3) We showed that RCT combined with Ang2 led to tumor clearance for the GL261-Ang2 group by acting on the tumor cells as well as on both vascular and immune compartments. (4) In vitro, Ang2 overexpression in GL261 cells exposed to RCT promoted senescence and induced robust genomic instability, leading to mitotic death. (5) Coculture experiments o

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Ertl, H., R. Mengele, S. Wenzl, J. Engel, and M. Sumper. "The extracellular matrix of Volvox carteri: molecular structure of the cellular compartment." Journal of Cell Biology 109, no. 6 (1989): 3493–501. http://dx.doi.org/10.1083/jcb.109.6.3493.

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The extracellular matrix (ECM) of Volvox contains insoluble fibrous layers that surround individual cells at a distance to form contiguous cellular compartments. Using immunological techniques, we identified a sulfated surface glycoprotein (SSG 185) as the monomeric precursor of this substructure within the ECM. The primary structure of the SSG 185 poly-peptide chain has been derived from cDNA and genomic DNA. A central domain of the protein, 80 amino acid residues long, consists almost exclusively of hydroxyproline residues. The chemical structure of the highly sulfated polysaccharide covalen

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Arnes, Luis, Zhaoqi Liu, Jiguang Wang, et al. "Comprehensive characterisation of compartment-specific long non-coding RNAs associated with pancreatic ductal adenocarcinoma." Gut 68, no. 3 (2018): 499–511. http://dx.doi.org/10.1136/gutjnl-2017-314353.

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ObjectivePancreatic ductal adenocarcinoma (PDA) is a highly metastatic disease with limited therapeutic options. Genome and transcriptome analyses have identified signalling pathways and cancer driver genes with implications in patient stratification and targeted therapy. However, these analyses were performed in bulk samples and focused on coding genes, which represent a small fraction of the genome.DesignWe developed a computational framework to reconstruct the non-coding transcriptome from cross-sectional RNA-Seq, integrating somatic copy number alterations (SCNA), common germline variants

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Bhattacharya, Arjun, Alina M. Hamilton, Melissa A. Troester, and Michael I. Love. "DeCompress: tissue compartment deconvolution of targeted mRNA expression panels using compressed sensing." Nucleic Acids Research 49, no. 8 (2021): e48-e48. http://dx.doi.org/10.1093/nar/gkab031.

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Abstract Targeted mRNA expression panels, measuring up to 800 genes, are used in academic and clinical settings due to low cost and high sensitivity for archived samples. Most samples assayed on targeted panels originate from bulk tissue comprised of many cell types, and cell-type heterogeneity confounds biological signals. Reference-free methods are used when cell-type-specific expression references are unavailable, but limited feature spaces render implementation challenging in targeted panels. Here, we present DeCompress, a semi-reference-free deconvolution method for targeted panels. DeCom

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Niscola, Pasquale, Valentina Gianfelici, Marco Giovannini, Daniela Piccioni, Carla Mazzone, and Paolo de Fabritiis. "Latest Insights and Therapeutic Advances in Myelodysplastic Neoplasms." Cancers 16, no. 8 (2024): 1563. http://dx.doi.org/10.3390/cancers16081563.

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Myelodysplastic syndromes/neoplasms (MDSs) encompass a range of hematopoietic malignancies, commonly affecting elderly individuals. Molecular alterations in the hematopoietic stem cell compartment drive disease pathogenesis. Recent advancements in genomic profiling have provided valuable insights into the biological underpinnings of MDSs and have expanded therapeutic options, particularly for specific molecularly defined subgroups. This review highlights the diagnostic principles, classification updates, prognostic stratification systems, and novel treatments, which could inform future clinica

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Plaisier, Christopher, Samantha O'Connor, Sonali Arora, Kevin Petrecca, Anoop Patel, and Patrick Paddison. "CCRG-02. DEVELOPMENTALLY PARTITIONED PROLIFERATIVE COMPARTMENTS IN GLIOBLASTOMA." Neuro-Oncology 25, Supplement_5 (2023): v38. http://dx.doi.org/10.1093/neuonc/noad179.0151.

