Aspects of the invention include methods and systems for identifying somatic mutational signatures for detecting, diagnosing, monitoring and/or classifying cancer in a patient known to have, or suspected of having cancer. In various embodiments, the methods of the invention use a non-negative matrix factorization (NMF) approach to construct a signature matrix that can be used to identify latent signatures in a patient sample for detection and classification of cancer. In some embodiments, the methods of the invention may use principal components analysis (PCA) or vector quantization (VQ) approaches to construct a signature matrix.

Systems and methods for identifying synthetic lethal (SL) and synthetic dosage lethal (SDL) interactions and networks are provided. Further provided are methods for predicting cancer gene essentiality, drug efficacy and survival of cancer patients using data-driven identification of synthetic lethality in cancer are provided. Novel drug candidates and drug combinations for use in cancer therapy and method for prioritizing existing cancer therapies are also provided.

A virtual cell simulator for generating virtual cell models is disclosed. The virtual cell simulator can be configured to model cells with a variety of different characteristics while adsorbing on various types of substrates. In some cases, the simulation technique can apply Molecular Dynamics. Furthermore, the simulation technique can implement Multi Particle Collision Dynamics to provide a powerful mesoscopic method for simulation of solvents. The virtual cell simulator provides a highly reliable means of predicting cell behavior prior to experimental evaluation. The virtual cell includes components that represent or virtually model outer membranes, nucleus membranes, cytoplasm, cytoskeleton, and/or chromatin fibers.

A method and system for planning a creation of a cement bore in a bone comprises obtaining a virtual model of a bone, the model of the bone including a proximal bone surface, a distal bone surface, and a depth profile between the proximal bone surface and the distal bone surface. A planned positioning of a first implant selected to be implanted in the proximal bone surface is obtained. An identity of at least one tool used to alter the proximal bone surface to receive the first implant in the planned positioning and obtaining geometry data for the at least one tool is obtained. A cement bore required in the bone using the geometry data of the at least one tool and the planned positioning of the first implant is generated. The virtual model of the bone with the cement bore indicative of a relation between the cement bore and the distal bone surface is output.

The present invention relates to purified and isolated DNA sequences having protein production increasing activity and more specifically to the use of matrix attachment regions (MARs) for increasing protein production activity in a eukaryotic cell. Also disclosed is a method for the identification of said active regions, in particular MAR nucleotide sequences, and the use of these characterized active MAR sequences in a new multiple transfection method.

Techniques and systems are disclosed for enabling a simulation environment for experimental design. The interactions of a configuration of molecules inside a biological structure or system, such as a cell (e.g., a neuron) or virtual test tube, are modeled using message-based techniques to communicate between molecules proximal to one another in a virtual 3-D geometric space. Some techniques and systems allow distributed processing of the individual molecular interactions across a plurality of work nodes. Some techniques and systems allow the storage of detailed information about the current state of the simulation of the biological model for each discrete time slice. This enables the ability for a 4-D playback/review of any particular spatial or temporal focus area of the simulation.

A process includes receiving information associated with a target molecule to be synthesized via a synthetic pathway engine user interface. The process also includes determining, using a synthetic pathway engine, synthetic pathway data for synthesis of the target molecule. In some cases, the process further includes generating a synthetic pathway report user interface that includes information associated with the synthetic pathway data. In other cases, the process further includes initiating automated synthesis of the target molecule using automated chemical synthesis equipment according to the synthetic pathway data.

Non-mechanistic, differential-equation-free approaches for predicting a particular pharmacokinetic and pharmacodynamic responses of a system to a given input are provided in the form of systems, methods, and devices. These approaches are generally directed to a non-compartmental method of predicting a time-dependent pharmacokinetic response, or pharmacodynamics response, of a component of a system to an input into the system. The systems, methods, and devices provide the ability to (i) reduce the cost of research and development by offering an accurate modeling of heterogeneous and complex physical systems; (ii) reduce the cost of creating such systems and methods by simplifying the modeling process; (iii) accurately capture and model inherent nonlinearities in cases where sufficient knowledge does not exist to a priori build a model and its parameters; and, (iv) provide one-to-one relationships between model parameters and model outputs, addressing the problem of the ambiguities inherent in the current, state-of-the-art systems and methods.

Provided herein are improved methods for detecting aneuploidy in a sample. The methods in certain embodiments are used for the analysis of circulating DNA in serum samples, such as circulating fetal DNA or circulating tumor DNA. In certain embodiments, chromosome or chromosome segments of interest are used to set a bias model and/or a control value for a z-score determination, in illustrative examples without the use of a control chromosome.

Provided herein are improved methods for detecting aneuploidy in a sample. The methods in certain embodiments are used for the analysis of circulating DNA in serum samples, such as circulating fetal DNA or circulating tumor DNA. In certain embodiments, chromosome or chromosome segments of interest are used to set a bias model and/or a control value for a z-score determination, in illustrative examples without the use of a control chromosome.