Andreas Dress

Andreas Dress
Chinese Academy of Sciences | CAS

About

403
Publications
30,901
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
12,537
Citations

Publications

Publications (403)
Article
Full-text available
Breast cancer is the second highest cause of carcinoma-related death caused by distant metastasis in women. Estrogen receptor (ER), human epidermal growth factor receptor 2 (HER2) and progesterone receptor (PR) are three classified makers of breast cancer, which are defined as ER + , HER2 + , and the most serious ER - PR - HER2- (triple-negative)....
Article
MAP kinase interacting serine/threonine kinase 2 (MKNK2) belongs to the protein kinase superfamily which phosphorylates and activates eukaryotic initiation factor 4E (elF4E), a rate limiting factor in protein synthesis that enhances the translation of some proteins involved in cell cycle, apoptosis and angiogenesis regulation. In this study, we fou...
Article
Angiogenesis has been found as an attractive target for drug therapy as it is necessary for tumor growth. Accumulating evidences show that microRNAs (miRNAs), which are a group of highly conserved, single-stranded, short non-coding RNAs, play important roles through directly targeting angiogenic factors and protein kinases. The purpose of this stud...
Article
Full-text available
In this paper, we present an analysis of oracle bone characters for animals from a “cognitive” point of view. After some general remarks on oracle-bone characters presented in Sec. 1 and a short outline of the paper in Sec. 2, we collect various oracle-bone characters for animals from published resources in Sec. 3. In the next section, we begin ana...
Article
Fuzzy rings are, on the one handside, an appropriate tool for a unified approach to representable, oriented, and valuated matroids. On the other hand, they also serve to unify the relatively new field of “Tropical Geometry” and “Classical Algebraic Geometry.” Therefore, these fuzzy rings deserve a more thorough examination. We study the arithmetic...
Article
Full-text available
Given a finite connected simple graph $G=(V,E)$ with vertex set $V$ and edge set $E\subseteq \binom{V}{2}$, we will show that $1.$ the (necessarily unique!) smallest block graph with vertex set $V$ whose edge set contains $E$ is uniquely determined by the $V$-indexed family ${\bf P}_G:=\big(\pi_0(G^{(v)})\big)_{v \in V}$ of the various partitions $...
Article
Full-text available
The article in PNAS by Gerdes et al. (1) adds to the evidence that spectral resolution limits of fluorescence microscopy can be overcome by reiterative cycles of tagging, imaging, and bleaching of fluorophores attached to ligands for target biomolecules. In fact, the robotic imaging cycler microscopes are based on this principle and have been used...
Chapter
We give an account of an approach to community-structure detection in networks using linear programming: given a finite simple graph G, we assign penalties for manipulating this graph by either deleting or adding edges, and then consider the problem of turning G, by performing these two operations, at minimal total cost into a graph that represents...
Article
The systems paradigm of modern medicine presents both, an opportunity and a challenge for current Information and Communication Technology (ICT): the opportunity to understand the dynamics of the human body as part of an integrated whole, incorporating bio-chemical, physiological, and environ-mental interactions that sustain life, provided we maste...
Article
Full-text available
A (pseudo-)metric $D$ on a finite set $X$ is said to be a `tree metric' if there is a finite tree with leaf set $X$ and non-negative edge weights so that, for all $x,y \in X$, $D(x,y)$ is the path distance in the tree between $x$ and $y$. It is well known that not every metric is a tree metric. However, when some such tree exists, one can always fi...
Article
To any metric D on a finite set X, one can associate a metric space T(D) known as its tight span. Properties of T(D) often reveal salient properties of D. For example, cut sets of T(D), i.e., subsets of T(D) whose removal disconnect T(D), can help to identify clusters suggested by D and indicate how T(D) (and hence D) may be decomposed into simpler...
Article
Full-text available
Fermat's principle of least time states that light rays passing through different media follow the fastest (and not the most direct) path between two points, leading to refraction at medium borders. Humans intuitively employ this rule, e.g., when a lifeguard has to infer the fastest way to traverse both beach and water to reach a swimmer in need. H...