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Abstract It is now well established from single-cell RNA-seq studies that glioblastoma (GBM) tumors are complex, maligned neuro-developmental ecosystems harboring diverse tumor cell types. Neoplastic cells can resemble astrocytes, neural progenitors, oligodendrocyte progenitor cells, mesenchymal cells, and radial glial cells that contribute to tumor growth and homeostasis in specific ways. However, GBM single-cell data sets have failed to produce general models for transitions in and out of specific developmental and proliferative states in tumors. One reason is that human GBM tumors do not ne

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Kumari, Poonam, Shahriar Tarighi, Thomas Braun, and Alessandro Ianni. "SIRT7 Acts as a Guardian of Cellular Integrity by Controlling Nucleolar and Extra-Nucleolar Functions." Genes 12, no. 9 (2021): 1361. http://dx.doi.org/10.3390/genes12091361.

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Sirtuins are key players for maintaining cellular homeostasis and are often deregulated in different human diseases. SIRT7 is the only member of mammalian sirtuins that principally resides in the nucleolus, a nuclear compartment involved in ribosomal biogenesis, senescence, and cellular stress responses. The ablation of SIRT7 induces global genomic instability, premature ageing, metabolic dysfunctions, and reduced stress tolerance, highlighting its critical role in counteracting ageing-associated processes. In this review, we describe the molecular mechanisms employed by SIRT7 to ensure cellul

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Saygin, Caner, Arletta Lozanski, Tzyy-Jye Doong, et al. "Genomic Analysis of Cellular Hierarchy in Acute Myeloid Leukemia Using Ultrasensitive LC-FACS-Seq." Blood 134, Supplement_1 (2019): 186. http://dx.doi.org/10.1182/blood-2019-125285.

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Normal hematopoiesis is organized in a hierarchical manner and it has been hypothesized that acute myeloid leukemia (AML) is organized in a similar way with leukemia-initiating cells (LIC) at the top of the hierarchy, giving rise to more differentiated blasts to sustain AML. Therefore, elimination of LIC population is critical for cure. This may be accomplished via novel molecular targeted therapies. The mutational composition of LIC and non-LIC compartments in AML has not been fully elucidated and could provide new insights into biology and treatment. We investigated the distribution and vari

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Niraj, Joshi, Anniina Färkkilä, and Alan D. D'Andrea. "The Fanconi Anemia Pathway in Cancer." Annual Review of Cancer Biology 3, no. 1 (2019): 457–78. http://dx.doi.org/10.1146/annurev-cancerbio-030617-050422.

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Fanconi anemia (FA) is a complex genetic disorder characterized by bone marrow failure (BMF), congenital defects, inability to repair DNA interstrand cross-links (ICLs), and cancer predisposition. FA presents two seemingly opposite characteristics: ( a) massive cell death of the hematopoietic stem and progenitor cell (HSPC) compartment due to extensive genomic instability, leading to BMF, and ( b) uncontrolled cell proliferation leading to FA-associated malignancies. The canonical function of the FA proteins is to collaborate with several other DNA repair proteins to eliminate clastogenic (chr

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Izzi, Valerio, Martin N. Davis, and Alexandra Naba. "Pan-Cancer Analysis of the Genomic Alterations and Mutations of the Matrisome." Cancers 12, no. 8 (2020): 2046. http://dx.doi.org/10.3390/cancers12082046.

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The extracellular matrix (ECM) is a master regulator of all cellular functions and a major component of the tumor microenvironment. We previously defined the “matrisome” as the ensemble of genes encoding ECM proteins and proteins modulating ECM structure or function. While compositional and biomechanical changes in the ECM regulate cancer progression, no study has investigated the genomic alterations of matrisome genes in cancers and their consequences. Here, mining The Cancer Genome Atlas (TCGA) data, we found that copy number alterations and mutations are frequent in matrisome genes, even mo

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Oki, Yasuhiro, Malek Faham, Victoria Carlton, Sattva S. Neelapu, and Anas Younes. "Detection of Diffuse Large B-Cell Lymphoma in Peripheral Blood Using High-Throughput Sequencing Assay." Blood 120, no. 21 (2012): 2666. http://dx.doi.org/10.1182/blood.v120.21.2666.2666.

