Relevant bibliographies by topics / Biochemistry – atlases

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  2. Dissertations / Theses
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Academic literature on the topic 'Biochemistry – atlases'

Author: Grafiati
Published: 28 July 2024
Last updated: 30 July 2024

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Journal articles on the topic "Biochemistry – atlases"

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Peng, Hanchuan, Phuong Chung, Fuhui Long, Lei Qu, Arnim Jenett, Andrew M. Seeds, Eugene W. Myers, and Julie H. Simpson. "BrainAligner: 3D registration atlases of Drosophila brains." Nature Methods 8, no. 6 (May 1, 2011): 493–98. http://dx.doi.org/10.1038/nmeth.1602.

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Krag, Sharon S. "Special Issue: Human and murine redox protein atlases." Biochimica et Biophysica Acta (BBA) - General Subjects 1810, no. 1 (January 2011): 1. http://dx.doi.org/10.1016/j.bbagen.2010.11.003.

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Ciric, Rastko, William H. Thompson, Romy Lorenz, Mathias Goncalves, Eilidh E. MacNicol, Christopher J. Markiewicz, Yaroslav O. Halchenko, et al. "TemplateFlow: FAIR-sharing of multi-scale, multi-species brain models." Nature Methods 19, no. 12 (December 2022): 1568–71. http://dx.doi.org/10.1038/s41592-022-01681-2.

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AbstractReference anatomies of the brain (‘templates’) and corresponding atlases are the foundation for reporting standardized neuroimaging results. Currently, there is no registry of templates and atlases; therefore, the redistribution of these resources occurs either bundled within existing software or in ad hoc ways such as downloads from institutional sites and general-purpose data repositories. We introduce TemplateFlow as a publicly available framework for human and non-human brain models. The framework combines an open database with software for access, management, and vetting, allowing scientists to share their resources under FAIR—findable, accessible, interoperable, and reusable—principles. TemplateFlow enables multifaceted insights into brains across species, and supports multiverse analyses testing whether results generalize across standard references, scales, and in the long term, species.
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Pliner, Hannah A., Jay Shendure, and Cole Trapnell. "Supervised classification enables rapid annotation of cell atlases." Nature Methods 16, no. 10 (September 9, 2019): 983–86. http://dx.doi.org/10.1038/s41592-019-0535-3.

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Haniffa, Muzlifah, Aidan Maartens, and Sarah A. Teichmann. "How developmental cell atlases inform stem cell embryo models." Nature Methods 20, no. 12 (December 2023): 1849–51. http://dx.doi.org/10.1038/s41592-023-02072-x.

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Ali, Mohamed T., Yaser ElNakieb, Ahmed Elnakib, Ahmed Shalaby, Ali Mahmoud, Mohammed Ghazal, Jawad Yousaf, et al. "The Role of Structure MRI in Diagnosing Autism." Diagnostics 12, no. 1 (January 11, 2022): 165. http://dx.doi.org/10.3390/diagnostics12010165.

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This study proposes a Computer-Aided Diagnostic (CAD) system to diagnose subjects with autism spectrum disorder (ASD). The CAD system identifies morphological anomalies within the brain regions of ASD subjects. Cortical features are scored according to their contribution in diagnosing a subject to be ASD or typically developed (TD) based on a trained machine-learning (ML) model. This approach opens the hope for developing a new CAD system for early personalized diagnosis of ASD. We propose a framework to extract the cerebral cortex from structural MRI as well as identifying the altered areas in the cerebral cortex. This framework consists of the following five main steps: (i) extraction of cerebral cortex from structural MRI; (ii) cortical parcellation to a standard atlas; (iii) identifying ASD associated cortical markers; (iv) adjusting feature values according to sex and age; (v) building tailored neuro-atlases to identify ASD; and (vi) artificial neural networks (NN) are trained to classify ASD. The system is tested on the Autism Brain Imaging Data Exchange (ABIDE I) sites achieving an average balanced accuracy score of 97±2%. This paper demonstrates the ability to develop an objective CAD system using structure MRI and tailored neuro-atlases describing specific developmental patterns of the brain in autism.
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Bryant, Katherine L., Longchuan Li, Nicole Eichert, and Rogier B. Mars. "A comprehensive atlas of white matter tracts in the chimpanzee." PLOS Biology 18, no. 12 (December 31, 2020): e3000971. http://dx.doi.org/10.1371/journal.pbio.3000971.

