Abstract: The invention refers to a method for diagnosing an individual who is to be subjected to or is being subjected to an anti-tumor necrosis factor alpha (TNF? or TNF) treatment to assess the responsiveness to an anti-TNF treatment which comprises the detection of immunoglobulin(s) against one or more biomarker proteins in a bodily fluid or an excrement of said patient, and sorting the individual into one of two categories based on detection of said immunoglobulin(s), wherein individuals are classified as NON-responder or responder. The invention refers to diagnostic kits comprising said one or more biomarker proteins and the use of these kits for assessing the responsiveness to an anti-TNF treatment of an individual who is to be subjected to or is being subjected to an anti-TNF? treatment.

Abstract: The invention refers to a method for diagnosing an individual who is to be subjected to or is being subjected to an anti-tumor necrosis factor alpha (TNF? or TNF) treatment to asses the responsiveness to an anti-TNF treatment which comprises the detection of immunoglobulin(s) against one or more biomarker proteins in a bodily fluid or an excrement of said patient, and sorting the individual into one of two categories based on detection of said immunoglobulin(s), wherein individuals are classified as NON-responder or responder. The invention refers to diagnostic kits comprising said one or more biomarker proteins and the use of these kits for assessing the responsiveness to an anti-TNF treatment of an individual who is to be subjected to or is being subjected to an anti-TNF? treatment.

Abstract: The invention relates to a method for linking at least two target nucleic acid molecules from a single biological compartment, comprising the steps of isolating a fraction from a sample, wherein the fraction comprises the compartment comprising at least two nucleic acid molecules, diluting the fraction and aliquoting the dilution in multiple separate reaction vessels such that each reaction vessel comprises preferably one compartment, or encapsulating the compartment in emulsion droplets such that each droplet comprises preferably one compartment; linking the at least two target nucleic acid molecules, preferably by overlap extension PCR. The method may be employed in the analysis of mutations present in a single cell and in the production of antibodies which are present in a single hybridoma.

Abstract: The invention relates to the identification and selection of novel genomic regions (biomarker) and the identification and selection of novel genomic region combinations which are hypermethylated in subjects with prostate cancer compared to subjects without prostate cancer. Nucleic acids which selectively hybridize to the genomic regions and products thereof are also encompassed within the scope of the invention as are compositions and kits containing said nucleic acids and nucleic acids for use in diagnosing prostate cancer. Further encompassed by the invention is the use of nucleic acids which selectively hybridize to one of the genomic regions or products thereof to monitor disease regression in a patient and the efficacy of therapeutic regimens.

Abstract: The idea of this invention is to prepare ordered oligonucleotides arrays from two or more pre-synthesized shorter parts—block-synthesis approach. The parts are linked together enzymatically to form a full-length oligonucleotide of a desired sequence. Such an approach allows splitting the oligonucleotide sequences into common and unique parts. It gives the possibility to place the functional group on a common part and to minimize the length of the unique parts. Method of the invention allows combinatorial synthesis of position-specific regions. Using combinatorial approach, position-specific regions are generated by linking two or more unique oligonucleotides, so that just few said unique oligonucleotides give rise to a large variety of codes, for example, 10 unique oligonucleotides linked pairwise can produce 100 position-specific regions.

Abstract: The present invention relates to a method for identifying a therapeutic drug combination against a cancer, wherein the cancer comprises at least two alterations in at least two different, but crosstalking signaling pathways, the method comprising the steps of: a) providing a kinetic model of a biological network for said cancer comprising the at least two different, but crosstalking signaling pathways, wherein the kinetic model is generated by choosing a network topology, wherein the nodes of said topology represent biological entities selected from the group comprising genes, transcripts, peptides, proteins, protein modification states, small molecules, complexes, metabolites and modifications thereof, and the edges of said topology represent interactions between said entities, assigning kinetic laws and kinetic constants to the interactions and assigning concentrations to the biological entities, such that the kinetic model reflects the genome, epi-genome, proteome and/or transcriptome of said cancer, b)sel