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Abstract Abstract 2666 Background: In patients with diffuse large B-cell lymphoma (DLBCL), circulating lymphoma cells in the bloodstream are rarely detected by conventional morphology or flow cytometry evaluation. We developed a high-throughput sequencing based platform, LymphoSIGHT, to detect evidence of lymphoid malignancies in peripheral blood samples, as this could potentially be used for detection of minimal residual disease after treatment. This sequencing method has a sensitivity to detect one lymphoma cell per million leukocytes in peripheral blood. We herein report the results of our

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Weiss, U., and K. Rajewsky. "The repertoire of somatic antibody mutants accumulating in the memory compartment after primary immunization is restricted through affinity maturation and mirrors that expressed in the secondary response." Journal of Experimental Medicine 172, no. 6 (1990): 1681–89. http://dx.doi.org/10.1084/jem.172.6.1681.

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The anti-(4-hydroxy-3-nitro-phenyl)acetyl (NP) response is dominated by lambda 1 chain-bearing antibodies expressing the VH gene V186.2 in combination with the D element DFL16.1. lambda 1-positive B cells were isolated from the spleens of mice immunized with NP-chicken gamma globulin 6 wk earlier. Rearranged V186.2 genes were amplified from the genomic DNA of these cells and sequenced. In cases where the rearrangement was typical for secondary anti-NP antibodies, the VHDJH sequences were generally heavily mutated. The frequency and the nature of the nucleotide exchanges mirrored those of secon

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Cannon, LaMont, Sophia Fehrman, Marilia Pinzone, Sam Weissman, and Una O'Doherty. "Machine Learning Bolsters Evidence That D1, Nef, and Tat Influence HIV Reservoir Dynamics." Pathogens and Immunity 8, no. 2 (2024): 37–58. http://dx.doi.org/10.20411/pai.v8i2.621.

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Background: The primary hurdle to curing HIV is due to the establishment of a reservoir early in infection. In an effort to find new treatment strategies, we and others have focused on understanding the selection pressures exerted on the reservoir by studying how proviral sequences change over time. Methods: To gain insights into the dynamics of the HIV reservoir we analyzed longitudinal near full-length sequences from 7 people living with HIV between 1 and 20 years following the initiation of antiretroviral treatment. We used this data to employ Bayesian mixed effects models to characterize t

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Boultwood, Jacqueline, Carrie Fidler, Amanda J. Strickson, et al. "Narrowing and genomic annotation of the commonly deleted region of the 5q− syndrome." Blood 99, no. 12 (2002): 4638–41. http://dx.doi.org/10.1182/blood.v99.12.4638.

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The 5q− syndrome is the most distinct of the myelodysplastic syndromes, and the molecular basis for this disorder remains unknown. We describe the narrowing of the common deleted region (CDR) of the 5q− syndrome to the approximately 1.5-megabases interval at 5q32 flanked by D5S413 and theGLRA1 gene. The Ensembl gene prediction program has been used for the complete genomic annotation of the CDR. The CDR is gene rich and contains 24 known genes and 16 novel (predicted) genes. Of 40 genes in the CDR, 33 are expressed in CD34+ cells and, therefore, represent candidate genes since they are express

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Alvarez-Breckenridge, Christopher, Sanjay Prakadan, Samuel Markson, et al. "IMMU-02. GENOMIC AND TRANSCRIPTOMIC CORRELATES OF IMMUNOTHERAPY RESPONSE WITHIN THE TUMOR MICROENVIRONMENT OF LEPTOMENINGEAL METASTASES." Neuro-Oncology 23, Supplement_6 (2021): vi92. http://dx.doi.org/10.1093/neuonc/noab196.362.

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Abstract Leptomeningeal disease (LMD) is a devastating complication of solid tumor malignancies, with dire prognosis and no effective systemic treatment options. Over the past decade, the incidence of LMD has steadily increased due to therapeutics that have extended the survival of cancer patients, highlighting the need for new interventions. To examine the efficacy of immune checkpoint inhibitors (ICI) in patients with LMD, we completed two phase II clinical trials utilizing either Pembrolizumab alone or the combination of Ipilimumab and Nivolumab. We investigated the cellular and molecular f

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Matlock, William, Kevin K. Chau, Manal AbuOun, et al. "Genomic network analysis of environmental and livestock F-type plasmid populations." ISME Journal 15, no. 8 (2021): 2322–35. http://dx.doi.org/10.1038/s41396-021-00926-w.