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Chimpanzees (Pan troglodytes) are, along with bonobos, humans’ closest living relatives. The advent of diffusion MRI tractography in recent years has allowed a resurgence of comparative neuroanatomical studies in humans and other primate species. Here we offer, in comparative perspective, the first chimpanzee white matter atlas, constructed from in vivo chimpanzee diffusion-weighted scans. Comparative white matter atlases provide a useful tool for identifying neuroanatomical differences and similarities between humans and other primate species. Until now, comprehensive fascicular atlases have been created for humans (Homo sapiens), rhesus macaques (Macaca mulatta), and several other nonhuman primate species, but never in a nonhuman ape. Information on chimpanzee neuroanatomy is essential for understanding the anatomical specializations of white matter organization that are unique to the human lineage.
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Ruffins, Seth W., and Russell E. Jacobs. "MRI in Developmental Biology and the Construction of Developmental Atlases." Cold Spring Harbor Protocols 2011, no. 3 (March 2011): top100. http://dx.doi.org/10.1101/pdb.top100.

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Younes, Subhi Talal, and Betty Herrington. "In silico analysis identifies a putative cell-of-origin for BRAF fusion-positive cerebellar pilocytic astrocytoma." PLOS ONE 15, no. 11 (November 18, 2020): e0242521. http://dx.doi.org/10.1371/journal.pone.0242521.

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Childhood cancers are increasingly recognized as disorders of cellular development. This study sought to identify the cellular and developmental origins of cerebellar pilocytic astrocytoma, the most common brain tumor of childhood. Using publicly available gene expression data from pilocytic astrocytoma tumors and controlling for driver mutation, a set of developmental-related genes which were overexpressed in cerebellar pilocytic astrocytoma was identified. These genes were then mapped onto several developmental atlases in order to identify normal cells with similar gene expression patterns and the developmental trajectory of those cells was interrogated. Eight known neuro-developmental genes were identified as being expressed in cerebellar pilocytic astrocytoma. Mapping those genes or their orthologs onto mouse neuro-developmental atlases identified overlap in their expression within the ventricular zone of the cerebellar anlage. Further analysis with a single cell RNA-sequencing atlas of the developing mouse cerebellum defined this overlap as occurring in ventricular zone progenitor cells at the division point between GABA-ergic neuronal and glial lineages, a developmental trajectory which closely mirrors that previously described to occur within pilocytic astrocytoma cells. Furthermore, ventricular zone progenitor cells and their progeny exhibited evidence of MAPK pathway activation, the paradigmatic oncogenic cascade known to be active in cerebellar pilocytic astrocytoma. Gene expression from developing human brain atlases recapitulated the same anatomic localizations and developmental trajectories as those found in mice. Taken together, these data suggest this population of ventricular zone progenitor cells as the cell-of-origin for BRAF fusion-positive cerebellar pilocytic astrocytoma.
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Ruffins, Seth W., Melanie Martin, Lindsey Keough, Salina Truong, Scott E. Fraser, Russell E. Jacobs, and Rusty Lansford. "Digital Three-Dimensional Atlas of Quail Development Using High-Resolution MRI." Scientific World JOURNAL 7 (2007): 592–604. http://dx.doi.org/10.1100/tsw.2007.125.

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We present an archetypal set of three-dimensional digital atlases of the quail embryo based on microscopic magnetic resonance imaging (μMRI). The atlases are composed of three modules: (1) images of fixedex ovoquail, ranging in age from embryonic day 5 to 10 (e05 to e10); (2) a coarsely delineated anatomical atlas of the μMRI data; and (3) an organ system-based hierarchical graph linked to the anatomical delineations. The atlas is designed to be accessed using SHIVA, a free Java application. The atlas is extensible and can contain other types of information including anatomical, physiological, and functional descriptors. It can also be linked to online resources and references. This digital atlas provides a framework to place various data types, such as gene expression and cell migration data, within the normal three-dimensional anatomy of the developing quail embryo. This provides a method for the analysis and examination of the spatial relationships among the different types of information within the context of the entire embryo.
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Dissertations / Theses on the topic "Biochemistry – atlases"

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Schmahl, Michelle Jordan. "Metabolic Profiling of Urine, Fecal, and Serum Samples and Pancreatic Tumors and Evaluation of HMGA1 Expression Levels in Pancreatic Intraepithelial Neoplasia Cells in the Ptf1a-Cre; LSL-KrasG12D Transgenic Mouse Model of Pancreatic Cancer." Miami University / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=miami1523977530802748.

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Books on the topic "Biochemistry – atlases"

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Klaus-Heinrich, Rohm, ed. Color atlas of biochemistry. [electronic resource]. 2nd ed. Stuttgart: Thieme, 2005.

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Marbas, Laurie L. Visual mnemonics for biochemistry. Malden, Mass: Blackwell Pub., 2004.

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Marbas, Laurie L. Visual mnemonics for biochemistry. Malden, Mass: Blackwell Pub, 2004.

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Koolman, Jan. Taschenatlas der Biochemie. 3rd ed. Stuttgart: Georg Thieme, 2003.

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Schwarz, Siegfried. Molecules of life & mutations: Understanding diseases by understanding proteins. Basel: Karger, 2002.

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Schwarz, Siegfried. Molecules of life & mutations: Understanding diseases by understanding proteins. Basel: Karger, 2002.

