Results for 'proteins'

497 found
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  1. Toward a History of Epistemic Things: Synthesizing Proteins in the Test Tube.Hans-Jorg Rheinberger - 1997 - Stanford University Press.
    In this powerful work of conceptual and analytical originality, the author argues for the primacy of the material arrangements of the laboratory in the dynamics of modern molecular biology. In a post-Kuhnian move away from the hegemony of theory, he develops a new epistemology of experimentation in which research is treated as a process for producing epistemic things. A central concern of the book is the basic question of how novelty is generated in the empirical sciences. In addressing this question, (...)
     
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  2.  96
    TGF-Beta Signaling Proteins and the Protein Ontology.Arighi Cecilia, Liu Hongfang, Natale Darren, Barker Winona, Drabkin Harold, Blake Judith, Barry Smith & Wu Cathy - 2009 - BMC Bioinformatics 10 (Suppl 5):S3.
    The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO (...)
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  3.  18
    Persistent Biases in the Amino Acid Composition of Prokaryotic Proteins.Géraldine Pascal, Claudine Médigue & Antoine Danchin - 2006 - Bioessays 28 (7):726-738.
    Correspondence analysis of 28 proteomes selected to span the entire realm of prokaryotes revealed universal biases in the proteins’ amino acid distribution. Integral Inner Membrane Proteins always form an individual cluster, which can then be used to predict protein localisation in unknown proteomes, independently of the organism’s biotope or kingdom. Orphan proteins are consistently rich in aromatic residues. Another bias is also ubiquitous: the amino acid composition is driven by the GþC content of the first codon position. (...)
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  4.  5
    Intrinsically Disordered Proteins and Desiccation Tolerance: Elucidating Functional and Mechanistic Underpinnings of Anhydrobiosis.Thomas C. Boothby & Gary J. Pielak - 2017 - Bioessays 39 (11):1700119.
    Over 300 years ago the father of microscopy, Antonie van Leeuwenhoek, observed dried rotifers “coming back to life” upon rehydration. Since then, scientists have been fascinated by the enduring mystery of how certain organisms survive losing essentially drying out completely. Historically sugars, such as the disaccharide trehalose, have been viewed as major functional mediators of desiccation tolerance. However, some desiccation tolerant organisms do not produce this sugar, hinting that additional mediators, and potentially novel mechanisms exist. It has become apparent that (...)
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  5.  11
    A New Insight Into Sanger’s Development of Sequencing: From Proteins to DNA, 1943–1977. [REVIEW]Miguel García-Sancho - 2010 - Journal of the History of Biology 43 (2):265 - 323.
    Fred Sanger, the inventor of the first protein, RNA and DNA sequencing methods, has traditionally been seen as a technical scientist, engaged in laboratory bench work and not interested at all in intellectual debates in biology. In his autobiography and commentaries by fellow researchers, he is portrayed as having a trajectory exclusively dependent on technological progress. The scarce historical scholarship on Sanger partially challenges these accounts by highlighting the importance of professional contacts, institutional and disciplinary moves in his career, spanning (...)
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  6.  16
    LRRC8 Proteins Share a Common Ancestor with Pannexins, and May Form Hexameric Channels Involved in Cell‐Cell Communication.Federico Abascal & Rafael Zardoya - 2012 - Bioessays 34 (7):551-560.
  7.  10
    Ribosomal Proteins Control Tumor Suppressor Pathways in Response to Nucleolar Stress.Frédéric Lessard, Léa Brakier‐Gingras & Gerardo Ferbeyre - 2019 - Bioessays 41 (3):1800183.
  8.  26
    Origin and Evolution of Chromosomal Sperm Proteins.José M. Eirín-López & Juan Ausió - 2009 - Bioessays 31 (10):1062-1070.
  9.  1
    Heat Shock Proteins in the “Hot” Mitochondrion: Identity and Putative Roles.Mohamed A. Nasr, Galina I. Dovbeshko, Stephen L. Bearne, Nagwa El‐Badri & Chérif F. Matta - 2019 - Bioessays 41 (9):1900055.
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  10.  19
    Chaperoning Stem Cells: A Role for Heat Shock Proteins in the Modulation of Stem Cell Self‐Renewal and Differentiation?Earl Prinsloo, Mokgadi M. Setati, Victoria M. Longshaw & Gregory L. Blatch - 2009 - Bioessays 31 (4):370-377.
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  11.  13
    Rnd Proteins: Multifunctional Regulators of the Cytoskeleton and Cell Cycle Progression.Philippe Riou, Priam Villalonga & Anne J. Ridley - 2010 - Bioessays 32 (11):986-992.
