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Dissertations / Theses on the topic 'Biological interactions data'

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Published: 3 June 2025

Last updated: 1 August 2025

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1

Bar-Joseph, Ziv 1971. "Inferring interactions, expression programs and regulatory networks from high throughput biological data." Thesis, Massachusetts Institute of Technology, 2003. http://hdl.handle.net/1721.1/28289.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2003.<br>Includes bibliographical references (leaves 171-180).<br>(cont.) For the networks level I present an algorithm that efficiently combines complementary large-scale expression and protein-DNA binding data to discover co-regulated modules of genes. This algorithm is extended so that it can infer sub-networks for specific systems in the cell. Finally, I present an algorithm which combines some of the above methods to automatically infer a dynamic sub-network for the cell cycle sys

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2

Lasher, Christopher Donald. "Discovering contextual connections between biological processes using high-throughput data." Diss., Virginia Tech, 2011. http://hdl.handle.net/10919/77217.

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Hearkening to calls from life scientists for aid in interpreting rapidly-growing repositories of data, the fields of bioinformatics and computational systems biology continue to bear increasingly sophisticated methods capable of summarizing and distilling pertinent phenomena captured by high-throughput experiments. Techniques in analysis of genome-wide gene expression (e.g., microarray) data, for example, have moved beyond simply detecting individual genes perturbed in treatment-control experiments to reporting the collective perturbation of biologically-related collections of genes, or "proce

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3

Sachse, René. "Influence of climate change on lake ecosystems - disentangling physical, chemical and biological interactions." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2015. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-167312.

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Climate change affects lake ecosystems in many ways by direct and indirect temperature impacts on hydrophysical structure, hydrology, chemical cycles and on biological interactions. The identification of these climate signals can be complicated and superimposed by other environmental changes, such as land use changes. The aim of this thesis was to seperate temperature effects from effects of management and other environmental influences and to understand the underlying complex processes causing significant changes of ecosystem states. This understanding is important for decisions of lake and r

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4

López-Blanco, Efrén. "Ecosystem-atmosphere interactions in the Arctic : using data-model approaches to understand carbon cycle feedbacks." Thesis, University of Edinburgh, 2018. http://hdl.handle.net/1842/33101.

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The terrestrial CO2 exchange in the Arctic plays an important role in the global carbon (C) cycle. The Arctic ecosystems, containing a large amount of organic carbon (C), are experiencing ongoing warming in recent decades, which is affecting the C cycling and the feedback interactions between its different components. To improve our understanding of the atmosphere-ecosystem interactions, the Greenland Ecosystem Monitoring (GEM) program measures ecosystem CO2 exchange and links it to biogeochemical processes. However, this task remains challenging in northern latitudes due to an insufficient nu

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5

bickel, thomas. "Interactions polymères-membranes: une approche locale." Phd thesis, Université Louis Pasteur - Strasbourg I, 2001. http://tel.archives-ouvertes.fr/tel-00002391.

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L'insertion d'objets polymériques dans les solutions de molécules tensioactives conduit à des changements importants des propriétés macroscopiques: modification des constantes élastiques, séparations de phases, augmentation ou diminution de la viscosité. En particulier, le problème de polymères greffés sur des membranes fluides est l'objet d'intenses recherches du fait de ces nombreuses applications industrielles. L'objectif de cette thèse est de mieux comprendre les couplages entre conformations de la surface et des macromolécules: quand un polymère est greffé sur une paroi repulsive, certain

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6

Tiwari, Purushottam Babu. "Multimode Analysis of Nanoscale Biomolecular Interactions." FIU Digital Commons, 2015. http://digitalcommons.fiu.edu/etd/1923.

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Biomolecular interactions, including protein-protein, protein-DNA, and protein-ligand interactions, are of special importance in all biological systems. These interactions may occer during the loading of biomolecules to interfaces, the translocation of biomolecules through transmembrane protein pores, and the movement of biomolecules in a crowded intracellular environment. The molecular interaction of a protein with its binding partners is crucial in fundamental biological processes such as electron transfer, intracellular signal transmission and regulation, neuroprotective mechanisms, and reg

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7

Dessinges, Marie Noelle. "Proprietes elastiques d'une molécule d'ADN simple brin, et interactions ADN hélicases à l'échelle de la molécule unique." Phd thesis, Université Pierre et Marie Curie - Paris VI, 2002. http://tel.archives-ouvertes.fr/tel-00001765.

