Floer HomologySimilarityPleckstrinPractical Guide to Homology ModelingMolecularHomoloGeneGeneAmino AcidMedicinesEvolutionary developInduces a homologyExample of homologyExamples of homologyDefinition of homologyCategories as homologies2019SingularCohomologySerial homologyCalponin homologyPersistent homologySimplicial homology1994StructuresCombinatorialAnalogyComputeAlgebraicProtein structureSpeciesBioinformaticsSequence alignmentGeneticsDonor plasmidsPlasmidsHomotopy2000InstantonSpectral sequenceDetectionInvariantHomoplasyPhylogenyFunctorialityDomainsSearchComparativeBiology and Philosophy

- In mathematics , Floer homology is a tool for studying symplectic geometry and low-dimensional topology . (wikipedia.org)
- Floer homology is a novel invariant that arises as an infinite-dimensional analogue of finite-dimensional Morse homology . (wikipedia.org)
- Andreas Floer introduced the first version of Floer homology, now called Lagrangian Floer homology, in his proof of the Arnold conjecture in symplectic geometry. (wikipedia.org)
- Floer homology is typically defined by associating to the object of interest an infinite-dimensional manifold and a real valued function on it. (wikipedia.org)
- Loosely speaking, Floer homology is the Morse homology of the function on the infinite-dimensional manifold. (wikipedia.org)
- Floer homology is the homology of this chain complex. (wikipedia.org)
- The Gromov compactness theorem is then used to show that the differential is well-defined and squares to zero, so that the Floer homology is defined. (wikipedia.org)
- For instanton Floer homology, the gradient flow equations is exactly the Yang-Mills equation on the three-manifold crossed with the real line. (wikipedia.org)
- Symplectic Floer Homology (SFH) is a homology theory associated to a symplectic manifold and a nondegenerate symplectomorphism of it. (wikipedia.org)
- The symplectic Floer homology of a Hamiltonian symplectomorphism of a compact manifold is isomorphic to the singular homology of the underlying manifold. (wikipedia.org)
- For the cotangent bundle of a manifold M, the Floer homology depends on the choice of Hamiltonian due to its noncompactness. (wikipedia.org)
- For Hamiltonians that are quadratic at infinity, the Floer homology is the singular homology of the free loop space of M (proofs of various versions of this statement are due to Viterbo, Salamon-Weber, Abbondandolo-Schwarz, and Cohen). (wikipedia.org)
- There are more complicated operations on the Floer homology of a cotangent bundle that correspond to the string topology operations on the homology of the loop space of the underlying manifold. (wikipedia.org)
- Honda, Kazez and Matic defined maps on sutured Floer homology induced by a contact structure. (princeton.edu)
- These estimates are obtained by studying Floer homology for fiberwise quadratic Hamiltonian functions on negative line bundles. (aimsciences.org)
- Floer homology in disk bundles and symplectically twisted geodesic flows. (aimsciences.org)
- Transport, flux and growth of homoclinic Floer homology. (aimsciences.org)
- Spectral invariants in Rabinowitz-Floer homology and global Hamiltonian perturbations. (aimsciences.org)
- In early 80s, David Gabai introduced the theory of "sutured manifolds" to study these objects and more than 20 years later, Andres Juhasz developed a Floer type theory, namely "Sutured Floer Homology", that turned out to be very useful in answering the question of when a 3-manifold with boundary supports a taut foliation. (gatech.edu)

