Results for 'spatial transcriptomics'

982 found
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  1.  25
    Spatially Resolved Transcriptomes—Next Generation Tools for Tissue Exploration.Michaela Asp, Joseph Bergenstråhle & Joakim Lundeberg - 2020 - Bioessays 42 (10):1900221.
    Recent advances in spatially resolved transcriptomics have greatly expanded the knowledge of complex multicellular biological systems. The field has quickly expanded in recent years, and several new technologies have been developed that all aim to combine gene expression data with spatial information. The vast array of methodologies displays fundamental differences in their approach to obtain this information, and thus, demonstrate method‐specific advantages and shortcomings. While the field is moving forward at a rapid pace, there are still multiple challenges (...)
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  2.  17
    Deep into the niche: Deciphering local endoderm‐microenvironment interactions in development, homeostasis, and disease of pancreas and intestine.Wojciech J. Szlachcic, Katherine C. Letai, Marissa A. Scavuzzo & Malgorzata Borowiak - 2023 - Bioessays 45 (4):2200186.
    Unraveling molecular and functional heterogeneity of niche cells within the developing endoderm could resolve mechanisms of tissue formation and maturation. Here, we discuss current unknowns in molecular mechanisms underlying key developmental events in pancreatic islet and intestinal epithelial formation. Recent breakthroughs in single‐cell and spatial transcriptomics, paralleled with functional studies in vitro, reveal that specialized mesenchymal subtypes drive the formation and maturation of pancreatic endocrine cells and islets via local interactions with epithelium, neurons, and microvessels. Analogous to this, (...)
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  3.  25
    “Hit-and-run”: Transcription factors get caught in the act.Varodom Charoensawan, Claudia Martinho & Philip A. Wigge - 2015 - Bioessays 37 (7):748-754.
    A key challenge for understanding transcriptional regulation is being able to measure transcription factor (TF)‐DNA binding events with sufficient spatial and temporal resolution; that is, when and where TFs occupy their cognate sites. A recent study by Para et al. has highlighted the dynamics underlying the activation of gene expression by a master regulator TF. This study provides concrete evidence for a long‐standing hypothesis in biology, the “hit‐and‐run” mechanism, which was first proposed decades ago. That is, gene expression is (...)
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  4.  25
    The transcriptome: malariologists ride the wave.R. J. M. Wilson - 2004 - Bioessays 26 (4):339-342.
    The Plasmodium falciparum genome‐sequencing project has provided malariologists with vast amounts of new information pertinent to a multitude of cellular processes that previously were only guessed about. In exploring this morass of predicted genes and proteins, there is now a danger of simply re‐inventing the cell. Fortunately, new global transcriptional analyses reassure malariologists that they are not dealing with just “any old cell.” The informative papers on the plasmodial transcriptome by Le Roch et al. (2003)1 and Bozdech et al. (2003)2 (...)
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  5.  60
    Population transcriptomics with single‐cell resolution: A new field made possible by microfluidics.Charles Plessy, Linda Desbois, Teruo Fujii & Piero Carninci - 2013 - Bioessays 35 (2):131-140.
    Tissues contain complex populations of cells. Like countries, which are comprised of mixed populations of people, tissues are not homogeneous. Gene expression studies that analyze entire populations of cells from tissues as a mixture are blind to this diversity. Thus, critical information is lost when studying samples rich in specialized but diverse cells such as tumors, iPS colonies, or brain tissue. High throughput methods are needed to address, model and understand the constitutive and stochastic differences between individual cells. Here, we (...)
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  6. Cross-species transcriptomic analysis elucidates constitutive aryl hydrocarbon receptor activity.Ren X. Sun, Lauren C. Chong, Trent T. Simmons, Kathleen E. Houlahan, Stephenie D. Prokopec, John D. Watson, Ivy D. Moffat, Sanna Lensu, Jere Lindén, Christine P'ng, Allan B. Okey, Raimo Pohjanvirta & Paul C. Boutros - unknown
    Background. Research on the aryl hydrocarbon receptor (AHR) has largely focused on variations in toxic outcomes resulting from its activation by halogenated aromatic hydrocarbons. But the AHR also plays key roles in regulating pathways critical for development, and after decades of research the mechanisms underlying physiological regulation by the AHR remain poorly characterized. Previous studies identified several core genes that respond to xenobiotic AHR ligands across a broad range of species and tissues. However, only limited inferences have been made regarding (...)
