One of the greatest challenges that modern molecular biology is facing is the understanding of the complex mechanisms regulating gene expression. A fundamental step in this process requires the characterization of regulatory motifs playing key roles in the regulation of gene expression at transcriptional and post-transcriptional levels. In particular, transcription is modulated by the interaction of transcription factors with their corresponding binding sites. Weeder Web is a web interface to Weeder, an algorithm for the automatic discovery of conserved motifs in a set of related regulatory DNA sequences. The motifs found are in turn likely to be instances of binding sites for some transcription factor. Other than providing access to the program, the interface has been designed so to make usage of the program itself as simple as possible, and to require very little prior knowledge about the length and the conservation of the motifs to be found. In fact, the interface automatically starts different runs of the program, each one with different parameters, and provides the user with an overall summary of the results as well as some 'advice' on which motifs look more interesting according to their statistical significance and some simple considerations. The web interface is available at the address www.pesolelab.it by following the 'Tools' link.

In medical imaging, it remains a challenging and valuable goal how to generate realistic medical images completely different from the original ones; the obtained synthetic images would improve diagnostic reliability, allowing for data augmentation in computer-assisted diagnosis as well as physician training. In this paper, we focus on generating synthetic multi-sequence brain Magnetic Resonance (MR) images using Generative Adversarial Networks (GANs). This involves difficulties mainly due to low contrast MR images, strong consistency in brain anatomy, and intra-sequence variability. Our novel realistic medical image generation approach shows that GANs can generate 128 χ 128 brain MR images avoiding artifacts. In our preliminary validation, even an expert physician was unable to accurately distinguish the synthetic images from the real samples in the Visual Turing Test.

Pattern discovery in unaligned DNA sequences is a challenging problem in both computer science and molecular biology. Several different methods and techniques have been proposed so far, but in most of the cases signals in DNA sequences are very complicated and avoid detection. Exact exhaustive methods can solve the problem only for short signals with a limited number of mutations. In this work, we extend exhaustive enumeration also to longer patterns. More in detail, the basic version of algorithm presented in this paper, given as input a set of sequences and an error ratio ε < 1, finds all patterns that occur in at least q sequences of the set with at most εm mutations, where m is the length of the pattern. The only restriction is imposed on the location of mutations along the signal. That is, a valid occurrence of a pattern can present at most ⌈εi⌉ mismatches in the first i nucleotides, and so on. However, we show how the algorithm can be used also when no assumption can be made on the position of mutations. In this case, it is also possible to have an estimate of the probability of finding a signal according to the signal length, the error ratio, and the input parameters. Finally, we discuss some significance measures that can be used to sort the patterns output by the algorithm. Contact: pavesi@disco.unimib.it