bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hidden Markov Models
Authors: Przytycka Teresa M 
Published: September 2006

Abstract
A hidden Markov model is a statistical tool that is frequently used for modeling biological sequences. In applying it, a sequence is modeled as an output of a discrete stochastic process, which progresses through a series of states that are ‘hidden’ from the observer. At each state, the process outputs a symbol from a finite alphabet according to a given probability distribution.
RNA Gene Prediction
Authors: Holbrook Stephen R , Carter Richard J , Meraz Richard F 
Published: September 2006

Abstract
The rapid growth of sequenced genomes and the discovery of numerous novel RNA species has made the development of methods for the computational identification of genes encoding functional RNA a high priority. Recent developments of algorithms for RNA gene prediction are based on diverse criteria, including location of promoters and terminators, sequence conservation among related genomes, RNA base‐pairing and nucleotide composition.
Transcriptional Regulation: Coordination
Authors: Egly Jean‐Marc , Rochette‐Egly Cécile 
Published: September 2006

Abstract
In higher eukaryotes, gene expression is tightly coordinated at multiple stages with other events that orchestrate the life of the cell. Prompted by an initial signal, regulatory transcription factors are activated, assemble at specific enhancer sequences and trigger a cascade of reactions, resulting in an appropriately remodeled chromatin template, with functional transcription machinery on the promoter. Phosphorylation, acetylation and methylation orchestrate the interconnection of the different steps.
Tissue‐specific Locus Control: Structure and Function
Authors: Bonifer Constanze 
Published: September 2006

Abstract
All developmental processes involve decisions in which the developmental fate of precursor cells is restricted to a single lineage by establishing a unique gene expression pattern. The activation at each of these gene loci involves restructuring chromatin as a necessary prerequisite for the assembly of the transcription apparatus. Tissue‐specific locus activation is controlled by the interplay between sequence‐specific transcription factors, chromatin‐modifying activities and basic chromatin components.
Hominids
Authors: Wood Bernard 
Published: September 2006

Abstract
‘Hominid’ is the term traditionally used to refer to the human clade, that is, all the extinct taxa that are more closely related to modern humans than they are to any other living animal. Given the molecular and other evidence for the close relationship between modern humans and the other higher primates (chimps, gorilla and the orang), there is an emerging consensus that the latter should be included in the Hominidae.
Gene Structure: Evolution
Authors: Ohta Tomoko 
Published: September 2006

Abstract
Two fundamental processes in the evolution of gene structure in populations are the production of variations by mutations and the natural selection that filters these variations. Mutations occur randomly in genomes of germ cell lineages and are rejected or selected for, so that genes perform needed functions. As a result of minute effects of most mutations, both genetic drift and natural selection influence their fate in a population.
Mammalian Phylogeny
Authors: Penny David , Phillips Matthew 
Published: September 2006

Abstract
The evolutionary tree of mammals is being resolved rapidly by the increased availability of DNA sequences. Highlights include the placement of humans within the African apes (chimpanzees and gorillas), and the uniting of primates as a whole with flying lemurs and tree shrews to form paraprimates. These join with rodents and rabbits to form the group Supraprimates.
Neanderthal DNA
Authors: Goodwin William , Ovchinnikov Igor 
Published: September 2006

Abstract
Mitochondrial deoxyribonucleic acid (mtDNA) has been successfully extracted and analyzed from three Neanderthal specimens recovered from the Feldhofer Cave in Germany, the Mezmaiskaya Cave in the Caucasus Mountains and the Vindija Cave in Croatia. The Neanderthals' mtDNA pool is distinct from modern human mtDNA and forms a separate phylogenetic clade. Using mtDNA as a molecular clock, the split between the mtDNA of modern humans and Neanderthals has been dated at approximately 600000 years. Like modern humans, the Neanderthals of 30000–40000 years ago display a low level of sequence diversity.
Optical Mapping
Authors: Mishra Bud 
Published: September 2006