- The term "percent homology" is often used to mean "sequence similarity. (wikipedia.org)
- The percentage of identical residues ( percent identity ) or the percentage of residues conserved with similar physicochemical properties ( percent similarity ), e.g. leucine and isoleucine , is usually used to "quantify the homology. (wikipedia.org)
- Based on the definition of homology specified above this terminology is incorrect since sequence similarity is the observation, homology is the conclusion. (wikipedia.org)
- This unit provides an overview of the inference of homology from significant similarity, and introduces other units in this chapter that provide more details on effective strategies for identifying homologs. (merlot.org)
- If you know the author of An Introduction to Sequence Similarity ("Homology") Searching , please help us out by filling out the form below and clicking Send. (merlot.org)
- In biology, homology is commonly defined as any similarity between structures of organisms in different taxa that derives from similar structures in their shared ancestry. (newworldencyclopedia.org)
- Historically, homology was defined as similarity in structure and position, such as the pattern of bones in a bat's wing and those in a porpoise's flipper (Wells, 2000). (newworldencyclopedia.org)
- Homology in the classical sense, as similarity in structure and position of anatomical features between different organisms, was important evidence used by Darwin. (newworldencyclopedia.org)
- Furthermore, he finds even retaining the pre-Darwinian definition of homology as structural similarity problematic because of such factors as the lack of correspondence between homology and development pathways, since there are examples of similar structures in adult forms where ancestry is assumed that actually are products of radically different development processes. (newworldencyclopedia.org)
- Homology refers to similarity in structure, which, according to the theory of evolution, is due to common ancestry. (creation.com)
- Please call it sequence SIMILARITY In a search you may find many sequence similarities but only few of the matches may represent homologies. (bio.net)
- Homology involves the theory that macroevolutionary relationships can be proven by the similarity in the anatomy and physiology of different animals. (answersingenesis.org)
- Homology, in general biology, pertains to the degree of similarity, as in position or structure, and that may indicate a common origin. (biology-online.org)
- In evolutionary biology, homology pertains to a state of similarity in structure and anatomical position but not necessarily in function between different organisms . (biology-online.org)
- Homology modeling, also termed as Comparative modeling refers to modeling of 3D structure of a protein by exploiting structural information from other known protein structures with good sequence similarity. (igi-global.com)
- CMG}} __NOTOC__ ==Overview== In [[biology]], homology refers to the general and quite ancient observation of ''similarity of form seen in the biological world'' of animals or plants. (wikidoc.org)

- The discovery of PHLPP, which stands for Pleckstrin Homology Domain Leucine-Rich Repeat Protein Phosphatase, contributes to the cast of phosphate-controlling enzymes in cell signaling. (wikibooks.org)
- The pleckstrin homology domain of Gab-2 is required for optimal interleukin-3 signalsome-mediated responses. (sigmaaldrich.com)
- To investigate the role of the pleckstrin homology domain of Gab-2 in this process, epitope-tagged wild type Gab-2 (WTGab-2), Gab-2 lacking its PH domain (DeltaPHGab-2) and the Gab-2 PH domain alone (PHGab-2) were inducibly expressed in IL-3-dependent BaF/3 cells. (sigmaaldrich.com)

- If you wish to make a homology model, please see Practical Guide to Homology Modeling . (proteopedia.org)

- At a molecular level, the term "homology" describes sequences, either DNA or protein, that share a common evolutionary origin. (encyclopedia.com)
- Furthermore, increased knowledge about the genetic and molecular basis of life has revealed many major exceptions and contradictions to the theory which, as a result, have largely negated homology as a proof of evolution. (answersingenesis.org)
- Circular plasmids are commonly used as donor DNA for HDR because they can carry a large DNA insert (≤ 10 kb) and homology arms corresponding to the target locus are added by molecular cloning. (genetics.org)
- Homology models contain sufficient information about the spatial arrangement of important residues in the protein and are often used in drug design for screening of large libraries by molecular docking techniques. (igi-global.com)
- Using integrated in-silico computational techniques, including homology modeling, structure-based and pharmacophore-based virtual screening, molecular dynamic simulations, per-residue energy decomposition analysis and atom-based 3D-QSAR analysis, we proposed ten novel compounds as potential CCR5-dependent HIV-1 entry inhibitors. (mdpi.com)

- Homology information is based on Homologene . (wikigenes.org)