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Dans la première partie de cette thèse, nous avons étudié l'élasticité d'une molécule d'ADN simple brin à l'aide de pinces magnétiques. Les modèles de polymères idéaux ne rendent pas bien compte de l'élasticité de cette molécule, alors qu'ils décrivent très bien l'ADN double brin. Nous avons donc étudié expérimentalement l'élasticité d'une molécule simple brin dans différentes conditions salines, i.e. d'écrantage de charges, et dans des conditions modulant les interactions internes du polymère. En utilisant des conditions dénaturantes, nous avons pu séparer les effets des différentes interacti

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8

Chen, Li. "Searching for significant feature interaction from biological data." Diss., Online access via UMI:, 2007.

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9

LEVY, Raphael. "Interactions intra et inter moléculaires, conformation des polymères adsorbés, transition de phase sous étirement : que peut-on apprendre des mesures de force." Phd thesis, Université Louis Pasteur - Strasbourg I, 2002. http://tel.archives-ouvertes.fr/tel-00001565.

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Le microscope à force atomique (AFM) est un outil privilégié pour sonder la matière à l'échelle nanométrique. Dans cette thèse, nous l'utilisons comme instrument de mesure de force. Nous montrons que la mesure des fluctuations thermiques des ressorts permet de déterminer précisément leur raideur à condition d'utiliser un modèle qui prend en compte la forme des modes et la méthode de détection. A l'aide de nouvelle méthodes d'analyse des courbes de rétraction, nous étudions la conformation de polymères et de copolymères adsorbés, ainsi que l'interaction spécifique entre un complexe du nickel (N

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10

Rodriguez, Palacios Miguel Andres. "Reversed Voodoo Dolls: An exploration of physical visualizations of biological data." Thesis, KTH, Skolan för datavetenskap och kommunikation (CSC), 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-175796.

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Physical visualizations are artifacts that materialize abstract data. They take advantage of human natural abilities to interact with information in the physical world. These visualizations present an opportunity to be applied on new application domains. With the objective of discovering if physical visualizations can support remote monitoring of biological data, a technology probe is presented in the form of a reversed voodoo doll. This probe uses the natural affordance of an anthropomorphic figure to represent a person and reverses the concept of voodoo dolls in a playful way. The scenario o

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11

Korkmaz, Gulberal Kircicegi Yoksul. "Mining Microarray Data For Biologically Important Gene Sets." Phd thesis, METU, 2012. http://etd.lib.metu.edu.tr/upload/12614266/index.pdf.

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Microarray technology enables researchers to measure the expression levels of thousands of genes simultaneously to understand relationships between genes, extract pathways, and in general understand a diverse amount of biological processes such as diseases and cell cycles. While microarrays provide the great opportunity of revealing information about biological processes, it is a challenging task to mine the huge amount of information contained in the microarray datasets. Generally, since an accurate model for the data is missing, first a clustering algorithm is applied and then the resulting

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12

Bebek, Gurkan. "Analyzing and Modeling Large Biological Networks: Inferring Signal Transduction Pathways." Case Western Reserve University School of Graduate Studies / OhioLINK, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=case1157723743.

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13

Coelho, Edgar Duarte de Jesus Valente Marques. "Computational prediction of inter-species protein-protein interactions." Doctoral thesis, Universidade de Aveiro, 2017. http://hdl.handle.net/10773/19165.

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Doutoramento em Ciências da Computação<br>O estudo em larga escala de proteínas e das suas eventuais interações tem sido alvo de bastante atenção pela comunidade científica. Os métodos de análise experimentais têm produzido uma quantidade imensa de dados, que têm sido armazenados em diferentes repositórios. A disponibilidade destes dados, muitos deles curados por especialistas, abre um leque de oportunidades de investigação. Dado que as técnicas experimentais de identificação de interações proteína- proteína (PPIs) são dispendiosas, demoradas e requerem análise de um perito, os métodos comput

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14

Kachala, Mikhail [Verfasser], and Dmitri [Akademischer Betreuer] Svergun. "Development of Methods to analyze and represent Small-Angle Scattering Data from Interacting and Flexible Biological Macromolecules / Mikhail Kachala. Betreuer: Dmitri Svergun." Hamburg : Staats- und Universitätsbibliothek Hamburg, 2015. http://d-nb.info/1074642600/34.