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  7.  42
    Epigenetics and the brain: Transcriptome sequencing reveals new depths to genomic imprinting.Gavin Kelsey - 2011 - Bioessays 33 (5):362-367.
    Transcriptome sequencing has identified more than a thousand potentially imprinted genes in the mouse brain. This comes as a revelation to someone who cut his teeth on the identification of imprinted genes when only a handful was known. Genomic imprinting, an epigenetic mechanism that determines expression of alleles according to sex of transmitting parent, was discovered over 25 years ago in mice but remains an enigmatic phenomenon. Why do these genes disobey the normal Mendelian logic of inheritance, do they function (...)
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  8. Chris Butler.Spatial Abstraction, Legal Violence & the Promise Of Appropriation - 2018 - In Andreas Philippopoulos-Mihalopoulos, Routledge Handbook of Law and Theory. New York, NY: Routledge.
     
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  9.  26
    Mouse‐centric comparative transcriptomics of protein coding and non‐coding RNAs.Masanori Suzuki & Yoshihide Hayashizaki - 2004 - Bioessays 26 (8):833-843.
    The largest transcriptome reported so far comprises 60,770 mouse full‐length cDNA clones, and is an effective reference data set for comparative transcriptomics. The number of mouse cDNAs identified greatly exceeds the number of genes predicted from the sequenced human and mouse genomes. This is largely because of extensive alternative splicing and the presence of many non‐coding RNAs (ncRNAs), which are difficult to predict from genomic sequences. Notably, ncRNAs are a major component of the transcriptomes of higher organisms, and many (...)
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  10.  53
    Exploiting human and mouse transcriptomic data: Identification of circadian genes and pathways influencing health.Emma E. Laing, Jonathan D. Johnston, Carla S. Möller-Levet, Giselda Bucca, Colin P. Smith, Derk-Jan Dijk & Simon N. Archer - 2015 - Bioessays 37 (5):544-556.
    The power of the application of bioinformatics across multiple publicly available transcriptomic data sets was explored. Using 19 human and mouse circadian transcriptomic data sets, we found that NR1D1 and NR1D2 which encode heme‐responsive nuclear receptors are the most rhythmic transcripts across sleep conditions and tissues suggesting that they are at the core of circadian rhythm generation. Analyzes of human transcriptomic data show that a core set of transcripts related to processes including immune function, glucocorticoid signalling, and lipid metabolism is (...)
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  11.  28
    Single neuron transcriptome analysis can reveal more than cell type classification.Lise J. Harbom, William D. Chronister & Michael J. McConnell - 2016 - Bioessays 38 (2):157-161.
    A recent single cell mRNA sequencing study by Dueck et al. compares neuronal transcriptomes to the transcriptomes of adipocytes and cardiomyocytes. Single cell ‘omic approaches such as those used by the authors are at the leading edge of molecular and biophysical measurement. Many groups are currently employing single cell sequencing approaches to understand cellular heterogeneity in cancer and during normal development. These single cell approaches also are beginning to address long‐standing questions regarding nervous system diversity. Beyond an innate interest in (...)
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  12.  22
    The Dictionary of Genomics, Transcriptomics, and Proteomics.Miguel A. Andrade-Navarro - 2009 - Bioessays 31 (12):1367-1369.
  13.  37
    Cajal body function in genome organization and transcriptome diversity.Iain A. Sawyer, David Sturgill, Myong-Hee Sung, Gordon L. Hager & Miroslav Dundr - 2016 - Bioessays 38 (12):1197-1208.
    Nuclear bodies contribute to non‐random organization of the human genome and nuclear function. Using a major prototypical nuclear body, the Cajal body, as an example, we suggest that these structures assemble at specific gene loci located across the genome as a result of high transcriptional activity. Subsequently, target genes are physically clustered in close proximity in Cajal body‐containing cells. However, Cajal bodies are observed in only a limited number of human cell types, including neuronal and cancer cells. Ultimately, Cajal body (...)