Data
RERANTZ V1.0. [refrantz1-0.xls], Excel file for the approximation of the fastest trail ρ . (ZIP)
Article
Full-text available
Background The large majority of optimization problems related to the inference of distance‐based trees used in phylogenetic analysis and classification is known to be intractable. One noted exception is found within the realm of ultrametric distances. The introduction of ultrametric trees in phylogeny was inspired by a model of evolution driven by...
Article
Full-text available
The systems paradigm of modern medicine presents both, an opportunity and a challenge, for current Information and Communication Technology (ICT). The opportunity is to understand the spatio-temporal organisation and dynamics of the human body as an integrated whole, incorporating the biochemical, physiological, and environmental interactions that...
Article
Full-text available
MiR-145 is known as a tumor suppressor in numerous human cancers. However, its role in tumor angiogenesis remains poorly defined. In this study, we found that miR-145 was significantly downregulated in breast cancer tissues by using 106 cases of normal and cancer tissues as well as in breast cancer cells. MiR-145 exhibited inhibitory role in tumor...
Article
Full-text available
Given a finite simplicial complex K, we construct a chain-complex isomorphism from the simplicial chain complex of K over F-2 endowed with the standard boundary operator partial derivative(K) ( that maps any simplex A is an element of K onto the sum of all of its maximal subsets) to that same complex endowed with the incidence operator I-K that map...
Article
Full-text available
Motivated by questions in biological classification, we discuss some elementary combinatorial and computational properties of certain set systems that generalize hierarchies, namely, 'patchworks', 'weak patchworks', 'ample patchworks' and 'saturated patchworks' and also outline how these concepts relate to an apparently new 'duality theory' for clu...
Article
The relatively new field of “Tropical Geometry” and “Classical Algebraic Geometry” have much in common. In this paper, we present a unified approach to both of these fields by studying more general “Fuzzy Geometries” over fuzzy rings. It turns out that the fuzzy ring which underlies “Tropical Geometry” is the same as that belonging to “Valuated Mat...
Article
Full-text available
A classical result, fundamental to evolutionary biology, states that an edge-weighted tree T with leaf set X, positive edge weights, and no vertices of degree 2 can be uniquely reconstructed from the leaf-to-leaf distances between any two elements of X. In biology, X corresponds to a set of taxa (e.g. extant species), the tree T describes their phy...
Article
Full-text available
We analyze a rather simple system in which some substance is being stored, released, and replenished simultaneously in some interdependent way. We investigate the dynamic behavior of such a system, using a two-dimensional map-based discrete-time model, and derive an integrated dynamical scene for this model. More specifically, we show the existence...
Article
For F a \({\wp}\)-adic field together with a \({\wp}\)-adic valuation, we present a new characterization for a map \({p: F^{n} \rightarrow {\mathbb R}\cup\{-\infty}\}\) to be a \({\wp}\)-adic norm on the vector space F n . This characterization was motivated by the concept of tight maps — maps that naturally arise within the theory of valuated matr...
Article
Full-text available
To investigate expression, regulation, potential role and targets of miR-195 and miR-497 in breast cancer. The expression patterns of miR-195 and miR-497 were initially examined in breast cancer tissues and cell lines by Northern blotting and quantitative real-time PCR. Combined bisulfite restriction analysis and bisulfite sequencing were carried o...
Article
Phylogenetic combinatorics is a branch of discrete applied mathematics concerned with the combinatorial description and analysis of phylogenetic trees and related mathematical structures such as phylogenetic networks and tight spans. Based on a natural conceptual framework, the book focuses on the interrelationship between the principal options for...
Article
Full-text available
Given a set $\Sg$ of bipartitions of some finite set $X$ of cardinality at least 2, one can associate to $\Sg$ a canonical $X$-labeled graph $\B(\Sg)$, called the Buneman graph. This graph has several interesting mathematical properties - for example, it is a median network and therefore an isometric subgraph of a hypercube. It is commonly used as...