- Such partial homology may result from a gene fusion event. (wikipedia.org)
- Abouheif E (1999) Establishing homology criteria for regulatory gene networks: Prospects and challenges. (springer.com)
- Homology Medicines, Inc. (FIXX), a genetic medicines company, announced that it achieved all corporate goals for 2018, positioning the Company to start a Phase 1/2 clinical trial of the Company's first gene therapy program in adults with phenylketonuria (PKU), with initial data expected in 2019. (yahoo.com)
- Homology Medicines, Inc. (FIXX), a genetic medicines company, announced today that it has nominated an in vivo gene editing development candidate and initiated IND-enabling studies for the treatment of pediatric patients with phenylketonuria (PKU). (yahoo.com)
- Homology also completed its internal GMP manufacturing facility with capabilities to support both gene editing and gene therapy programs. (yahoo.com)
- A group of biotech veterans have debuted today a new company, Homology Medicines, with a bold claim that their underlying science is a better version of the gene editing methods, such as CRISPR-Cas9, that have captured the attention of patients, doctors, and scientists looking to treat desperate diseases. (xconomy.com)
- Homology now says its method of genetic manipulation might have advantages over both gene editing and gene therapy. (xconomy.com)
- Homology aims to use homologous recombination to "flip in a gene that's normal for a gene that's abnormal," Tzianabos says. (xconomy.com)
- Homology aims to engineer a piece of "healthy" DNA, pack it into a type of adeno-associated virus, or AAV-a delivery tool commonly used in gene therapy, and now CRISPR technologies as well-and infuse it into the body. (xconomy.com)
- Therefore, homology-independent insertion in Drosophila is a fast and simple alternative to HDR that will enable researchers to dissect gene function. (genetics.org)
- Now that we have IND clearance for HMI-102, our lead gene therapy candidate for PKU, we are approaching the clinic and are on track to report initial data from our Phase 1/2 pheNIX trial later this year," said Arthur Tzianabos, Ph.D., President and Chief Executive Officer of Homology Medicines. (einpresswire.com)
- have been devised to survey gene functions en masse either computationally (Marcotte et al. (psu.edu)

- Overall, the predicted amino acid homologies of the surface glycoproteins, F and G, of NV-B and NV-M are high (Table). (thefreedictionary.com)
- You don't need a homology model if the amino acid sequence of interest (the query sequence) already has an empirically determined 3D structure. (proteopedia.org)
- The overall homology based on two separate matrix scoring systems (minimum base change per codon and amino acid homology per residue) is significant. (rice.edu)

- FIXX - Homology Medicines, Inc. (yahoo.com)
- Is Homology Medicines, Inc. (FIXX) A Good Stock To Buy? (yahoo.com)
- The Qatar Investment Authority, created to handle the windfall from the country's gas and oil exports, has invested in companies including Foursquare Labs Inc., biotech firm Rubius Therapeutics Inc., Homology Medicines Inc., Thoughtspot Inc. and Grail Inc., said the people, asking not to be identified because the deals are private. (yahoo.com)
- Homology Medicines, Inc. (FIXX), a genetic medicines company, announced today data demonstrating that Homology's proprietary vectors are able to cross the blood-brain-barrier and have a positive impact on the rare neurological disorder metachromatic leukodystrophy (MLD). (yahoo.com)
- Homology is a genetic medicines company dedicated to transforming the lives of patients suffering from rare genetic diseases with significant unmet medical needs by curing the underlying cause of the disease. (yahoo.com)
- Homology Medicines Sees Hammer Chart Pattern: Time to Buy? (nasdaq.com)

- Here, Lewis I. Held, Jr compares the genetics and development of the two to review the evidence for deep homology, the biggest discovery from the emerging field of evolutionary developmental biology. (cambridge.org)

- Having these numbers naturally leads to the definition of a boundary operator, which induces a homology. (archives-ouvertes.fr)
- Suppose we have a map of fiber sequence $[A\rightarrow B\rightarrow C]\rightarrow [A^{'}\rightarrow B^{'}\rightarrow C^{'}]$ where all involved spaces are connected and the maps $A\rightarrow A^{'}$, $B\rightarrow B^{'}$ induce homology isomorphism, could we conclude that the map $C\rightarrow C^{'}$ induces a homology isomorphism. (mathoverflow.net)

- To evolutionists, the vertebrate forelimbs are a classic example of homology. (creation.com)
- Aside from the aforementioned double pair of wings found in insects, other examples of homology include the forearm structure of tetrapod limbs, this is perhaps the most famous example of homology, and is featured in many textbooks. (rationalwiki.org)
- Forelimb]]s in [[mammal]]s provide one example of homology. (wikidoc.org)

- Examples of homology occur at different levels of organization. (newworldencyclopedia.org)
- A review of the literature on homology indicates that the theory does not provide evidence for evolutionary naturalism, and that the common examples of homology can be better explained by Creation. (answersingenesis.org)