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15

Messié, Monique. "Contrôle de la dynamique de la biomasse phytoplanctonique dans le Pacifique tropical ouest." Phd thesis, Université Paul Sabatier - Toulouse III, 2006. http://tel.archives-ouvertes.fr/tel-00137145.

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Le Pacifique tropical ouest (120°E-160°W, 20°S-20°N) est une région complexe où coexistent deux écosystèmes aux frontières variables, et aux caractéristiques physiques et biologiques très différentes : la warm pool à l'ouest, écosystème oligotrophe limité par le nitrate, et la cold tongue à l'est, limitée par le fer. Nous utilisons les concentrations en chlorophylle SeaWiFS comme proxy pour la biomasse phytoplanctonique sur la période septembre 1997 à décembre 2004. Une analyse statistique nous permet de dégager les principaux modes spatiaux-temporels où se concentre la variabilité de la chlor

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16

Siegelman, Lia. "Ageostrophic dynamics in the ocean interior A correction for the thermal mass–induced errors of CTD tags mounted on marine mammals, in the Journal of Atmospheric and Oceanic Technology 35 (6), June 2018 Submesoscale ocean fronts act as biological hotspot for southern elephant seal, in Scientific Reports 9, 2019 Ocean‐scale interactions from space, in Earth and Space Science 6(5), May 2019 Correction and accuracy of high- and low-resolution CTD data from animal-borne instruments, in the Journal of Atmospheric and Oceanic Technology 36 (5), May 2019 Diagnosing ocean‐wave‐turbulence interactions from space, in Geophysical Research Letters 46(15), August 2019 Sub‐mesoscale fronts modify elephant seals foraging behavior, in Limnology and Oceanography Letters, 4(6), December 2019." Thesis, Brest, 2019. http://www.theses.fr/2019BRES0094.

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L'océan est le plus grand réservoir d'énergie solaire de notre planète. La quantité de chaleur qu'il est capable de stocker est modulée par sa circulation complexe, opérant sur une vaste gamme d’échelles allant du centimètre à la dizaine de milliers de kilomètres. Cette thèse s'intéresse à deux types de processus océaniques: les tourbillons de mésoéchelle, d'une taille de 100 à 300 km, et les fronts de sous-mésoéchelle, d'une taille inférieure à 50 km. L'idée communément admise est que les mouvements agéostrophiques de sous-mésoéchelle sont principalement confinés à la couche de mélange océani

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17

Aragüés, Peleato Ramón. "Protein Interaction networks and their applications to protein characterization and cancer genes prediction." Doctoral thesis, Universitat Pompeu Fabra, 2007. http://hdl.handle.net/10803/7148.

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La importancia de comprender los procesos biológicos ha estimulado el desarrollo de métodos para la detección de interacciones proteína-proteína. Esta tesis presenta PIANA (Protein Interactions And Network Analysis), un programa informático para la integración y el análisis de redes de interacción proteicas. Además, describimos un método que identifica motivos de interacción basándose en que las proteínas con parejas de interacción comunes tienden a interaccionar con esas parejas a través del mismo motivo de interacción. Encontramos que las proteínas altamente conectadas (i.e., hubs) con múl

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18

Toufighi, Kiana 1980. "Integrative study of gene expression and protein complexes." Doctoral thesis, Universitat Pompeu Fabra, 2014. http://hdl.handle.net/10803/380907.

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Over the last several decades, the emerging ‘integrated’ view of the cell has triumphed over the ‘one gene/one protein/one function’ paradigm. This is illustrated by the biologically opposite effects of key regulatory proteins in different cell types, in established versus primary cells, and in vitro versus in vivo situations. The persistent theme throughout this dissertation is the integration of a wide range of data sources for the purpose of understanding distinct cellular contexts. We first use circadian expression data from human epidermal stem cells to discover waves of transcripts

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19

Sachse, René. "Influence of climate change on lake ecosystems - disentangling physical, chemical and biological interactions." Doctoral thesis, 2014. https://tud.qucosa.de/id/qucosa%3A28696.