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  14.  7
    AI-driven transcriptome profile-guided hit molecule generation.Chen Li & Yoshihiro Yamanishi - 2025 - Artificial Intelligence 338 (C):104239.
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  15.  24
    Untranslated Parts of Genes Interpreted: Making Heads or Tails of High-Throughput Transcriptomic Data via Computational Methods.Krzysztof J. Szkop & Irene Nobeli - 2017 - Bioessays 39 (12):1700090.
    In this review we highlight the importance of defining the untranslated parts of transcripts, and present a number of computational approaches for the discovery and quantification of alternative transcription start and poly-adenylation events in high-throughput transcriptomic data. The fate of eukaryotic transcripts is closely linked to their untranslated regions, which are determined by the position at which transcription starts and ends at a genomic locus. Although the extent of alternative transcription starts and alternative poly-adenylation sites has been revealed by sequencing (...)
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  16.  20
    The Genomic Fabric Perspective on the Transcriptome Between Universal Quantifiers and Personalized Genomic Medicine.Dumitru Andrei Iacobas - 2016 - Biological Theory 11 (3):123-137.
    Numerous groups race to discover the gene biomarker whose alteration alone is indicative of a particular disease in all humans. Biomarkers are selected from the most frequently altered genes in large population cohorts. However, thousands of other genes are simultaneously affected, and, in each person, the same disease results from a unique, never-repeatable combination of gene alterations. Therefore, our Genomic Fabric Paradigm (GFP) switches the focus from the alteration of one particular gene to the overall change in selected groups of (...)
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  17.  25
    Understanding Animal Evolution: The Added Value of Sponge Transcriptomics and Genomics.Emmanuelle Renard, Sally P. Leys, Gert Wörheide & Carole Borchiellini - 2018 - Bioessays 40 (9):1700237.
    Sponges are important but often‐neglected organisms. The absence of classical animal traits (nerves, digestive tract, and muscles) makes sponges challenging for non‐specialists to work with and has delayed getting high quality genomic data compared to other invertebrates. Yet analyses of sponge genomes and transcriptomes currently available have radically changed our understanding of animal evolution. Sponges are of prime evolutionary importance as one of the best candidates to form the sister group of all other animals, and genomic data are essential to (...)
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  18.  37
    Experience and the ever‐changing brain: What the transcriptome can reveal.Todd G. Rubin, Jason D. Gray & Bruce S. McEwen - 2014 - Bioessays 36 (11):1072-1081.
    The brain is an ever‐changing organ that encodes memories and directs behavior. Neuroanatomical studies have revealed structural plasticity of neural architecture, and advances in gene expression technology and epigenetics have demonstrated new mechanisms underlying the brain's dynamic nature. Stressful experiences challenge the plasticity of the brain, and prolonged exposure to environmental stress redefines the normative transcriptional profile of both neurons and glia, and can lead to the onset of mental illness. A more thorough understanding of normal and abnormal gene expression (...)
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  19. How 'paternalistic' is spatial perception? Why wearing a heavy backpack doesn't -- and couldn't -- make hills look steeper.Chaz Firestone - 2013 - Perspectives on Psychological Science 8 (4):455-473.
  20. Three puzzles about spatial experience.David Chalmers - 2018 - In Adam Pautz & Daniel Stoljar, Blockheads! Essays on Ned Block’s Philosophy of Mind and Consciousness. new york: MIT Press.
     
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  21.  35
    Failure of spatial selectivity in vision.Suzanne V. Gatti & Howard E. Egeth - 1978 - Bulletin of the Psychonomic Society 11 (3):181-184.
  22.  50
    The embodied nature of spatial perspective taking: Embodied transformation versus sensorimotor interference.Klaus Kessler & Lindsey Anne Thomson - 2010 - Cognition 114 (1):72-88.