AbstractOptical mapping generates an ordered restriction map of a DNA molecule, that is, an ordered enumeration of the restriction sites along with the estimated lengths of the restriction fragments between consecutive restriction sites and various statistics, which model the errors in estimating the restriction fragment lengths and due to unrepresented and misrepresented restriction sites in the map. They have applications in improving the accuracy and algorithmic efficiency of sequence assembly, validating assembled sequences, characterizing gaps in the assembly and identifying candidates for finishing steps in a sequencing project, etc.
Insulin‐dependent Diabetes Mellitus (IDDM): Identifying the Disease‐causing Gene at the
IDDM11
Locus
Authors: Zollo Massimo , Dear Paul , Pociot Flemming 
Published: September 2006

Abstract
In complex diseases, genome linkage analysis, fine mapping and association studies are used to identify disease‐causing genes. With the completion of the human genome sequence and its annotation, positional candidate gene studies have become an attractive method to identify genes involved in complex disorders by screening for selected chromosomal interval regions.
Primer Walking
Authors: Sverdlov Eugene , Azhikina Tatyana 
Published: September 2006

Abstract
Primer walking is a step‐by‐step approach to sequencing long DNA templates from end to end that overcomes the inability of the Sanger chain termination method to read more than a few hundred bases in a single reaction. After an initial round of sequencing from a known sequence at one end of the template, each subsequent round is initiated from a new primer, which is based on the end of the sequence obtained from the previous reaction.
Sequence Accuracy and Verification
Authors: Beck Stephan 
Published: September 2006

AbstractAnalyses involving deoxyribonucleic acid sequences have to consider three main parameters concerning accuracy: sequence quality, sequence contiguity and sequence fidelity. Here, sequence quality defines the probability of error for any base‐call, contiguity defines the completeness and correctness of the assembly of subsequences and fidelity defines the correctness of the genomic representation of the assembly.
Single Nucleotide Polymorphisms (
SNPs
): Identification and Scoring
Authors: Kwok Pui‐Yan 
Published: September 2006

Abstract
Single nucleotide polymorphisms (SNPs) are the most abundant DNA sequence variations in the human genome. Numerous methods have been developed to identify and score them. A large set of human SNPs have been identified and mapped to the reference human genome sequence. The SNP markers are useful for the study of the genetic basis of many human diseases.
Model‐based Linkage Analysis
Authors: Teare Marion Dawn 
Published: September 2006

AbstractModel‐based linkage analysis is the analysis of the cosegregation of genetic loci in pedigrees. The most common form of linkage analysis uses pedigrees selected due to the presence of individuals affected by a disease that is assumed or known to have a major genetic component. Genetic markers are then examined to identify loci that appear to be cotransmitted with the predisposing disease locus.
Genetic Epidemiology of Complex Traits
Authors: Rana Brinda K , Schork Nicholas J 
Published: September 2006

Abstract
Genetic epidemiology evaluates the contribution of genetic factors to disease incidence, prevalence, diagnosis, prevention and treatment in the population at large. Since most traits and diseases are influenced by a number of genetic and nongenetic factors, the identification and characterization of such factors using population‐based studies is extremely difficult, although ‘assays’ that investigate aspects of genetic population structure make meaningful analysis possible.
Psychiatric Disorders: The Search for Genes
Authors: Craddock Nick 
Published: September 2006

Abstract
Psychiatric disorders are a set of common complex genetic disorders in which the core features include pathological disturbances of mood, cognition and behavior. Genes have already been identified for some psychiatric disorders such as Alzheimer disease, and large‐scale positional and candidate gene studies are ongoing for several others including schizophrenia, bipolar disorder, depression, alcohol abuse, autism and attention deficit hyperactivity disorder.
Polymorphisms: Origins and Maintenance
Authors: Weiss Kenneth M 
Published: September 2006

Abstract
Polymorphism is variation in specific locations in the deoxyribonucleic acid (DNA) sequence. Some authors use the term only for variant alleles with at least 1% frequency in a population. This shows the population dependence of the concept itself. Variation arises initially by some form of mutation in a single individual but, because DNA is transmitted from parent to offspring, over time the frequency and geographical distribution of a genetic variant is essentially a population concept that depends on history.
Stationary Allele Frequency Distributions
Authors: Rannala Bruce 
Published: September 2006