Abstract: The present invention relates to a method for identification of fragments originating from individual macromolecules (MM) or molecular complexes (MC) in a mixture of fragments of different MM or MC using labeling of MM or MC with oligonucleotide markers comprising the following steps: a) labeling of MM or MC with oligonucleotide markers wherein each particular MM or MC is labeled with identical oligonucleotide markers and preferentially the different MM or MC are labeled with different oligonucleotide markers and wherein the number of identical oligonucleotide markers is sufficient that after subsequent fragmentation or dissociation of fragments of the MM or the MC each fragment is preferentially labeled with at least one of the oligonucleotide marker; b) fragmentation or dissociation of MM or MC, wherein step a) and b) are optionally done in parallel; c) mixing labeled fragments of different MM or MC together; d) analyzing of fragments and determining the nucleotide sequence of the at least one oligonucleoti

Abstract: The present invention pertains to a diagnostic assay for the diagnosis of an autoimmune disease. The present invention provides an improved diagnostic assay for the diagnosis of an autoimmune disease, particularly rheumatoid arthritis (RA) and Systemic Lupus Erythematosus (SLE). In particular the invention pertains to a method of determining in a sample of a subject the presence of two or more antibodies comprising the step of determining whether an antibody is present in a sample that specifically recognizes a hnRNP-DL polypeptide or a fragment thereof or a splice variant thereof and the further step of determining whether at least one further antibody is present in the sample that specifically recognizes a at least one other hnRNP polypeptide which is not sequence homologue to said hnRNP-DL polypeptide or fragments thereof or splice variants thereof, and/or said CCP peptide and/or a polypeptide comprising at least the Fc-part of IgG, respectively.

Abstract: The invention relates to the identification and selection of novel genomic regions (biomarker) and the identification and selection of novel genomic region combinations which are hypermethylated in subjects with colorectal cancer compared to subjects without colorectal cancer. Nucleic acids which selectively hybridize to the genomic regions and products thereof are also encompassed within the scope of the invention as are compositions and kits containing said nucleic acids and nucleic acids for use in diagnosing prostate cancer. Further encompassed by the invention is the use of nucleic acids which selectively hybridize to one of the genomic regions or products thereof to monitor disease progression or regression in a patient and the efficacy of therapeutic regimens.

Abstract: Objective of the present invention is to provide a method for keeping of directional information in double-stranded DNA. We suggest to convert polynucleotide into a hybrid double-stranded DNA. One particular strand of this hybrid double-stranded DNA should be synthesised using at least one modified nucleotide. Thus, this particular strand would contain modified nucleotides along the whole length. Density of directional markers would not depend on the length of polynucleotides. Any internal fragments of the hybrid double-stranded DNA would have directional information. When it is necessary the modified strand may be easily degraded or separated from the other strand. It was found that such hybrid double-stranded DNA may be easily generated in a number of molecular biology tasks and may be used for molecular cloning, library preparation and strand separation.

Abstract: The present invention relates to a computer-implemented method of producing a kinetic model of a biological network. An example method can comprise choosing a network topology. The nodes of said topology represent biological entities and the edges of said topology represent interactions between said entities. An example method can comprise assigning kinetic laws and kinetic constants to said interactions and assigning starting concentrations to said biological entities. One part of said kinetic constants and independently one part of said starting concentrations are experimental data. The remaining part of said kinetic constants and independently the remaining part of said starting concentrations are chosen randomly.

Abstract: When sequencing is used for the analysis of composition of nucleic acid mixtures with a large dynamic range of concentrations of individual components, the reliability of results significantly differs for abundant and rare components. The present invention relates to methods for analysis of concentrations of components of nucleic acid mixtures by sequencing, wherein relative abundances of at least two components for which concentrations should be measured is changed before sequencing in a reproducible way using locus-specific oligonucleotides.

Abstract: The invention refers to a method for diagnosing an individual who is to be subjected to or is being subjected to an anti-tumour necrosis factor alpha (TNF? or TNF) treatment to asses the responsiveness to an anti-TNF treatment which comprises the detection of immunoglobulin(s) against one or more biomarker proteins in a bodily fluid or an excrement of said patient, and sorting the individual into one of two categories based on detection of said immunoglobulin(s), wherein individuals are classified as NON-responder or responder. The invention refers to diagnostic kits comprising said one or more biomarker proteins and the use of these kits for assessing the responsiveness to an anti-TNF treatment of an individual who is to be subjected to or is being subjected to an anti-TNF? treatment.