  23. What’s So Spatial about Time Anyway?Sam Baron & Peter W. Evans - 2021 - British Journal for the Philosophy of Science 72 (1):159-183.
    Skow ([2007]), and much more recently Callender ([2017]), argue that time can be distinguished from space due to the special role it plays in our laws of nature: our laws determine the behaviour of physical systems across time, but not across space. In this work we assess the claim that the laws of nature might provide the basis for distinguishing time from space. We find that there is an obvious reason to be sceptical of the argument Skow submits for distinguishing (...)
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  24.  57
    Tool-use changes multimodal spatial interactions between vision and touch in normal humans.Angelo Maravita, Charles Spence, Steffan Kennett & Jon Driver - 2002 - Cognition 83 (2):B25-B34.
  25.  56
    Plasticity of human spatial cognition: Spatial language and cognition covary across cultures.Daniel B. M. Haun, Christian J. Rapold, Gabriele Janzen & Stephen C. Levinson - 2011 - Cognition 119 (1):70-80.
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  26.  81
    Some primitive mechanisms of spatial attention.Zenon Pylyshyn - 1994 - Cognition 50 (1-3):363-384.
  27.  75
    Henri Lefebvre: Spatial Politics, Everyday Life and the Right to the City.Chris Butler - 2012 - Routledge.
    108 Lefebvre (2005:109). 109 Lefebvre (2005: 110,87). 110 Lefebvre (2005: 110) . 111 Lefebvre(1991b: 371¥2) (emphasis in original). 112 Lefebvre(1991b: 372); Lefebvre (1970: 20). 113 Lefebvre(1991b: 372) (emphasis in original).
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  28.  87
    Body-specific representations of spatial location.Tad T. Brunyé, Aaron Gardony, Caroline R. Mahoney & Holly A. Taylor - 2012 - Cognition 123 (2):229-239.
  29.  48
    Subitizing reflects visuo-spatial object individuation capacity.Manuela Piazza, Antonia Fumarola, Alessandro Chinello & David Melcher - 2011 - Cognition 121 (1):147-153.
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  30.  69
    Whence and whither in spatial language and spatial cognition?Barbara Landau & Ray Jackendoff - 1993 - Behavioral and Brain Sciences 16 (2):255-265.
  31.  27
    Information about spatial location based on knowledge about efference.Leon Festinger & Lance Kirkpatrick Canon - 1965 - Psychological Review 72 (5):373-384.
  32. Concrete Universals and Spatial Relations.Antti Keskinen, Jani Hakkarainen & Markku Keinänen - 2015 - European Journal of Analytic Philosophy 11 (1):57-71.
    According to strong immanent realism, proposed for instance by David M. Armstrong, universals are concrete, located in their instances. E.J. Lowe and Douglas Ehring have presented arguments to the effect that strong immanent realism is incoherent. Cody Gilmore has defended strong immanent realism against the charge of incoherence. Gilmore’s argument has thus far remained unanswered. We argue that Gilmore’s response to the charge of incoherence is an ad hoc move without support independent of strong immanent realism itself. We conclude that (...)
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  33.  49
    Linguistic and non-linguistic spatial categorization.L. Elizabeth Crawford, Terry Regier & Janellen Huttenlocher - 2000 - Cognition 75 (3):209-235.
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  34.  43
    Modularity and spatial reorientation in a simple mind: encoding of geometric and nongeometric properties of a spatial environment by fish.Valeria Anna Sovrano, Angelo Bisazza & Giorgio Vallortigara - 2002 - Cognition 85 (2):B51-B59.
  35. Temporal and spatial relations in sentential reasoning.Csongor Juhos, Ana Cristina Quelhas & Philip N. Johnson-Laird - 2012 - Cognition 122 (3):393-404.
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  36.  35
    Everyday life and spatial transformation: The construction of a community’s interiority in the void deck.Jiawen Han - 2022 - Technoetic Arts 20 (3):183-201.
    The void deck, originally developed for housing projects in Singapore, refers to the open space located on the ground floor of a residential building. The model of the void deck was exported to Suzhou Industrial Park and later used in a growing number of high-rise residential developments in China. Taking community interiority as a new perspective, the discussion of void decks and everyday life investigates whether the void deck endows a new layer of interiority to communal life as a special (...)