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  12.  7
    The DING Family of Proteins: Ubiquitous in Eukaryotes, but Where Are the Genes?Anne Berna, Ken Scott, Eric Chabrière & François Bernier - 2009 - Bioessays 31 (5):570-580.
  13. Microstructuralism and Macromolecules: The Case of Moonlighting Proteins[REVIEW]Emma Tobin - 2010 - Foundations of Chemistry 12 (1):41-54.
    Microstructuralism in the philosophy of chemistry is the thesis that chemical kinds can be individuated in terms of their microstructural properties (Hendry in Philos Sci 73:864–875, 2006 ). Elements provide paradigmatic examples, since the atomic number should suffice to individuate the kind. In theory, Microstructuralism should also characterise higher-level chemical kinds such as molecules, compounds, and macromolecules based on their constituent atomic properties. In this paper, several microstructural theses are distinguished. An analysis of macromolecules such as moonlighting proteins suggests (...)
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  14.  21
    Semiotic Selection of Mutated or Misfolded Receptor Proteins.Franco Giorgi, Luis Emilio Bruni & Roberto Maggio - 2013 - Biosemiotics 6 (2):177-190.
    Receptor oligomerization plays a key role in maintaining genome stability and restricting protein mutagenesis. When properly folded, protein monomers assemble as oligomeric receptors and interact with environmental ligands. In a gene-centered view, the ligand specificity expressed by these receptors is assumed to be causally predetermined by the cell genome. However, this mechanism does not fully explain how differentiated cells have come to express specific receptor repertoires and which combinatorial codes have been explored to activate their associated signaling pathways. It is (...)
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  15.  19
    A New Way to Treat Brain Tumors: Targeting Proteins Coded by Microcephaly Genes?Patrick Y. Lang & Timothy R. Gershon - 2018 - Bioessays 40 (5):1700243.
    New targets for brain tumor therapies may be identified by mutations that cause hereditary microcephaly. Brain growth depends on the repeated proliferation of stem and progenitor cells. Microcephaly syndromes result from mutations that specifically impair the ability of brain progenitor or stem cells to proliferate, by inducing either premature differentiation or apoptosis. Brain tumors that derive from brain progenitor or stem cells may share many of the specific requirements of their cells of origin. These tumors may therefore be susceptible to (...)
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  16.  24
    Support Vector Machines for Predicting Apoptosis Proteins Types.Jing Huang & Feng Shi - 2005 - Acta Biotheoretica 53 (1):39-47.
    Apoptosis proteins have a central role in the development and homeostasis of an organism. These proteins are very important for understanding the mechanism of programmed cell death, and their function is related to their types. According to the classification scheme by Zhou and Doctor (2003), the apoptosis proteins are categorized into the following four types: (1) cytoplasmic protein; (2) plasma membrane-bound protein; (3) mitochondrial inner and outer proteins; (4) other proteins. A powerful learning machine, the (...)
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  17.  26
    Microtubule Inner Proteins: A Meshwork of Luminal Proteins Stabilizing the Doublet Microtubule.Muneyoshi Ichikawa & Khanh Huy Bui - 2018 - Bioessays 40 (3):1700209.
    Motile eukaryotic cilia and flagella are hair-like organelles responsible for cell motility and mucociliary clearance. Using cryo-electron tomography, it has been shown that the doublet microtubule, the cytoskeleton core of the cilia and flagella, has microtubule inner protein structures binding periodically inside its lumen. More recently, single-particle cryo-electron microscopy analyses of isolated doublet microtubules have shown that microtubule inner proteins form a meshwork inside the doublet microtubule. High-resolution structures revealed new types of interactions between the microtubule inner proteins (...)
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  18.  14
    Primary Cilia Reconsidered in the Context of Ciliopathies: Extraciliary and Ciliary Functions of Cilia Proteins Converge on a Polarity Theme?Kiet Hua & Russell J. Ferland - 2018 - Bioessays 40 (8):1700132.
    Once dismissed as vestigial organelles, primary cilia have garnered the interest of scientists, given their importance in development/signaling, and for their implication in a new disease category known as ciliopathies. However, many, if not all, “cilia” proteins also have locations/functions outside of the primary cilium. These extraciliary functions can complicate the interpretation of a particular ciliopathy phenotype: it may be a result of defects at the cilium and/or at extraciliary locations, and it could be broadly related to a unifying (...)