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AbstractF-type plasmids are diverse and of great clinical significance, often carrying genes conferring antimicrobial resistance (AMR) such as extended-spectrum β-lactamases, particularly in Enterobacterales. Organising this plasmid diversity is challenging, and current knowledge is largely based on plasmids from clinical settings. Here, we present a network community analysis of a large survey of F-type plasmids from environmental (influent, effluent and upstream/downstream waterways surrounding wastewater treatment works) and livestock settings. We use a tractable and scalable methodology to

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Kim, Jun Hyun, Alexander V. Penson, Barry S. Taylor, and John H. J. Petrini. "Nbn−Mre11 interaction is required for tumor suppression and genomic integrity." Proceedings of the National Academy of Sciences 116, no. 30 (2019): 15178–83. http://dx.doi.org/10.1073/pnas.1905305116.

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We derived a mouse model in which a mutant form of Nbn/Nbs1mid8 (hereafter Nbnmid8) exhibits severely impaired binding to the Mre11−Rad50 core of the Mre11 complex. The Nbnmid8 allele was expressed exclusively in hematopoietic lineages (in Nbn−/mid8vav mice). Unlike Nbnflox/floxvav mice with Nbn deficiency in the bone marrow, Nbn−/mid8vav mice were viable. Nbn−/mid8vav mice hematopoiesis was profoundly defective, exhibiting reduced cellularity of thymus and bone marrow, and stage-specific blockage of B cell development. Within 6 mo, Nbn−/mid8 mice developed highly penetrant T cell leukemias. N

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Gruel, Nadège, Chloé Quignot, Julien Vibert, et al. "Abstract 96: Integrated molecular analysis of human dedifferentiated liposarcoma identifies a population of liposarcoma progenitors vulnerable to TGF beta inhibition." Cancer Research 83, no. 7_Supplement (2023): 96. http://dx.doi.org/10.1158/1538-7445.am2023-96.

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Abstract Introduction: Dedifferentiated liposarcomas (DDLPS) are the most frequent high-grade soft tissue sarcoma in adults. From a pathological point of view, these tumors are composed of high-grade undifferentiated tumor cells (DD), often showing an abrupt transition from a compartment of well-differentiated adipocytic tumor cells (WD). Tumor cells from both WD and DD compartments are characterized by recurrent MDM2 amplification, but their cellular origin and the molecular mechanisms associated with dedifferentiation are poorly understood. Methods: We performed an integrated molecular analy

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Sobel, Eric S., Chandra Mohan, Laurence Morel, Joel Schiffenbauer, and Edward K. Wakeland. "Genetic Dissection of SLE Pathogenesis: Adoptive Transfer of Sle1 Mediates the Loss of Tolerance by Bone Marrow-Derived B Cells." Journal of Immunology 162, no. 4 (1999): 2415–21. http://dx.doi.org/10.4049/jimmunol.162.4.2415.

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Abstract Sle1 is a potent autoimmune susceptibility locus on chromosome 1 originally identified in a genome scan of testcross progeny between the systemic lupus erythematosus-prone NZM2410 strain and C57BL/6. We subsequently produced B6.NZMc1, a congenic strain carrying the NZM2410-derived Sle1 genomic interval on the B6 background and demonstrated that Sle1 mediated the loss of tolerance to chromatin in both the B and T cell compartments. In this communication, we show by adoptive transfer experiments that the autoimmune phenotypes of Sle1 are completely reconstituted in B6 radiation chimeras

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Sur, Inderpreet, Wenshuo Zhao, Jilin Zhang, et al. "Shared requirement for MYC upstream super-enhancer region in tissue regeneration and cancer." Life Science Alliance 8, no. 6 (2025): e202403090. https://doi.org/10.26508/lsa.202403090.