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Siegfried, Schwarz. Molecules of life & mutations: Understanding diseases by understanding proteins. Basel: Karger, 2002.

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Rohm, Klaus-Heinrich, and Jan Koolman. Color Atlas Of Biochemistry. 2nd ed. Thieme Medical Publishers, 2004.

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Color Atlas of Biochemistry. Thieme Medical Publishers, Incorporated, 2012.

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Roehm, Klaus Heinrich. Color Atlas of Biochemistry. Thieme, 2012.

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Book chapters on the topic "Biochemistry – atlases"

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Atkins, Peter, George Ratcliffe, Mark Wormald, and Julio de Paula. "Coupled reactions in biochemistry." In Physical Chemistry for the Life Sciences. Oxford University Press, 2023. http://dx.doi.org/10.1093/hesc/9780198830108.003.0020.

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This chapter explores coupled reactions. A spontaneous reaction may be able to drive forward a non-spontaneous reaction. In cells, every reaction is a part of a wider network of reactions and transmembrane transport processes. Here, inspection of metabolic pathways often reveals steps that can be considered to be a coupling between an energetically unfavourable process and an energetically favourable process. To better study these concepts, the chapter presents two case studies. The first involves the function of adenosine triphosphate, ATP (Atlas N3), which is to drive endergonic, energetically unfavourable processes such as protein synthesis, muscle contraction, and vision by the process of parallel coupling. The second concerns the oxidation of glucose and sequentially coupled reactions.
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Chatterjea, Dr. "Chapter-45 Environmental Biochemistry." In Jaypee Gold Standard Mini Atlas Series Biochemistry, 723–32. Jaypee Brothers Medical Publishers (P) Ltd., 2007. http://dx.doi.org/10.5005/jp/books/10408_45.

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Chatterjea, Dr. "Chapter-46 Biochemistry of Cancer." In Jaypee Gold Standard Mini Atlas Series Biochemistry, 733–57. Jaypee Brothers Medical Publishers (P) Ltd., 2007. http://dx.doi.org/10.5005/jp/books/10408_46.

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Chatterjea, Dr. "Chapter-49 Biochemistry of AIDS." In Jaypee Gold Standard Mini Atlas Series Biochemistry, 780–92. Jaypee Brothers Medical Publishers (P) Ltd., 2007. http://dx.doi.org/10.5005/jp/books/10408_49.

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Chatterjea, Dr. "Chapter-50 Biochemistry of Ageing." In Jaypee Gold Standard Mini Atlas Series Biochemistry, 793–800. Jaypee Brothers Medical Publishers (P) Ltd., 2007. http://dx.doi.org/10.5005/jp/books/10408_50.

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Garrison, R. G., and W. N. Arnold. "Atlas of Cell Morphology." In Yeast Cell Envelopes: Biochemistry, Biophysics, and Ultrastructure, 5–24. CRC Press, 2018. http://dx.doi.org/10.1201/9781351077798-2.

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Chatterjea, Dr. "Chapter-21 Biochemistry of Cholera-Vibrio Toxins, Pathogenesis." In Jaypee Gold Standard Mini Atlas Series Biochemistry, 289–96. Jaypee Brothers Medical Publishers (P) Ltd., 2007. http://dx.doi.org/10.5005/jp/books/10408_21.

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Maroni, Gustavo. "The Dopa Decarboxylase Cluster: Ddc, l(2)amd, Cs, DoxA2." In An Atlas of Drosophila Genes, 109–25. Oxford University PressNew York, NY, 1993. http://dx.doi.org/10.1093/oso/9780195071160.003.0011.

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Abstract The Ddc cluster is arbitrarily defined as those genes that fail to complement Df(2L)TW130, 37B9-C1 to 37D1-2, an 8-12-band deletion in the left arm of chromosome 2. The cluster contains 18 genetically identified genes plus three transcription units for which no mutations are known. Some of the genes in this cluster seem to be functionally related, most of them being involved in the formation, sclerotization and pigmentation of cuticle. Several genes in the cluster have mutant alleles that are female sterile. For three genes, Ddc, l(2)amd and DoxA2, some of the gene-product biochemistry is known; these genes are involved in catecholamine metabolism (Fig. 11.1) (Wright 1987).
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Chatterjea, Dr. "Chapter-01 Cell and Cell Organelles: Chemistry and Functions." In Jaypee Gold Standard Mini Atlas Series Biochemistry, 1–9. Jaypee Brothers Medical Publishers (P) Ltd., 2007. http://dx.doi.org/10.5005/jp/books/10408_1.

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Chatterjea, Dr. "Chapter-10 Biological Oxidation." In Jaypee Gold Standard Mini Atlas Series Biochemistry, 126–38. Jaypee Brothers Medical Publishers (P) Ltd., 2007. http://dx.doi.org/10.5005/jp/books/10408_10.

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