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  37.  35
    How are the spatial characteristics of the body represented? A reply to Pitron & de Vignemont.Stephen Gadsby - 2018 - Consciousness and Cognition 62:163-168.
    In their article, Pitron and de Vignemont (2017) provide an insightful and well overdue discussion of the relationship between long-term body representation models and Alice in Wonderland syndrome. Here, I supplement their discussion with a number of observations. First, I present a cautionary note regarding the interpretation of experiential changes in body size as reflective of changes in the content of body representations. Second, I show how their evidence contradicts an alternative model of body representation arising from research into anorexia (...)
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  38.  48
    Sex differences in the spatial representation of number.Rebecca Bull, Alexandra A. Cleland & Thomas Mitchell - 2013 - Journal of Experimental Psychology: General 142 (1):181.
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  39. Studies in spatial learning. II. Place learning versus response learning.E. C. Tolman, B. F. Ritchie & D. Kalish - 1946 - Journal of Experimental Psychology 36 (3):221.
  40.  63
    Happiness increases verbal and spatial working memory capacity where sadness does not: Emotion, working memory and executive control.Justin Storbeck & Raeya Maswood - 2016 - Cognition and Emotion 30 (5).
  41.  58
    Are Leibnizian Monads Spatial?J. A. Cover & Glenn A. Hartz - 1994 - History of Philosophy Quarterly 11 (3):295 - 316.
  42.  38
    Have sex differences in spatial ability evolved from male competition for mating and female concern for survival?Isabelle Ecuyer-Dab & Michèle Robert - 2004 - Cognition 91 (3):221-257.
  43.  62
    Time drawings: Spatial representation of temporal concepts.María Juliana Leone, Alejo Salles, Alejandro Pulver, Diego Andrés Golombek & Mariano Sigman - 2018 - Consciousness and Cognition 59:10-25.
  44.  24
    Impact of Spatial and Verbal Short-Term Memory Load on Auditory Spatial Attention Gradients.Edward J. Golob, Jenna Winston & Jeffrey R. Mock - 2017 - Frontiers in Psychology 8.
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  45.  90
    From Euler to Navier–Stokes: A Spatial Analysis of Conceptual Changes in Nineteenth-century Fluid Dynamics.Graciana Petersen & Frank Zenker - 2014 - International Studies in the Philosophy of Science 28 (3):235-253.
    This article provides a spatial analysis of the conceptual framework of fluid dynamics during the nineteenth century, focusing on the transition from the Euler equation to the Navier–Stokes equation. A dynamic version of Peter Gärdenfors's theory of conceptual spaces is applied which distinguishes changes of five types: addition and deletion of special laws; change of metric; change in importance; change in separability; addition and deletion of dimensions. The case instantiates all types but the deletion of dimensions. We also provide (...)
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  46.  38
    When endogenous spatial attention improves conscious perception: Effects of alerting and bottom-up activation.Fabiano Botta, Juan Lupiáñez & Ana B. Chica - 2014 - Consciousness and Cognition 23:63-73.
  47.  46
    Number-induced shifts in spatial attention: a replication study.Kiki Zanolie & Diane Pecher - 2014 - Frontiers in Psychology 5.
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  48. Kant on Spatial Orientation.Sven Bernecker - 2010 - European Journal of Philosophy 20 (4):519-533.
    This paper develops a novel interpretation of Kant's argument from incongruent counterparts to the effect that the representations of space and time are intuitions rather than concepts. When properly understood, the argument anticipates the contemporary position whereby the meaning of indexicals cannot be captured by descriptive contents.
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  49.  28
    Foundations of spatial vision: From retinal images to perceived shapes.Joseph S. Lappin & Warren D. Craft - 2000 - Psychological Review 107 (1):6-38.
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  50.  27
    Unmasking the Perky Effect: Spatial Extent of Image Interference on Visual Acuity.Adam Reeves & Catherine Craver-Lemley - 2012 - Frontiers in Psychology 3.
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