Abstract: Objective of the present invention is to provide a method for keeping of directional information in double-stranded DNA. We suggest to convert polynucleotide into a hybrid double-stranded DNA. One particular strand of this hybrid double-stranded DNA should be synthesised using at least one modified nucleotide. Thus, this particular strand would contain modified nucleotides along the whole length. Density of directional markers would not depend on the length of polynucleotides. Any internal fragments of the hybrid double-stranded DNA would have directional information. When it is necessary the modified strand may be easily degraded or separated from the other strand. It was found that such hybrid double-stranded DNA may be easily generated in a number of molecular biology tasks and may be used for molecular cloning, library preparation and strand separation.

Abstract: The invention encompasses the identification and selection of novel miRNAs as biomarkers so as to provide a method for the diagnosis of colorectal cancer. The miRNAs identified are differentially expressed in subjects with colorectal cancer compared to subjects without colorectal cancer. Further, some of the identified miRNAs were found to play a critical role for the progression of colorectal cancer into metastasis and, thus, facilitate a differential diagnosis between tumor and metastasis. Nucleic acids which are capable of specifically detecting the miRNAs identified are also encompassed within the scope of the invention as are sets of said nucleic acids, which arc particularly suited for being used in multiplex RT-PCR or in array techniques. Further encompassed are compositions and kits containing said nucleic acids and nucleic acids for use in diagnosing colorectal cancer.

Abstract: The invention refers to a method for diagnosing an individual who is to be subjected to or is being subjected to an anti-tumor necrosis factor alpha (TNF? or TNF) treatment to assess the responsiveness to an anti-TNF treatment which comprises the detection of immunoglobulin(s) against one or more biomarker proteins in a bodily fluid or an excrement of said patient, and sorting the individual into one of two categories based on detection of said immunoglobulin(s), wherein individuals are classified as NON-responder or responder. The invention refers to diagnostic kits comprising said one or more biomarker proteins and the use of these kits for assessing the responsiveness to an anti-TNF treatment of an individual who is to be subjected to or is being subjected to an anti-TNF? treatment.

Abstract: The present invention provides methods for replication of nucleic acid molecules distributed on a surface or within a layer by transferring them to a target surface covered with oligonucleotides, and fixation of transferred molecules by hybridization to complementary sequences.

Abstract: Objective of the present invention is to provide a method for keeping of directional information in double-stranded DNA. We suggest to convert polynucleotide into a hybrid double-stranded DNA. One particular strand of this hybrid double-stranded DNA should be synthesised using at least one modified nucleotide. Thus, this particular strand would contain modified nucleotides along the whole length. Density of directional markers would not depend on the length of polynucleotides. Any internal fragments of the hybrid double-stranded DNA would have directional information. When it is necessary the modified strand may be easily degraded or separated from the other strand. It was found that such hybrid double-stranded DNA may be easily generated in a number of molecular biology tasks and may be used for molecular cloning, library preparation and strand separation.

Abstract: Objective of the present invention is to provide a method for keeping of directional information in double-stranded DNA. We suggest to convert polynucleotide into a hybrid double-stranded DNA. One particular strand of this hybrid double-stranded DNA should be synthesized using at least one modified nucleotide. Thus, this particular strand would contain modified nucleotides along the whole length. Density of directional markers would not depend on the length of polynucleotides. Any internal fragments of the hybrid double-stranded DNA would have directional information. When it is necessary the modified strand may be easily degraded or separated from the other strand. It was found that such hybrid double-stranded DNA may be easily generated in a number of molecular biology tasks and may be used for molecular cloning, library preparation and strand separation.

Abstract: The present invention describes a method for identification of areas of a sample from which nucleic acid molecules originate using labeling of said nucleic acid molecules by two-dimensionally distributed oligonucleotide markers. Further analysis of hybrids between the nucleic acid molecules and the oligonucleotide markers allow identification of the original position of the labelled nucleic acid molecules in the sample.