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Climate change affects lake ecosystems in many ways by direct and indirect temperature impacts on hydrophysical structure, hydrology, chemical cycles and on biological interactions. The identification of these climate signals can be complicated and superimposed by other environmental changes, such as land use changes. The aim of this thesis was to seperate temperature effects from effects of management and other environmental influences and to understand the underlying complex processes causing significant changes of ecosystem states. This understanding is important for decisions of lake and r

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20

Luna, Augustin. "Formalization of molecular interaction maps in systems biology; Application to simulations of the relationship between DNA damage response and circadian rhythms." Thesis, 2013. https://hdl.handle.net/2144/14143.

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Quantitative exploration of biological pathway networks must begin with a qualitative understanding of them. Often researchers aggregate and disseminate experimental data using regulatory diagrams with ad hoc notations leading to ambiguous interpretations of presented results. This thesis has two main aims. First, it develops software to allow researchers to aggregate pathway data diagrammatically using the Molecular Interaction Map (MIM) notation in order to gain a better qualitative understanding of biological systems. Secondly, it develops a quantitative biological model to study the effect

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21

Blakney, Gregory Terrell. "Investigations of biological interactions by hydrogen deuterium exchange Fourier transform ion cyclotron mass spectrometry novel methods, automated analysis and data reduction /." Thesis, 2003. http://wwwlib.umi.com/cr/utexas/fullcit?p3110730.

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22

Grassa, F. "Geochemical processes governing the chemistry of groundwater hosted within the Hyblean aquifers." Thesis, 2002. http://hdl.handle.net/2122/416.

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A raingauge network made of six stations was installed in the Hyblean region. Stations were located at different altitudes (from 5 m to 986 m a.s.l.) and along two directions (E-W and SW-NE). Rainwater samples were monthly collected for stable isotope measurements. Spatial distribution of rainwater isotope composition has confirmed the wet air masses move from South-East/South-West toward North. Water balance has highlighted that the annual volume of infiltrating waters is in the range of 1-1.5 *105 m3 Km-2. 82 well waters and 12 spring waters located within the Hyblean Plateau (South-Ester

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23

Li, Pin. "Effects of carbon nanotubes on airway epithelial cells and model lipid bilayers : proteomic and biophysical studies." Thesis, 2014. http://hdl.handle.net/1805/5968.

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Indiana University-Purdue University Indianapolis (IUPUI)<br>Carbon nanomaterials are widely produced and used in industry, medicine and scientific research. To examine the impact of exposure to nanoparticles on human health, the human airway epithelial cell line, Calu-3, was used to evaluate changes in the cellular proteome that could account for alterations in cellular function of airway epithelia after 24 h exposure to 10 μg/mL and 100 ng/mL of two common carbon nanoparticles, singleand multi-wall carbon nanotubes (SWCNT, MWCNT). After exposure to the nanoparticles, label-free quantitative

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24

Zhao, Huiying. "Protein function prediction by integrating sequence, structure and binding affinity information." Thesis, 2014. http://hdl.handle.net/1805/3913.

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Indiana University-Purdue University Indianapolis (IUPUI)<br>Proteins are nano-machines that work inside every living organism. Functional disruption of one or several proteins is the cause for many diseases. However, the functions for most proteins are yet to be annotated because inexpensive sequencing techniques dramatically speed up discovery of new protein sequences (265 million and counting) and experimental examinations of every protein in all its possible functional categories are simply impractical. Thus, it is necessary to develop computational function-prediction tools that complemen

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25

Yesmunt, Garrett Scot. "Design, analysis, and simulation of a humanoid robotic arm applied to catching." Thesis, 2014. http://hdl.handle.net/1805/5610.

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Indiana University-Purdue University Indianapolis (IUPUI)<br>There have been many endeavors to design humanoid robots that have human characteristics such as dexterity, autonomy and intelligence. Humanoid robots are intended to cooperate with humans and perform useful work that humans can perform. The main advantage of humanoid robots over other machines is that they are flexible and multi-purpose. In this thesis, a human-like robotic arm is designed and used in a task which is typically performed by humans, namely, catching a ball. The robotic arm was designed to closely resemble a human arm,

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