- Such a definition of homology is a redefinition from the classical understanding of the term, which predated Charles Darwin 's theory of evolution , having been coined by Richard Owen in the 1840s. (newworldencyclopedia.org)

- Ereshefsky M (2007a) Psychological categories as homologies: Lessons from ethology. (springer.com)
- This paper takes up the project of studying psychological categories as homologies. (pitt.edu)

- Our anticipated near-term transition to a clinical stage company with the potential for initial safety and efficacy data by the end of 2019 makes this a significant year for Homology. (einpresswire.com)

- armed with chains - formal sums - of singular cubes we can use them to come up with a homology theory. (wordpress.com)
- This is, of course, the case in singular homology, but in a general theory stable under suspension it is far from true. (mathoverflow.net)
- INTRODUCTION Poincare duality Morse theory for siningular spac es de Rham cohomology and L2-c -cohomol ology The cohomology of pr projective vari ties REVIEW OF HOMOLOGY AND COHOMOLOGY Simplicial homology Singular homology Homology with close closed support Conclusion Further reading REVIEW OF SHEAF COHOMOLOGY AND DERIVED CATEGORIES Sheaves Cech cohomology of sheaves Hypercohomology Functors and exactness Resolution of sheaves of complexes Cohomology and hypercohomology via derived functors Derived categories. (hugendubel.de)
- THE DEFINITION OF INTERSECTION HOMOLOGY Stratified spaces and pseudomanifolds Simplicial intersection homology Singular intersection homology Simple examples of intersection homology Normalisati ons Relative groups and the Mayer-Vietoris sequence. (hugendubel.de)

- The talk Spectral sequence and homology of currents for operator algebras given by AC at the 1981 Oberwolfach meeting introduced for instance the SBI long exact sequence and described the cyclic cohomology of the NC torus. (blogspot.com)
- One of them is the nuance between cyclic homology and archimedean cyclic homology (this is the one taken up in the above result) which parallels and reflects, in cyclic homology, the difference between reduced and unreduced real Deligne cohomology (we refer to the paper for more details). (blogspot.com)

- What Is Serial Homology? (reference.com)
- Serial homology is the development of special features from a structure that occurs in each section of an organism's body. (reference.com)
- A common example of serial homology is the specialized limb structure of arthropods. (reference.com)
- Vertebrates also demonstrate serial homology, though vertebrate segmentation is less pronounced than it is among arthropods. (reference.com)
- Serial homology works to the advantage of organisms in several ways. (reference.com)

- leucine-rich repeats and calponin homology. (wikigenes.org)

- We present a promising new system that applies the two-parameter persistent homology to the complex task of finding good drug candidates, by finding similarities in the 3D shapes of the molecules. (umn.edu)
- In this talk, we will discuss a variety of applications of persistent homology. (umn.edu)
- Further, we construct Vietoris-Rips complexes from the Jaccard distances and compute the persistent homology associated with those. (harvard.edu)

- Homology computation on such structures is usually achieved by computing simplicial homology on a simplicial analog. (archives-ouvertes.fr)
- By using simplicial homology, the complex geometrical calculation of the coverage is reduced to simple matrix computation. (archives-ouvertes.fr)

- Lauder G (1994) Homology, form, and function. (springer.com)
- one cannot test hypotheses of homology" (Lauder, 1994:188). (thefreedictionary.com)

- Homology, as stated above, refers to the occurrence of shared traits or structures in different but related taxa that is a result of shared ancestry. (rationalwiki.org)
- While homology and analogy both concern themselves with similarities, the former differs from the latter in that homology refers to any similar structure found in related taxa that has been inherited as a result of common descent, whereas analogy refers to similar structures that have been derived independently of one another in different, unrelated taxa. (rationalwiki.org)
- This paper focuses on homology computation over 'cellular' structures that allow multi-incidence between cells. (archives-ouvertes.fr)
- So far, a number of different MT 1 and MT 2 receptor homology models, built either from the prototypic structure of rhodopsin or from recently solved X-ray structures of druggable GPCRs, have been proposed. (mdpi.com)
- Homology of structures in evolution == Shared ancestry can be [[evolution]]ary or developmental. (wikidoc.org)
- Structures determined empirically, by X-ray crystallography or (much less often) by solution NMR or cryo-EM, will almost always be more accurate than a homology model. (proteopedia.org)
- Three structural models for PAR2 have been constructed based on sequence homology with known crystal structures for bovine rhodopsin, human ORL-1 (also called nociceptin/orphanin FQ receptor), and human PAR1. (sigmaaldrich.com)