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  19.  22
    Prenylation of Viral Proteins by Enzymes of the Host: Virus-Driven Rationale for Therapy with Statins and FT/GGT1 Inhibitors.S. Marakasova Ekaterina, Eisenhaber Birgit, Maurer‐Stroh Sebastian, Eisenhaber Frank & Baranova Ancha - 2017 - Bioessays 39 (10):1700014.
    Intracellular bacteria were recently shown to employ eukaryotic prenylation system for modifying activity and ensuring proper intracellular localization of their own proteins. Following the same logic, the proteins of viruses may also serve as prenylation substrates. Using extensively validated high-confidence prenylation predictions by PrePS with a cut-off for experimentally confirmed farnesylation of hepatitis delta virus antigen, we compiled in silico evidence for several new prenylation candidates, including IRL9 and few other proteins encoded by Herpesviridae, Nef, E1A, NS5A, (...)
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  20.  15
    Loss and Rebirth of the Animal Microtubule Organizing Center: How Maternal Expression of Centrosomal Proteins Cooperates with the Sperm Centriole in Zygotic Centrosome Reformation.Daigo Inoue, Joachim Wittbrodt & Oliver J. Gruss - 2018 - Bioessays 40 (4):1700135.
    Centrosomes are the main microtubule organizing centers in animal cells. In particular during embryogenesis, they ensure faithful spindle formation and proper cell divisions. As metazoan centrosomes are eliminated during oogenesis, they have to be reassembled upon fertilization. Most metazoans use the sperm centrioles as templates for new centrosome biogenesis while the egg's cytoplasm re-prepares all components for on-going centrosome duplication in rapidly dividing embryonic cells. We discuss our knowledge and the experimental challenges to analyze zygotic centrosome reformation, which requires genetic (...)
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  21.  20
    Protein Folding and Evolution Are Driven by the Maxwell Demon Activity of Proteins.Alejandro Balbín & Eugenio Andrade - 2004 - Acta Biotheoretica 52 (3):173-200.
    In this paper we propose a theoretical model of protein folding and protein evolution in which a polypeptide (sequence/structure) is assumed to behave as a Maxwell Demon or Information Gathering and Using System (IGUS) that performs measurements aiming at the construction of the native structure. Our model proposes that a physical meaning to Shannon information (H) and Chaitin's algorithmic information (K) parameters can be both defined and referred from the IGUS standpoint. Our hypothesis accounts for the interdependence of protein folding (...)
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  22.  32
    Engineering Novel Proteins with Orthogonal tRNA: Artificial Causes That Make a Difference.Janella Baxter - manuscript
    Model organisms, the use of green fluorescent proteins, and orthogonal transfer RNA are examples of artificial causes being used in biology. Recent work characterizing the research interests of biologists in terms of a common set of values has ruled out artificial causes as biologically interesting. For instance, Kenneth Waters argues that biologists are primarily interested in causes that actually obtain. Similarly, Marcel Weber argues that biologists are primarily concerned with biologically normal interventions. Both views express a widely received attitude (...)
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  23.  27
    Evolution of the Gelsolin Family of Actin-Binding Proteins as Novel Transcriptional Coactivators.Stuart K. Archer, Charles Claudianos & Hugh D. Campbell - 2005 - Bioessays 27 (4):388-396.
    The gelsolin gene family encodes a number of higher eukaryotic actin-binding proteins that are thought to function in the cytoplasm by severing, capping, nucleating or bundling actin filaments. Recent evidence, however, suggests that several members of the gelsolin family may have adopted unexpected nuclear functions including a role in regulating transcription. In particular, flightless I, supervillin and gelsolin itself have roles as coactivators for nuclear receptors, despite the fact that their divergence appears to predate the evolutionary appearance of nuclear (...)
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  24.  34
    Proteins and Genes, Singletons and Species.Branko Kozulić - unknown
    Recent experimental data from proteomics and genomics are interpreted here in ways that challenge the predominant viewpoint in biology according to which the four evolutionary processes, including mutation, recombination, natural selection and genetic drift, are sufficient to explain the origination of species. The predominant viewpoint appears incompatible with the finding that the sequenced genome of each species contains hundreds, or even thousands, of unique genes - the genes that are not shared with any other species. These unique genes and (...), singletons, define the very character of every species. Moreover, the distribution of protein families from the sequenced genomes indicates that the complexity of genomes grows in a manner different from that of self-organizing networks: the dominance of singletons leads to the conclusion that in living organisms a most unlikely phenomenon can be the most common one. In order to provide proper rationale for these conclusions related to the singletons, the paper first treats the frequency of functional proteins among random sequences, followed by a discussion on the protein structure space, and it ends by questioning the idea that protein domains represent conserved units of evolution. (shrink)
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  25.  34
    Proteins, the Chaperone Function and Heredity.Valeria Mosini - 2013 - Biology and Philosophy 28 (1):53-74.