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Cancer has been characterized as a wound that does not heal. Malignant cells are morphologically distinct from normal proliferating cells but have extensive similarities to tissues undergoing wound healing and/or regeneration. The mechanistic basis of this similarity has, however, remained enigmatic. Here, we show that the genomic region upstream ofMyc, which carries more cancer susceptibility in humans than any other genomic region, is required for intestinal regeneration after radiation damage. Failure to regenerate is associated with inefficientLy6a/Sca1+stem/progenitor cell mobilization, a

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Darmastuti, Arum, Pratama N. Hasan, Rachma Wikandari, Tyas Utami, Endang S. Rahayu, and Dian Anggraini Suroto. "Adhesion Properties of Lactobacillus plantarum Dad-13 and Lactobacillus plantarum Mut-7 on Sprague Dawley Rat Intestine." Microorganisms 9, no. 11 (2021): 2336. http://dx.doi.org/10.3390/microorganisms9112336.

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Adhesion capacity is considered one of the selection criteria for probiotic strains. The purpose of this study was to determine the adhesion properties of two candidate probiotics, Lactobacillus plantarum Dad-13 and Lactobacillus plantarum Mut-7. The evaluation included the hydrophobicity of the cell surface using microbial adhesion to hydrocarbons (MATH), autoaggregation, and the adhesion of L. plantarum Dad-13 and L. plantarum Mut-7 to the intestinal mucosa of Sprague Dawley rat, followed by genomic analysis of the two L. plantarum strains. L. plantarum Dad-13 and L. plantarum Mut-7 showed a

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Merbach, Anne Kathrin, Christian Rohde, Sergi Beneyto-Calabuig, et al. "A Venetoclax/Azacytidine Single-Cell RNA-Seq Resistance Signature (VARS) Predicts Response and Relapse in AML Patients." Blood 144, Supplement 1 (2024): 5744. https://doi.org/10.1182/blood-2024-209706.

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Acute myeloid leukemia (AML) is a highly aggressive and fatal disease, predominantly affecting older adults with a median diagnosis age of 68 years. Venetoclax, a BCL-2 inhibitor, combined with azacitidine (VA) has emerged as a standard treatment for AML patients ineligible for intensive chemotherapy. Despite initial efficacy, resistance to VA therapy remains a significant challenge, with approximately 27% of patients failing to respond and most responders eventually relapsing. Targeting anti-apoptotic proteins or combining venetoclax with IDH or FLT3 inhibitors may overcome therapy resistance

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Li, Heng, Ji Li, Ming Luo, Peilong Wang, Yue Sheng, and Hongling Peng. "Aberrant c-AMP Signalling in Richter Syndrome Revealed By Single-Cell Transcriptome and 3D Chromatin Analysis." Blood 144, Supplement 1 (2024): 3230. https://doi.org/10.1182/blood-2024-194294.

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Background: Richter syndrome (RS) is a severe progression of chronic lymphocytic leukaemia (CLL) into aggressive lymphoma, with a poorly understood molecular basis and an urgent need for new treatments. The application of single-cell RNA sequencing (scRNA-seq) has yielded numerous insights into the genetic events of lymphoma. Within the genome, three-dimensional chromatin structures are dynamic and could play a crucial role in transcriptional regulation. Methods: We integrated scRNA-seq and high-throughput chromosome conformation capture (Hi-C) sequencing to analyze a patient with CLL that tra

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Veyhe, Sólja Remisdóttir, Oriane Cédile, Sara Kamuk Dahlmann, et al. "Molecular Composition and Kinetics of B Cells During Ibrutinib Treatment in Patients with Chronic Lymphocytic Leukemia." International Journal of Molecular Sciences 25, no. 23 (2024): 12569. http://dx.doi.org/10.3390/ijms252312569.

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Chronic lymphocytic leukemia (CLL) is characterized by the accumulation of B cells due to constitutive B-cell receptor (BCR) signaling, leading to apoptosis resistance and increased proliferation. This study evaluates the effects of the Bruton Tyrosine Kinase (BTK) inhibitor ibrutinib on the molecular composition, clonality, and kinetics of B cells during treatment in CLL patients. Employing a multi-omics approach of up to 3.2 years of follow-up, we analyzed data from 24 CLL patients, specifically focusing on nine patients treated with ibrutinib monotherapy. In this study, clonal stability was

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