- Minelli AM (1998) Molecules, developmental modules, and phenotypes: A combinatorial approach to homology. (springer.com)
- It is proved that, under specific conditions, the homology of a combinatorial map as defined in the paper is equivalent to the homology of its simplicial analogue. (archives-ouvertes.fr)
- begingroup$ I'm not really a topologist, but my impression was that ordinary homology is 'more computable' than homotopy because it satisfies excision (allowing more combinatorial attacks), and 'more computable' than K-theory because it satisfies the dimension axiom (meaning relatively small spaces have homology with low complexity). (mathoverflow.net)

- Homology is different from analogy. (newworldencyclopedia.org)
- In anthropology and archaeology, homology is a type of analogy whereby two human beliefs, practices or artifacts are separated by time but share similarities due to genetic or historical connections. (wikipedia.org)

- I'll explain how to compute these maps using holomorphic triangle counts and give some applications to computing sutured Floer homologies and sutured contact invariants. (princeton.edu)
- Our work aims at providing a way to compute homologies directly on a cellular structure. (archives-ouvertes.fr)
- That it enables us to compute the homology of certain spaces (such as spheres) which are built out of each other by suspension, by some kind of inductive argument? (mathoverflow.net)
- It might be quite hard to compute its homology then. (mathoverflow.net)

- In the context of algebraic geometry instead, the application of cyclic homology to schemes has a more recent evolution and it has been mainly promoted in the work of C. Weibel. (blogspot.com)
- infty} K_v$, of the operator $(2\pi)^{-1}(s-\Theta)$, where $\Theta$ generates the lambda operations which are the analogue in cyclic homology of the Adams operations in algebraic K-theory. (blogspot.com)
- This result promotes the development of the archimedean cyclic homology as a theory playing a natural role in the theory of motives in algebraic geometry, in view of its connection to algebraic K-theory by the regulator maps. (blogspot.com)

- These preliminary results show that our novel approach to use homology information can greatly improve the performance of ab-initio methods for protein structure prediction, both overcoming errors and approximation in the energy functions, improving the ability of the Monte Carlo method to avoid spurious local minima and allowing for a more efficient search of the conformational space. (omicsonline.org)

- 5 An early example of how homology was used to argue for macroevolution is a 1928 biology text which, in answer to the question 'Why do the individuals in a species have all of their parts homologous? (answersingenesis.org)
- Biologists carry this answer a step further and say that since homology within the species is the result of common ancestry therefore all homology is due to common ancestry and the closeness of relationship determines the number of homologous parts [emphasis in original]. (answersingenesis.org)
- The most extensive coverage of mammalian species homologies is the Mouse Genome Database of The Jackson Laboratory (21). (thefreedictionary.com)
- Conventional North American molt terminology for birds was developed by Humphrey and Parkes (1959) to facilitate identification of homologies among molts and plumages across species through use of the neutral terms 'basic', 'alternate', and 'supplemental' rather than terms that refer to breeding status, plumage, or season of the year. (thefreedictionary.com)

- This work covers sequence-based protein homology detection, a fundamental and challenging bioinformatics problem with a variety of real-world applications. (springer.com)

- Errors or uncertainties in the sequence alignment result in errors or uncertainties in the homology model. (proteopedia.org)
- Folding the query sequence identically to the template, guiding the registration by the sequence alignment, produces a homology model. (proteopedia.org)

- Abouheif E (1997) Developmental genetics and homology: A hierarchical approach. (springer.com)

- Here, we adapt the mammalian CRISPaint [clustered regularly interspaced short palindromic repeat (CRISPR)-assisted insertion tagging] homology-independent knock-in method for Drosophila melanogaster , which uses CRISPR/Cas9 and nonhomologous end joining to insert "universal" donor plasmids into the genome. (genetics.org)
- For HITI, donor plasmids lack homology arms and DSB does not occur through the HDR pathway. (golden.com)

