Related papers: Long non-coding RNAs as a source of new peptides

In this work we propose a method to compute continuous embeddings for kmers from raw RNA-seq data, without the need for alignment to a reference genome. The approach uses an RNN to transform kmers of the RNA-seq reads into a 2 dimensional…

This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…

This thesis deals with the problem of communicating and storing non-sequential data. We investigate this problem through the lens of lossless source coding, also sometimes referred to as lossless compression, from both an algorithmic and…

We develop a representation suitable for the unconstrained recognition of words in natural images: the general case of no fixed lexicon and unknown length. To this end we propose a convolutional neural network (CNN) based architecture which…

3' untranslated regions (3' UTRs) contain binding sites for many regulatory elements, and in particular for microRNAs (miRNAs). The importance of miRNA-mediated post-transcriptional regulation has become increasingly clear in the last few…

Recurrent Neural Networks are powerful machine learning frameworks that allow for data to be saved and referenced in a temporal sequence. This opens many new possibilities in fields such as handwriting analysis and speech recognition. This…

RNA is a vital biomolecule with numerous roles and functions within cells, and interest in targeting it for therapeutic purposes has grown significantly in recent years. However, fully understanding and predicting RNA behavior, particularly…

The process of polymerizing a protein by a ribosome, using a messenger RNA (mRNA) as the corresponding template, is called {\it translation}. Ribosome may be regarded as a molecular motor for which the mRNA template serves also as the…

Designing a practical, low complexity, close to optimal, channel decoder for powerful algebraic codes with short to moderate block length is an open research problem. Recently it has been shown that a feed-forward neural network…

Cancer ranks as one of the deadliest diseases worldwide. The high mortality rate associated with cancer is partially due to the lack of reliable early detection methods and/or inaccurate diagnostic tools such as certain protein biomarkers.…

The DNA storage channel is considered, in which the $M$ Deoxyribonucleic acid (DNA) molecules comprising each codeword are stored without order, sampled $N$ times with replacement, and then sequenced over a discrete memoryless channel. For…

Neural networks, specifically deep convolutional neural networks, have achieved unprecedented performance in various computer vision tasks, but the rationale for the computations and structures of successful neural networks is not fully…

We consider the problem of coding for the substring channel, in which information strings are observed only through their (multisets of) substrings. Due to existing DNA sequencing techniques and applications in DNA-based storage systems,…

A major challenge in structured prediction is to represent the interdependencies within output structures. When outputs are structured as sequences, linear-chain conditional random fields (CRFs) are a widely used model class which can learn…

Proteins are complex biomolecules that play a central role in various biological processes, making them critical targets for breakthroughs in molecular biology, medical research, and drug discovery. Deciphering their intricate, hierarchical…

Random Linear Network Coding (RLNC) provides a theoretically efficient method for coding. Some of its practical drawbacks are the complexity of decoding and the overhead due to the coding vectors. For computationally weak and battery-driven…

Gene expression is a readily-observed quantification of transcriptional activity and cellular state that enables the recovery of the relationships between regulators and their target genes. Reconstructing transcriptional regulatory networks…

DNA is a leading candidate as the next archival storage media due to its density, durability and sustainability. To read (and write) data DNA storage exploits technology that has been developed over decades to sequence naturally occurring…

RNA, whose functionality is largely determined by its structure, plays an important role in many biological activities. The prediction of pairwise structural proximity between each nucleotide of an RNA sequence can characterize the…

Transcription regulation is largely governed by the profile and the dynamics of transcription factors' binding to DNA. Stochastic effects are intrinsic to this dynamics and the binding to functional sites must be controled with a certain…