Abstract
Forces that determine the allele frequencies in natural populations include genetic drift, natural selection, migration and mutation. A balance of opposing forces can, in some cases, cause allele frequencies to approach a stationary distribution over time. The form of this distribution is not influenced by initial allele frequencies, but instead is determined by the relative magnitudes of different evolutionary forces.
Mutations in Human Genetic Disease
Authors: Antonarakis Stylianos E , Cooper David N 
Published: September 2006

AbstractMutations in human genetic disease include single base‐pair substitutions in coding, regulatory and splicing‐relevant regions of human genes. Other kinds of pathogenic mutations are micro‐deletions, micro‐insertions, duplications, repeat expansions, combined micro‐insertions/deflections (‘indels’), inversions, gross deletions and insertions, and complex rearrangements.
Imprinting Disorders
Authors: Feinberg Andrew P , Niemitz Emily L 
Published: September 2006

Abstract
Genomic imprinting is an example of epigenetic inheritance in which differences in gene function depend on whether the allele was inherited from the mother or father. Many disorders now appear to involve epigenetic alterations, and the mechanism of normal imprinting as well as its perturbation in disease is becoming understood and amenable to experimentation.
Linkage and Association Studies
Authors: Borecki Ingrid B 
Published: September 2006

Abstract
Identification of genetic factors underlying predisposition to complex human diseases has relied on linkage studies to map the relevant loci and on association studies to evaluate the putative role of specific genetic variants on the risk for disease or on levels of quantitative risk factors. While both approaches seek an association between a genetic sequence and a phenotype of interest, their respective utility and power depend on the specific problem.
Disease‐related Genes: Functional Analysis
Authors: Rugarli Elena I , Ballabio Andrea 
Published: September 2006

Abstract
Functional analysis of genes involved in human diseases is a critical step in understanding disease pathogenesis. The function of a given gene can be determined either at the cellular level or at the level of a whole organism in both normal and pathological conditions. Functional analysis is achieved through integration of information derived from various experimental strategies, for example, determination of gene‐expression pattern, exploitation of bioinformatic resources, and biochemical and cellular studies.
Cp
G
Dinucleotides and Human Disorders
Authors: Antonarakis Stylianos E 
Published: September 2006

Abstract
Analysis of the mutation spectra of single nucleotide substitutions associated with monogenic disorders strongly suggests that CG to TG mutations are among the most frequent causes of human genetic disease phenotypes. This is probably due to the mechanism of methylation–deamination of cytosine. In addition, this substitution mechanism results in a substantial fraction of the polymorphic variability of the human genome.
3′
UTR
Mutations and Human Disorders
Authors: Conne Béatrice , Stutz André , Vassalli Jean‐Dominique 
Published: September 2006

Abstract
The 3′ untranslated region (3′ UTR) of a number of messenger ribonucleic acids (mRNAs) is involved in the regulation of the processing, localization, translation or degradation of the transcript. Perturbations in such 3′ UTR‐mediated functions are implicated in a variety of human diseases.
Deafness: Hereditary
Authors: Hardelin Jean‐Pierre , Levilliers Jacqueline , Petit Christine 
Published: September 2006

Abstract
There are 35 genes known to cause nonsyndromic hearing loss, and many more are expected to come out in the next few years. However, difficulties inherent in genetic linkage analysis, coupled with the possible involvement of environmental causes, have prevented the characterization of the main genes causative or predisposing to the late‐onset forms of deafness.
Skeletal Dysplasias: Genetics
Authors: Superti‐Furga Andrea , Unger Sheila 
Published: September 2006

Abstract
The skeletal dysplasias and dysostoses are a group of genetic disorders that manifest as disproportionate short stature, deformity and various medical complications. Dysplasias may result from genetic mutations that affect structural components, metabolic pathways, signal transduction mechanisms or gene expression patterns involved in skeletal growth and development.
Kidney: Hereditary Disorders
Authors: Esquivel Ernie L , Somlo Stefan 
Published: September 2006