- Topology II: Homotopy and Homology. (google.co.uk)
- In essence, you have then (togehter with homotopy invariance) exactly the notion of a reduced homology theory. (mathoverflow.net)
- Thus, the fibrations $$ \Omega S^2 \to * \to S^2 $$ $$ \Omega(\mathbb{C}P^\infty\times S^3) \to * \to \mathbb{C}P^\infty\times S^3 $$ have homotopy equivalent fibre and total space, but the bases have non-isomorphic homology. (mathoverflow.net)

- Laubichler M (2000) Homology in development and the development of the homology concept. (springer.com)
- Wells (2000) notes that homology as now defined can no longer be used as evidence for evolution because of circular reasoning. (newworldencyclopedia.org)

- I will describe a spectral sequence that starts at reduced odd Khovanov homology and converges to a version of instanton homology for double branched covers. (princeton.edu)

- begingroup$ Often the information on the homology of $C$ can be understood from the Serre spectral sequence. (mathoverflow.net)

- The text first surveys a few popular homology detection methods, such as Position-Specific Scoring Matrix (PSSM) and Hidden Markov Model (HMM) based methods, and then describes a novel Markov Random Fields (MRF) based method developed by the authors. (springer.com)
- We introduce a greedy algorithm for filtering and enrichment of dynamic fragment libraries, compiled with remote-homology detection methods such as HHfrag. (ebscohost.com)
- In this paper, a new method for remote protein homology detection called remote-3DP, is presented. (ebscohost.com)

- I've heard it said that the reason why the homology groups of a space are a computable invariant is because they are a stable invariant in the sense that they are stable under suspension. (mathoverflow.net)
- In particular, the action on some $4$-dimensional invariant subspace of the homology leaves invariant a root system of $D_4$ type. (aimsciences.org)

- Hall BK (2003) Descent with modification: The unity underlying homology and homoplasy as seen through an analysis of development and evolution. (springer.com)
- Hall BK (2007) Homology and homoplasy. (springer.com)

- Ethologists have numerous theoretical ideas concerning the phylogeny and ontogeny of behavioral homologies. (pitt.edu)

- The intersection homology of a cone Functoriality of intersection homology Homology with local coefficients Quasi-projec tive complex varieties Further reading WITT SPACES AND DUALITY Generalised Poincare duality. (hugendubel.de)

- Probabilistic and numerical validation of homology computations for nodal domains. (aimsciences.org)
- In a pilot study on 40 different domains selected from the SCOP database, we observe that our method is able to improve the exploration of energy landscapes thanks to the exchange of homology information during the Monte Carlo simulation and to reach better solutions in terms of both lower energy and distance from the native structure. (omicsonline.org)

- Increased chromosome mobility facilitates homology search during recombination. (nih.gov)
- We propose a model for homology search in which increased chromosome mobility facilitates homologous pairing. (nih.gov)
- Here we describe a large-scale energy optimization-based refinement method that incorporates advances in both search and energy function accuracy that can substantially improve the accuracy of low-resolution homology models. (pnas.org)
- If the Rad51 -mediated homology search is successful, the 3′ end of the invading strand is extended by DNA synthesis. (genetics.org)
- Our objective was to define a strategy for this type of homology-tolerant database search. (pubmedcentralcanada.ca)
- Mascot) was compared with that obtained using homology search. (pubmedcentralcanada.ca)
- The highest-ranking protein was the same using Mascot, homology search using the 20 most intense peptides, or homology search using all peptides, for 63.4% of 112 spots from two-dimensional polyacrylamide gel electrophoresis gels. (pubmedcentralcanada.ca)
- After identifying the protein using MS-Homology, a peptide mass search may increase the percent coverage of the protein identified. (pubmedcentralcanada.ca)
- Your search returned 2 bromo adjacent homology domain containing 1 ELISA ELISA Kit across 1 supplier. (biocompare.com)

- In: Homology: The Hierarchical Basis of Comparative Biology (Hall B, ed), 151-196. (springer.com)
- Homology , also known as comparative anatomy , in biology is the occurrence and study of shared traits between different taxa due to common descent . (rationalwiki.org)
- Homology models , also called comparative models , are obtained by folding a query protein sequence (also called the target sequence) to fit an empirically-determined template model. (proteopedia.org)

- Presented as part of the symposium 'The Importance of Homology for Biology and Philosophy' at ISHPSSB 2007 (July 25-29, Exeter). (pitt.edu)