Article
Empirical clinical studies on the human interactome and phenome not only illustrates prevalent phenotypic overlap and genetic overlap between diseases, but also reveals a modular organization of the genetic landscape of human disease, providing new opportunities to reduce the complexity in dissecting the phenotype-genotype association. We here intr...
Article
Full-text available
The theory of the tight span, a cell complex that can be associated to every metric D, offers a unifying view on existing approaches for analyzing distance data, in particular for decomposing a metric D into a sum of simpler metrics as well as for representing it by certain specific edge-weighted graphs, often referred to as realizations of D. Many...
Article
In this note, we present a new method that allows us to determine threshold values for separating presence and absence of proteins in a stack of fluorescence images describing a spatial distribution of proteins across a biological object (like a slice of nervous tissue, a sample of blood cells, etc.). We apply this method to stacks of fluorescence...
Article
This paper introduces an efficient implementation of approaches to alignment-free comparative genome analysis and genome-based phylogeny relying on substring composition. Distances derived from substring statistics have been proposed recently as a meaningful alternative to distances derived from sequence alignment. In particular, procaryote phyloge...
Article
A hierarchical structure describing the inter-relationships of species has long been a fundamental concept in systematic biology, from Linnean classification through to the more recent quest for a 'Tree of Life'. In this paper we use an approach based on discrete mathematics to address a basic question: could one delineate this hierarchical structu...
Article
Full-text available
Empirical clinical studies on the human interactome and phenome not only illustrates prevalent phenotypic overlap and genetic overlap between diseases, but also reveals a modular organization of the genetic landscape of human disease, provding new opportunities to reduce the complexity in dissecting the phenotype-genotype association. We here intro...
Article
We introduce the concept of single-linkage equivalence of edge-weighted graphs, we apply it to characterise maximal spanning trees and “ultra-similarities”, and we discuss how it relates to the popular single-linkage clustering algorithm.
Conference Paper
In this note, we present a new method that allows us to determine threshold values for separating presence and absence of proteins in a stack of fluorescence images describing a spatial distribution of proteins across a biological object (like a slice of nervous tissue, a sample of blood cells etc.). This method is based on the so-called Multi-Info...
Article
Full-text available
We present a technique to find threshold values that allows the user to sepa-rate signal from noise in fluorescence grey-level images. It can be classified as a purely comparative method based upon the amount of "Mutual Information" between two or more florescence images, and we apply it to stacks of such images produced using the newly-developed M...
Conference Paper
Inspired by recent discovery that human disease phenome shows a modular organization on the genetic landscape, we introduce a network-module based method towards phenotype-genotype association inference and disease-gene identification. This approach integrates protein-protein interaction network, phenotype similarity network and known phenotype-gen...
Article
Full-text available
One of the most important aspects of cellular protein networks is the spatial distribution of the proteins across cell compartments (membranes, nucleus, mitochondria, etc.). That means that for some cellular function (like cell migration) to be exerted, a cell has not only * Andreas Dress acknowledges support by the BMBF/Germany, the Chinese Academ...
Article
Exploring recent developments in spectral clustering, we discovered that relaxing a spectral reformulation of Newman’s Q-measure (a measure that may guide the search for–and help to evaluate the fit of - community structures in networks) yields a new framework for use in detecting fuzzy communities and identifying so-called unstable nodes. In this...
Article
Defining a subset B of a connected topological space T to be a barrier (in T) if B is connected and its complement T−B is disconnected, we will investigate barriers B in the tight span T(D)={f∈RX:∀x∈Xf(x)=supy∈X(D(x,y)−f(y))} of a metric D defined on a finite set X (endowed, as a subspace of RX, with the metric and the topology induced by the ℓ∞-no...
