Heinrich Stamerjohanns

DNA Methylation Analysis by Bisulfite Conversion, Cloning, and Sequencing of Individual Clones

DNA methylation is an essential epigenetic modification in the human genome. For the investigation of DNA methylation patterns, bisulfite conversion and DNA sequencing is a method of choice, because it provides detailed information on the methylation pattern of individual DNA molecules at single CG site resolution. The method is based on the deamination of cytosine residues to uracils in the presence of NaOH and sodium bisulfite. Since methylcytosine is not converted under these conditions, the original methylation state of the DNA can be analyzed by sequencing of the converted DNA. After the conversion reaction, the DNA sequence under investigation is amplified by polymerase chain reaction (PCR) with primers specific for one strand of the bisulfite-converted DNA. The PCR product is cloned and individual clones are sequenced. Here, we describe an advanced protocol for bisulfite conversion, protocols for cloning, and tools for primer design (Methprimer, Bisearch). In addition, we present tools for the web display of primary data and data analysis (BiQ Analyzer, BDPC) and describe the setup of a sequencing and analysis pipeline for medium to high throughput.

Bisulfite sequencing Data Presentation and Compilation (BDPC) web server—a useful tool for DNA methylation analysis

During bisulfite genomic sequencing projects large amount of data are generated. The Bisulfite sequencing Data Presentation and Compilation (BDPC) web interface (http://biochem.jacobs-university.de/BDPC/) automatically analyzes bisulfite datasets prepared using the BiQ Analyzer. BDPC provides the following output: (i) MS-Excel compatible files compiling for each PCR product (a) the average methylation level, the number of clones analyzed and the percentage of CG sites analyzed (which is an indicator of data quality), (b) the methylation level observed at each CG site and (c) the methylation level of each clone. (ii) A methylation overview table compiling the methylation of all amplicons in all tissues. (iii) Publication grade figures in PNG format showing the methylation pattern for each PCR product embedded in an HMTL file summarizing the methylation data, the DNA sequence and some basic statistics. (iv) A summary file compiling the methylation pattern of different tissues, which is linked to the individual HTML result files, and can be directly used for presentation of the data in the internet. (v) A condensed file, containing all primary data in simplified format for further downstream data analysis and (vi) a custom track file for display of the results in the UCSC genome browser.

Capturing the content of physics: systems, observables, and experiments

We present a content markup language for physics realized by extending the OMDoc format by an infrastructure for the principal concepts of physics: observables, physical systems, and experiments. The formalization of the description of physics observables follows the structural essence of the operational theory of physics measurements. The representational infrastructure for systems and experiments allow to capture the distinctive practice of physics: natural laws are supported by evidence from experiments which are described, disseminated and reproduced by others.

Classification of phase transitions of finite Bose-Einstein condensates in power law traps by Fisher zeros

We present a detailed description of a classification scheme for phase transitions in finite systems based on the distribution of Fisher zeros of the canonical partition function in the complex temperature plane. We apply this scheme to finite Bose systems in power-law traps within a semi-analytic approach with a continuous one-particle density of states O(E)~Ed-1 for different values of d and to a three-dimensional harmonically confined ideal Bose gas with discrete energy levels. Our results indicate that the order of the Bose-Einstein condensation phase transition sensitively depends on the confining potential.

New clustering module in BDPC bisulfite sequencing data presentation and compilation web application for DNA methylation analyses

The Bisulfite Sequencing Data Presentation and Compilation (BDPC) web interface for compilation and presentation of data from bisulfite sequencing DNA methylation studies has been improved by adding a new module. This module allows visualization of the whole data set in form of a heatmap of DNA methylation levels and clustering and comparison of tissue methylation patterns. It can also be used for data not processed by BDPC. In addition, several functions of the existing BDPC compilation module have been improved.

Origins of phase transitions in small systems

The identification and classification of phases in small systems, e.g., nuclei, social and financial networks, clusters, and biological systems, where the traditional definitions of phase transitions are not applicable, is important to obtain a deeper understanding of the phenomena observed in such systems. Within a simple statistical model, we investigate the validity and applicability of different classification schemes for phase transtions in small systems. We show that the whole complex temperature plane contains necessary information in order to give a distinct classification.

Deceptive signals of phase transitions in small magnetic clusters

We present an analysis of the thermodynamic properties of small transition-metal clusters and show how the commonly used indicators of phase transitions such as peaks in the specific heat or magnetic susceptibility can lead to deceptive interpretations of the underlying physics. The analysis of the distribution of zeros of the canonical partition function in the whole complex temperature plane reveals the nature of the transition. We show that signals in the magnetic susceptibility at positive temperatures have their origin at zeros lying at negative temperatures.

Transforming the ar Χ iv to XML

We describe an experiment of transforming large collections of documents to more machine-understandable representations. Concretely, we are translating the collection of scientific publications of the Cornell e-Print Archive ( arXiv ) using the to XML converter which is currently under development. The main technical task of our arXMLiv project is to supply LaTeXML bindings for the (thousands of) classes and packages used in the arXiv collection. For this we have developed a distributed build system that reiteratively runs LaTeXML over the arXiv collection and collects statistics about e.g. the most sorely missing LaTeXML bindings and clusters common error events. This creates valuable feedback to both the developers of the LaTeXML package and to binding implementers. We have now processed the complete arXiv collection of more than 400,000 documents from 1993 until 2006 (one run is a processor-year-size undertaking) and have continuously improved our success rate to more than 56% (i.e. over 56% of the documents that are have been converted by LaTeXML without noticing an error and are available as XHTML+MathML documents).

The LaTeXML daemon: editable math on the collaborative web

The language of the \({T\kern-.1667em\lower.7ex\hbox{E}\kern-.125emX}/{\rm L\kern-.36em\raise.3ex\hbox{\sc a}\kern-.15em T\kern-.1667em\lower.7ex\hbox{E}\kern-.125emX}\) typesetting system has become all-pervasive in scientific publications and has proven its stability, convenience and expressivity in its three-decade history. With the advent of the Web 2.0 paradigm, it has also become the primary choice of various technical and scientific social platforms, most prominently online encyclopedias (e.g. Planet- Math [Pla]) and question-answer forums (e.g. MathOverflow [Mat]). On the other hand, the standardization of MathML and OpenMath and the adoption of the former in HTML5, have opened the floodgates for scientific content native to the browser.

Thermodynamics of finite magnetic two-isomer systems

We use Monte Carlo simulations to investigate the thermodynamical behavior of aggregates consisting of few superparamagnetic particles in a colloidal suspension. The potential energy surface of this classical two-isomer system with a stable and a metastable “ring” and “chain” configuration is tunable by an external magnetic field and temperature. We determine the complex “phase diagram” of this system and analyze thermodynamically the nature of the transition between the ring and the chain “phase.”