    In this paper I use a case study—the discovery of the chaperon function exerted by proteins in the various steps of the hereditary process—to re-discuss the question whether the nucleic acids are the sole repositories of relevant information as assumed in the information theory of heredity. The evidence I here present of a crucial role for molecular chaperones in the folding of nascent proteins, as well as in DNA duplication, RNA folding and gene control, suggests that the family (...)
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  26.  8
    Prenylation of Viral Proteins by Enzymes of the Host: Virus-Driven Rationale for Therapy with Statins and FT/GGT1 Inhibitors.Ekaterina S. Marakasova, Birgit Eisenhaber, Sebastian Maurer-Stroh, Frank Eisenhaber & Ancha Baranova - 2017 - Bioessays 39 (10):1700014.
    Intracellular bacteria were recently shown to employ eukaryotic prenylation system for modifying activity and ensuring proper intracellular localization of their own proteins. Following the same logic, the proteins of viruses may also serve as prenylation substrates. Using extensively validated high-confidence prenylation predictions by PrePS with a cut-off for experimentally confirmed farnesylation of hepatitis delta virus antigen, we compiled in silico evidence for several new prenylation candidates, including IRL9 and few other proteins encoded by Herpesviridae, Nef, E1A, NS5A, (...)
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  27.  13
    Unique Lipids and Unique Properties of Retinal Proteins.Kamon Sanada & Yoshitaka Fukada - 1995 - Behavioral and Brain Sciences 18 (3):486-487.
    Amino-terminal heteroacylation has been identified in retinal proteins including recoverin and α subunit of G-protein, transducin. The tissue-specific modification seems to mediate not only a proteinmembrane interaction but also a specific protein-protein interaction. The mechanism generating the heterogeneity and its physiological role are still unclear, but an interesting idea for the latter postulates a fine regulation of the signal transduction pathway by distinct N-acyl groups.
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  28.  9
    Insider Trading: Extracellular Matrix Proteins and Their Non-Canonical Intracellular Roles.Andrew L. Hellewell & Josephine C. Adams - 2016 - Bioessays 38 (1):77-88.
    In metazoans, the extracellular matrix (ECM) provides a dynamic, heterogeneous microenvironment that has important supportive and instructive roles. Although the primary site of action of ECM proteins is extracellular, evidence is emerging for non‐canonical intracellular roles. Examples include osteopontin, thrombospondins, IGF‐binding protein 3 and biglycan, and relate to roles in transcription, cell‐stress responses, autophagy and cancer. These findings pose conceptual problems on how proteins signalled for secretion can be routed to the cytosol or nucleus, or can function in (...)
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  29.  7
    Adenylyl Cyclase, G Proteins, and Synaptic Plasticity.Mark M. Rasenick - 1995 - Behavioral and Brain Sciences 18 (3):484-485.
    It has been suggested that type I adenylyl cyclase may play a unique role in long-term potentiation, due to both unique regulatory properties as well as a specialized distribution within the mammalian brain. This would allow an integration of the signals wrought by increased intracellular calcium with those conveyed into the cellular milieu via increased cAMP. These results are discussed in the context of changes in cellular structure, because of changing interactions between G proteins and cytoskeletal components, which might (...)
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  30.  5
    Glycosaminoglycan-Protein Interactions: Definition of Consensus Sites in Glycosaminoglycan Binding Proteins.Ronald E. Hileman, Jonathan R. Fromm, John M. Weiler & Robert J. Linhardt - 1998 - Bioessays 20 (2):156-167.
    Although interactions of proteins with glycosaminoglycans (GAGs), such as heparin and heparan sulphate, are of great biological importance, structural requirements for protein‐GAG binding have not been well‐characterised. Ionic interactions are important in promoting protein‐GAG binding. Polyelectrolyte theory suggests that much of the free energy of binding comes from entropically favourable release of cations from GAG chains. Despite their identical charges, arginine residues bind more tightly to GAGs than lysine residues. The spacing of these residues may determine protein‐GAG affinity and (...)
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  31.  1
    Cellular Adaptation Relies on Regulatory Proteins Having Episodic Memory.Razvan C. Stan, Darshak K. Bhatt & Maristela M. De Camargo - forthcoming - Bioessays.
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  32. Mammalian Chromodomain Proteins: Their Role in Genome Organisation and Expression.David O. Jones, Ian G. Cowell & Prim B. Singh - 2000 - Bioessays 22 (2):124-137.