Article
Full-text available
Identification of interaction patterns in complex networks via community structures has gathered a lot of attention in recent research studies. Local community structures provide a better measure to understand and visualise the nature of interaction when the global knowledge of networks is unknown. Recent research on local community structures, how...
Article
Full-text available
In phylogenetic combinatorics, the analysis of split systems is a fundamental issue. Here, we observe that there is a canonical one-to-one correspondence between split systems on the one, and “even” set systems on the other hand, i.e., given any finite set X, we show that there is a canonical one-to-one correspondence between the set P (S (X ) ){\m...
Article
Full-text available
Split-decomposition theory deals with relations between \mathbb R{\mathbb R}-valued split systems and metrics. Here, we generalize (parts of) this theory, considering group-valued split systems that take their values in an arbitrary abelian group, and replacing metrics by certain, appropriately defined maps (some of which appear to exhibit a deci...
Article
Given a collection $\C$ of subsets of a finite set $X$, let $\bigcup \C = \cup_{S \in \C}S$. Philip Hall's celebrated theorem \cite{hall} concerning `systems of distinct representatives' tells us that for any collection $\C$ of subsets of $X$ there exists an injective (i.e. one-to-one) function $f: \C \to X$ with $f(S) \in S$ for all $S \in \C$ if...
Article
Networks_in Computational_Biology/). Computational biology is one of the many currently emerging areas of applied mathematics and science. During the last century, cooperation between biology and chemistry, physics, mathematics and other sciences increased dramatically, thus providing a solid foundation for, and initiating an enormous momentum in,...
Article
Split-decomposition theory deals with relations between R-valued split systems and metrics. In a previous publication (the first of a series of papers on split decomposition over an abelian group), a general conceptual framework has been set up to study these relationships from an essentially algebraic point of view, replacing metrics by certain mo...
Article
Given a topological space T and a finite subset T0 of T, we associate two graphs with T and T0 that, under rather mild conditions, turn out to be a block graph and a tree, respectively. This construction is of interest, e.g., in the context of phylogenetic analysis where T may model a full “orbit” of a dynamical branching process, and T0 the set of...
Article
Given a finite set X and a proper metric D:X×X→R≥0 defined on X, we show that every block realization of D can be “embedded” canonically into the tight span T(D) of D and characterize the subsets of T(X) that can be obtained in that way as the “canonical image” of the vertex set of a block realization.
Article
Full-text available
Sequence-based phylogeny reconstruction is a fundamental task in Bioinformatics. Practically all methods for phylogeny reconstruction are based on multiple alignments. The quality and stability of the underlying alignments is therefore crucial for phylogenetic analysis. In this short report, we investigate alignments and alignment-based phylogenies...
Chapter
Dieses Kapitel beinhaltet: Vorsokratiker Pflasterungstheorie und mathematische Kristallographie Quasikristalle Anregbare Medien Vergleichende Sequenzanalyse Abschlussbemerkung: Sapere aude! Habe den Mut dich deines eigenen Verstandes zu bedienen. Vorsokratiker Pflasterungstheorie und mathematische Kristallographie Quasikristalle Anregbare Medien Ve...
Article
Abstract Given a metric D defined on a finite set X, we define a finite collec- tion D of metrics on X to be a compatible decomposition of D if any two distinct metrics in D are linearly independent (considered as vectors in R,,y) = 0 holds for every y 2 X. In this paper, we show that such decomposi- tions are in one-to-one correspondence with (iso...
Article
Full-text available
One of the problems arising when exploring toponome or other multivariate-image data is the following: Given a family of n gray-value images of, e.g., a given sample of cell tissue, indexed by a collection of n proteins under investigation (so-called MELK data) — each single image representing the varying local concentration of one of those n prote...
Article
Full-text available
This paper is concerned with the design and analysis of a fully adaptive eigenvalue solver for linear symmetric operators. After transforming the original problem into an equivalent one formulated on ℓ 2, the space of square summable sequences, the problem becomes sufficiently well conditioned so that a gradient type iteration can be shown to reduc...
