DeepSort: deep convolutional networks for sorting haploid maize seeds.

Background: Maize is a leading crop in the modern agricultural industry that accounts for more than 40% grain production worldwide. THe double haploid technique that uses fewer breeding generations for generating a maize line has accelerated the pace of development of superior commercial seed varieties and has been transforming the agricultural industry. In this technique the chromosomes of the haploid seeds are doubled and taken forward in the process while the diploids marked for elimination.

Systems biology-based identification of Mycobacterium tuberculosis persistence genes in mouse lungs.

Unlabelled: Identifying Mycobacterium tuberculosis persistence genes is important for developing novel drugs to shorten the duration of tuberculosis (TB) treatment. We developed computational algorithms that predict M. tuberculosis genes required for long-term survival in mouse lungs.

Predicting functional associations from metabolism using bi-partite network algorithms.

Background: Metabolic reconstructions contain detailed information about metabolic enzymes and their reactants and products. These networks can be used to infer functional associations between metabolic enzymes. Many methods are based on the number of metabolites shared by two enzymes, or the shortest path between two enzymes.

Metabolic flux correlations, genetic interactions, and disease.

Many diseases are caused by failures of metabolic enzymes. These enzymes exist in the context of networks defined by the static topology of enzyme-metabolite interactions and by the reaction fluxes that are feasible at steady state. We use the local topology and the flux correlations to identify how failures in the metabolic network may lead to disease.

Adaptive epileptic seizure prediction system.

Current epileptic seizure "prediction" algorithms are generally based on the knowledge of seizure occurring time and analyze the electroencephalogram (EEG) recordings retrospectively. It is then obvious that, although these analyses provide evidence of brain activity changes prior to epileptic seizures, they cannot be applied to develop implantable devices for diagnostic and therapeutic purposes. In this paper, we describe an adaptive procedure to prospectively analyze continuous, long-term EEG recordings when only the occurring time of the first seizure is known.

Measuring information flow in nonlinear systems--a modeling approach in the state space.

Directional information flow between coupled nonlinear systems is of practical interest in many areas like bioengineering, chemistry, physics and electrical engineering. Due to the high complexity and nonlinearity of the coupled chaotic systems, linear modeling approaches may fail to capture the proper dynamics and thus the proper directional information flow. This necessitates novel approaches to analyze signals derived from such systems.