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  33.  12
    Genomic Accumulation of Retrotransposons Was Facilitated by Repressive RNA‐Binding Proteins: A Hypothesis.Jan Attig & Jernej Ule - 2019 - Bioessays 41 (2):1800132.
  34. Mechanics of Motor Proteins and the Cytoskeleton (Review).Lincoln E. Ford - 2002 - Perspectives in Biology and Medicine 45 (2):305-307.
  35.  15
    A New Insight Into Sanger’s Development of Sequencing: From Proteins to DNA, 1943–1977.Miguel García-Sancho - 2010 - Journal of the History of Biology 43 (2):265-323.
    Fred Sanger, the inventor of the first protein, RNA and DNA sequencing methods, has traditionally been seen as a technical scientist, engaged in laboratory bench work and not interested at all in intellectual debates in biology. In his autobiography and commentaries by fellow researchers, he is portrayed as having a trajectory exclusively dependent on technological progress. The scarce historical scholarship on Sanger partially challenges these accounts by highlighting the importance of professional contacts, institutional and disciplinary moves in his career, spanning (...)
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  36.  21
    Converging Images: Techniques of Intervention and Forms of Representation of Sodium-Channel Proteins in Nerve Cell Membranes. [REVIEW]Maria Trumpler - 1997 - Journal of the History of Biology 30 (1):55 - 89.
  37.  22
    RNA Binding Proteins as Regulators of Retrotransposon‐Induced Exonization.John LaCava - 2019 - Bioessays 41 (2):1800263.
  38.  22
    Back From the Brink: Retrieval of Membrane Proteins From Terminal Compartments.Matthew N. J. Seaman - 2019 - Bioessays 41 (3):1800146.
  39.  19
    Therefore, What Are Recombination Proteins There For?Justin Courcelle, Ann K. Ganesan & Philip C. Hanawalt - 2001 - Bioessays 23 (5):463-470.
  40.  7
    The Evolution of Meiosis: Recruitment and Modification of Somatic DNA-Repair Proteins.Edyta Marcon & Peter B. Moens - 2005 - Bioessays 27 (8):795-808.
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  41.  28
    Methyl CpG‐Binding Proteins and Transcriptional Repression.Paul A. Wade - 2001 - Bioessays 23 (12):1131-1137.
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  42.  5
    Hypothesis: Motor Proteins and Ion Pumps, Not Ciliary Motion, Initiate LR Asymmetry.M. Levin - 2003 - Bioessays 25 (10):1002-1010.
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  43.  3
    Structural and Functional Properties of the Evolutionarily Ancient Y‐Box Family of Nucleic Acid Binding Proteins.Alan P. Wolffe - 1994 - Bioessays 16 (4):245-251.
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  44.  26
    Are Nicotinic Acetylcholine Receptors Coupled to G Proteins?Nadine Kabbani, Jacob C. Nordman, Brian A. Corgiat, Daniel P. Veltri, Amarda Shehu, Victoria A. Seymour, David J. Adams, Zeljko Durdevic, Matthias Schaefer & Ron Milo - 2013 - Bioessays 35 (12):1025-1034.
  45.  28
    Are Nicotinic Acetylcholine Receptors Coupled to G Proteins?Nadine Kabbani, Jacob C. Nordman, Brian A. Corgiat, Daniel P. Veltri, Amarda Shehu, Victoria A. Seymour & David J. Adams - 2013 - Bioessays 35 (12):1025-1034.
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  46.  12
    More Than the Sum of Their Parts: On the Evolution of Proteins From Peptides.Johannes Söding & Andrei N. Lupas - 2003 - Bioessays 25 (9):837-846.
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  47.  25
    Cell Death Proteins: An Evolutionary Role in Cellular Adaptation Before the Advent of Apoptosis.Sarah A. Dick & Lynn A. Megeney - 2013 - Bioessays 35 (11):974-983.
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  48.  24
    Aggregation of polyQ‐Extended Proteins is Promoted by Interaction with Their Natural Coiled‐Coil Partners.Spyros Petrakis, Martin H. Schaefer, Erich E. Wanker & Miguel A. Andrade-Navarro - 2013 - Bioessays 35 (6):503-507.
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  49.  9
    A Role for Y-Box Proteins in Cell Proliferation.Michael Ladomery & John Sommerville - 1995 - Bioessays 17 (1):9-11.
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  50.  16
    Position Effect Variegation and Chromatin Proteins.Gunter Reute & Pierre Spierer - 1992 - Bioessays 14 (9):605-612.
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