Article
In this note, we present three methods to discover the most consistent features in the World Atlas of Languages Structures (WALS). These methods measure the fit between each individual WALS feature and the overall dataset of all features combined. Features that show a strong fit to the overall dataset are hypothesised to be more central for the str...
Article
Full-text available
Motivation Sequence-based methods for phylogenetic reconstruction from (nucleic acid) sequence data are notoriously plagued by two effects: homoplasies and alignment errors. Large evolutionary distances imply a large number of homoplastic sites. As most protein-coding genes show dramatic variations in substitution rates that are not uncorrelated ac...
Article
In this note, we will define topological and virtual cut points of finite metric spaces and show that, though their definitions seem to look rather distinct, they actually coincide. More specifically, let X denote a finite set, and let D:X×X→R:(x,y)↦xy denote a metric defined on X. The tight span T(D) of D consists of all maps f∈RX for which f(x)=s...
Chapter
Here we re-interpret this task in the context of a rather naturally defined injective map \( \mathcal{D}_ \bullet \) from the ℝ-vectorspace of all ℝ-weighted split systems into the ℝ-vectorspace \( \mathcal{B} \)(X | ℝ) of ℝ-valued Boolean functions defined on X (i.e., the ℝ-vectorspace consisting of all maps from the power set \( \mathcal{P} \)(X)...
Article
Full-text available
We present an approach to studying the community structures of networks by using linear programming (LP). Starting with a network in terms of (a) a collection of nodes and (b) a collection of edges connecting some of these nodes, we use a new LP-based method for simultaneously (i) nding, at minimal cost, a second edge set by deleting existing and i...
Conference Paper
Full-text available
Article
Full-text available
We investigate the reliability of a recent approach to use parameter- ized linear programming for detecting community structures in networks. Using a one-parameter family of objective functions, a number of \perturbation experi- ments" document that our approach works rather well. We also analyze a real-life network and a family of benchmark networ...
Conference Paper
In this note, we consider algorithms for computing virtual cut points in finite metric spaces and explain how these points can be used to study compatible decompositions of metrics generalizing the well-known decomposition of a tree metric into a sum of pairwise compatible split metrics.
Article
An important procedure in the mathematics of phylogenetic analysis is to associate, to any collection of weighted splits, the metric given by the corresponding linear combination of split metrics. In this note, we study necessary and sufficient conditions for a collection of splits of a given finite set X to give rise to a linearly independent coll...
Article
Full-text available
There is a natural way to associate to any tree T with leaf set X, and with edges weighted by elements from an abelian group G, a map from the power set of X into G—simply add the elements on the edges that connect the leaves in that subset. This map has been well-studied in the case where G has no elements of order 2 (particularly when G is the ad...
Article
Full-text available
. In 1970, Farris introduced a procedure that can be used to transform a tree metric into an ultra metric. Since its discovery, Farris’ procedure has been used extensively within phylogenetics where it has become commonly known as the Farris transform. Remarkably, the Farris transform has not only been rediscovered several times within phylogenetic...
Article
Full-text available
We present QNet, a method for constructing split networks from weighted quartet trees. QNet can be viewed as a quartet analogue of the distance-based Neighbor-Net (NNet) method for network construction. Just as NNet, QNet works by agglomeratively computing a collection of circular weighted splits of the taxa set which is subsequently represented by...
Article
The dependence polynomial PG=PG(z) of a graph G is defined by PG(z)≔∑i=0n(−1)icizi where ci=ci(G) is the number of complete subgraphs of G of cardinality i. It is clear that the complete subgraphs of G form a poset relative to subset inclusion. Using Möbius inversion, this yields various identities involving dependence polynomials implying in parti...
Article
Full-text available
The concept of X-nets is introduced as a convenient tool for dealing with taxonomic problems in terms of phylogenetic networks; in the same formalized quantitative fashion the concept of X-trees is used as a tool for dealing with taxonomic analysis in terms of phylogenetic trees. According to the definition proposed here, a net is considered to be...