AbstractHereditary disorders of the kidney consist of a heterogeneous group of diseases characterized by abnormalities in the ability of the kidneys to filter waste products and/or maintain acid–base and fluid homeostasis. Elucidation of the underlying genetic lesions has enhanced our basic understanding of renal physiology, as well as of normal kidney development and cellular differentiation.
Infertility: Genetic Disorders
Authors: Vogt Peter H 
Published: September 2006

Abstract
Identification of genetic disorders causing human male or female infertility is of paramount importance in each infertility clinic that has to consider the possible risk of transfer of a specified genetic abnormality (i.e. a distinct chromosomal aberration and/or a specific gene mutation) to the offspring created by the applied artificial fertilization protocol. This is useful especially for those men and women where no obstructions of the germ line can be observed and who are therefore diagnosed in the clinic as having idiopathic infertility.
Hemochromatosis
Authors: Beutler Ernest 
Published: September 2006

Abstract

Essentially a clinical diagnosis, classically the term
hemochromatosis
has denoted iron storage disease of varying etiology accompanied by tissue damage. Common pathologic manifestations are cirrhosis of the liver, diabetes, darkening of the skin and cardiac arrhythmias and failure. The cause can be hereditary, as in the HLA‐linked form most common in Europeans, or acquired, as the result of transfusions and/or disordered erythropoiesis as in thalassemia. With the positional cloning of the
HFE
gene, the term hemochromatosis has been increasingly taken to represent an
HFE
genotype, with or without pathologic changes.
Mitochondrial Disorders
Authors: Hofmann Sabine , Bauer Matthias F 
Published: September 2006

Abstract
Mitochondria are double‐membrane organelles which play a pivotal role in cellular metabolism and are responsible for creating free energy, in the form of ATP, essential for the normal function and maintenance of all human organ systems. Genetic defects of mitochondrial functions cause human diseases associated with a wide spectrum of clinical phenotypes.
Microdeletion Syndromes
Authors: Schinzel Albert , Riegel Mariluce , Baumer Alessandra 
Published: September 2006

Abstract

A microdeletion syndrome is the clinical consequence of a submicroscopic chromosome deletion leading to the monosomic state of a small chromosomal segment. Clinical pictures of well‐known microdeletion syndromes are mostly specific, and cytogenetic confirmation is done by either fluorescent
in situ
hybridization or microsatellite marker analysis.
Multiple Sclerosis (
MS
): Genetics
Authors: Dyment D A , Ebers G C 
Published: September 2006

Abstract
Multiple sclerosis is a complex trait and highlights the interplay between nature, nurture and chance. Genetic–epidemiological and prevalence studies demonstrate the importance of genes and that environmental factors operate on a population‐based level. There is an association with HLA polymorphisms located at 6p21; genome searches have not yet identified a novel susceptibility locus.
Databases in Genetics Clinics
Authors: Pagon Roberta A , Tarczy‐Hornoch Peter , Beahler Christine 
Published: September 2006

Abstract
Medical geneticists, genetics counselors and nurses in genetics who staff medical genetics clinics rely upon internet‐accessible and stand‐alone databases for access to the medical literature, for disease recognition, for current information on genetic test availability and use, for patient‐support materials, and for locating other genetics professionals.
Yeast as a Model for Human Diseases
Authors: Fridovich‐Keil Judith L 
Published: September 2006

Abstract
Yeasts are single‐celled eukaryotes that provide a genetically and biochemically amenable model system for biomedical research. Over the past decades, studies in yeast have established a foundation for much of our current knowledge on such fundamental processes as eukaryotic cell cycle control, genetic instability and colon cancer, metabolism and metabolic disease and even aging. Through basic science and pharmaceutical applications, studies in yeast hold promise for even greater contributions in the future.
Olfactory Receptors
Authors: Giorgi Dominique , Gaillard Isabelle , Rouquier Sylvie 
Published: September 2006

Abstract
The sense of smell is mediated by olfactory receptors belonging to the seven‐transmembrane G‐protein‐coupled receptor superfamily. They are expressed at the surface of the cilia of olfactory sensory neurons that emerge in the olfactory epithelium of the nasal cavity. The specific binding of odorant ligands initiates signals transmitted to the central nervous system through different relays, allowing an individual to identify precisely a particular odor.
Cytochrome P450 (
CYP
) Gene Superfamily
Authors: Nebert Daniel W , Nelson David R 
Published: September 2006

