Cancer-associated mutations of the core splicing factor 3 B1 (SF3B1) result in selection of novel 3’ splice sites (3’SS), but precise molecular mechanisms of oncogenesis remain unclear. SF3B1 stabilizes the interaction between U2 snRNP and branch point (BP) on the pre-mRNA. It has hence been s... Read more
Strand displacement reactions are widely used in DNA nanotechnology as a building block for engineering molecular computers and machines. Here, we demonstrate that strand displacement-based probes can be triggered by RNA expressed in mammalian cells, thus taking a step toward adapting the DNA ... Read more
Life operates at the intersection of chemistry and mechanics. Over the years, we have made remarkable progress in understanding life from a biochemical perspective and the mechanics of life at the single-molecule scale. Yet the full integration of physical and mechanical models into mainstream... Read more
We present strand and codeword design schemes for a DNA database capable of approximate similarity search over a multidimensional dataset of content-rich media. Our strand designs address cross-talk in associative DNA databases, and we demonstrate a novel method for learning DNA sequence encod... Read more
We show that discrete distributions on the $d$-dimensional non-negative integer lattice can be approximated arbitrarily well via the marginals of stationary distributions for various classes of stochastic chemical reaction networks. We begin by providing a class of detailed balanced networks a... Read more
MicroRNA mediated incoherent feed forward loops (IFFLs) are recurrent network motifs in mammalian cells and have been a topic of study for their noise rejection and buffering properties. Previous work showed that IFFLs can adapt to varying promoter activity and are less prone to noise than sim... Read more
Specifications for complex engineering systems are typically decomposed into specifications for individual subsystems in a manner that ensures they are implementable and simpler to develop further. We describe a method to algorithmically construct component specifications that implement a give... Read more
Algorithmic DNA tile systems have the potential to allow the construction by self-assembly of large structures with complex nanometer-scale details out of relatively few monomer types, but are constrained by errors in growth and the limited sequence space of orthogonal DNA sticky ends that pro... Read more
The interest in channel models in which the data is sent as an unordered set of binary strings has increased lately, due to emerging applications in DNA storage, among others. In this paper we analyze the minimal redundancy of binary codes for this channel under substitution errors, and provid... Read more
Simulation and bisimulation relations define pre-orders on processes which serve as the basis for approximation based verification techniques, and have been extended towards the design of continuous and hybrid systems with complex logic specifications. We study pre-orders between hybrid system... Read more
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URL: http://dx.doi.org/10.1109/MCS.2018.2830084
Read moreDynamic DNA nanotechnology has yielded nontrivial autonomous behaviours such as stimulus-guided locomotion, computation and programmable molecular assembly. Despite these successes, DNA-based nanomachines suffer from slow kinetics, requiring several minutes or longer to carry out a handful of ... Read more
We (people) are memory machines. Our decision processes, emotions, and interactions with the world around us are based on and driven by associations to our memories. This natural association paradigm will become critical in future memory systems, namely, the key question will not be “How do I ... Read more
In the version of this article initially published, the references in the reference list were in the wrong order; the references have been renumbered as follows: 3 as 2; 5 as 3; 6 as 8; 7 as 9; 8 as 11; 9 as 6; 10 as 12; 11 as 5; 12 as 13; 13 as 7; 16 as 10; and no. 2, “Hoch, J.A. & Losick... Read more
Identifying the gene regulatory networks that control development or disease is one of the most important problems in biology. Here, we introduce a computational approach, called PIPER (ProgressIve network PERturbation), to identify the perturbed genes that drive differences in the gene regula... Read more
Despite its early promise as a diagnostic and prognostic tool, gene expression profiling remains cost-prohibitive and challenging to implement in a clinical setting. Here, we introduce a molecular computation strategy for analysing the information contained in complex gene expression signature... Read more
From bacteria following simple chemical gradients to the brain distinguishing complex odour information, the ability to recognize molecular patterns is essential for biological organisms. This type of information-processing function has been implemented using DNA-based neural networks, but has... Read more
In situ hybridization based on the mechanism of the hybridization chain reaction (HCR) has addressed multi-decade challenges that impeded imaging of mRNA expression in diverse organisms, offering a unique combination of multiplexing, quantitation, sensitivity, resolution and versatility. Here,... Read more
When sensitive data is stored in the cloud, the only way to ensure its secrecy is by encrypting it before it is uploaded. The emerging multi-cloud model, in which data is stored redundantly in two or more independent clouds, provides an opportunity to protect sensitive data with secret-sharing... Read more
Construction of capacity achieving deletion correcting codes has been a baffling challenge for decades. A recent breakthrough by Brakensiek et al., alongside novel applications in DNA storage, have reignited the interest in this longstanding open problem. In spite of recent advances, the amoun... Read more
Proving properties of a minimal covering algorithm … Control & Dynamical Systems California Institute of Technology … Filippidis and Murray ( Caltech ) Proving properties of a minimal covering algorithm July 18, 2018 1 / 27 … Motivation: Converting binary decision diagrams to minimal …
... Read moreDevelopmental programs sculpt plant morphology to meet environmental challenges, and these same programs have been manipulated to increase agricultural productivity (Doebley et al., 1997; Khush, 2001). Hormones coordinate these programs, creating chemical circuitry (Vanstraelen and Benková, 20... Read more
To facilitate scalable profiling of single cells, we developed split-pool ligation-based transcriptome sequencing (SPLiT-seq), a single-cell RNA-seq (scRNA-seq) method that labels the cellular origin of RNA through combinatorial barcoding. SPLiT-seq is compatible with fixed cells or nuclei, al... Read more
Alternative polyadenylation (APA) is a major driver of transcriptome diversity in human cells. Here, we use deep learning to predict APA from DNA sequence alone. We trained our model (APARENT, APA REgression NeT) on isoform expression data from over three million …
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Deep neural networks are vulnerable to adversarial examples, which dramatically alter model output using small input changes. We propose Neural Fingerprinting, a simple, yet effective method to detect adversarial examples by verifying whether model behavior is consistent with a set of secret f... Read more