Abstract

Cytochrome P450, which was first named a ‘pigment in the cell’ and thought to be a single enzyme in the early 1960s, was correlated with drug and steroid metabolism by the late 1960s and recognized eventually to comprise an ancient gene superfamily encoding numerous ubiquitous enzymes that participate in countless essential life processes. Defects in many of the 57 human functional
CYP
genes are involved in some inborn errors of metabolism and other clinical diseases.
Potassium Channels
Authors: Coetzee William A , Rudy Bernardo 
Published: September 2006

Abstract

Potassium channels constitute a highly diverse class of ion channel and thus participate in multiple modulatory functions. There are several functional types of K
+
channel, including voltage‐gated K
+
channels, Ca
2+
‐activated K
+
channels, inward rectifiers, leak K
+
channels and Na
+
‐activated K
+
channels. Principal or pore‐forming subunits of at least the first four types have been identified and are classified into three groups of proteins on the basis of their structural properties.
DNA Chip Revolution
Authors: Lockhart David J 
Published: September 2006

Abstract
The deoxyribonucleic acid (DNA) chips, arrays or microarrays are powerful new tools, designed and built based on genomic sequence information, that are changing the face of biological and biomedical research. The arrays enable massively parallel measurements of gene expression and genetic variation, and are dramatically increasing our understanding of biology and disease, and promise to have a great impact on drug development and the practice of medicine.
Rett Syndrome
Authors: Hoffman Eric P , Moses Linda , Scacheri Cheryl AG , Hoffbuhr Kristen C 
Published: September 2006

Abstract

Rett syndrome is a neurological disease of early postnatal brain growth found almost exclusively in girls. Typically girls with Rett syndrome show developmental regression including loss of communication and motor skills, stereotypic hand movements and a deceleration of head growth. The defective gene, methyl CpG binding protein 2 (Rett syndrome) (
MECP2
) is normally involved in the transcription silencing of genes (turning genes ‘off’): in Rett syndrome, the MECP2 protein does not work properly in approximately half of the patient's cells (heterozygous), leading to the aberrant expression of a cascade of other genes, normally regulated by MECP2.
Turner Syndrome
Authors: Hall Laura L 
Published: September 2006

Abstract

Turner syndrome (TS) results from the absence of some or all of the X chromosome, with a karyotype of 45,X in the fully developed syndrome. Because not all genes on the X chromosome are inactivated normally, the diminished expression of these genes presumably leads to the TS phenotype, including short stature, incomplete sexual development and reproductive function, and other structural and cognitive abnormalities. Research has begun to identify genes that are potentially linked to TS, including the short stature homeobox (
SHOX
) gene and
DFRX
, the human homolog of a fruitfly gene involved in oogenesis.
Chromatin in the Cell Nucleus: Higher‐order Organization
Authors: Cremer Thomas , Cremer Christoph G 
Published: September 2006

Abstract
The cell nucleus contains chromosome territories (CTs) and an interchromatin compartment (IC). The CT–IC model provides a framework for the functional nuclear architecture with a set of testable predictions. In particular, it predicts a topological level of gene regulation based on a cell‐type‐specific 3D architecture of higher‐order chromatin domains.
Synchronous and Asynchronous Replication
Authors: Selig Sara 
Published: September 2006

Abstract
Replication of nuclear DNA in animal cells is carried out according to a temporal program that is conserved from one cell division to the next. The order of replication of genomic regions can be determined by various methods. In most genomic regions both allelic copies replicate synchronously, with the exception of the X chromosomes in female mammals, regions containing imprinted genes or genes with one randomly inactivated allele.
Fluorescence Microscopy
Authors: Tanke Hans J 
Published: September 2006

Abstract

Fluorescence microscopy is applied to visualize gene and gene transcripts as stained
in situ
by methods such as fluorescence
in situ
hybridization. Instrumentation includes the use of cameras and interferometers for recording multicolor microscopic images, and confocallaser scanning microscopes for optical sectioning and subsequent reconstruction of three‐dimensional images of (living) cells.