### Recent Submissions

• #### Robonaut 2 and you: Specifying and executing complex operations ﻿

(2017)
Crew time is a precious resource due to the expense of trained human operators in space. Efficient caretaker robots could lessen the manual labor load required by frequent vehicular and life support maintenance tasks, ...
• #### Interpreting T-Cell Cross-reactivity through Structure: Implications for TCR-Based Cancer Immunotherapy ﻿

(2017)
Immunotherapy has become one of the most promising avenues for cancer treatment, making use of the patient’s own immune system to eliminate cancer cells. Clinical trials with T-cell-based immunotherapies have shown dramatic ...
• #### SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models ﻿

(2017-09-19)
Abstract Single-cell sequencing enables the inference of tumor phylogenies that provide insights on intra-tumor heterogeneity and evolutionary trajectories. Recently introduced methods perform this task under ...
• #### Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis ﻿

(2016)
The role of hybridization and subsequent introgression has been demonstrated in an increasing number of species. Recently, Fontaine et al. (Science, 347, 2015, 1258524) conducted a phylogenomic analysis of six members of ...
• #### A review of parameters and heuristics for guiding metabolic pathfinding ﻿

(2017-09-15)
Abstract Recent developments in metabolic engineering have led to the successful biosynthesis of valuable products, such as the precursor of the antimalarial compound, artemisinin, and opioid precursor, ...
• #### Strong $\mu$-Bases for Rational Tensor Product Surfaces and Extraneous Factors Associated to Bad Base Points and Anomalies at Infinity ﻿

(2017)
We investigate conditions under which the resultant of a $\mu$-basis for a rational tensor product surface is the implicit equation of the surface without any extraneous factors. In this case, we also derive a formula for ...
• #### Continuous checkpointing of HTM transactions in NVM ﻿

(2017)
This paper addresses the challenges of coupling byte addressable non-volatile memory (NVM) and hardware transaction memory (HTM) in high-performance transaction processing. We first show that HTM transactions can be ordered ...
• #### Reconstructing rooms using photon echoes: A plane based model and reconstruction algorithm for looking around the corner ﻿

(2017)
Can we reconstruct the entire internal shape of a room if all we can directly observe is a small portion of one internal wall, presumably through a window in the room? While conventional wisdom may indicate that this is ...
• #### Persisting in-memory databases using SCM ﻿

(2016)
Big Data applications need to be able to access large amounts of variable data as fast as possible. Emerging Storage Class Memory (SCM) fit this need by making memory available in large capacity while making changes endure ...
• #### An Automated System for Interactively Learning Software Testing ﻿

(2017)
Testing is an important, time-consuming, and often difficult part of the software development process. It is therefore critical to introduce testing early in the computer science curriculum, and to provide students with ...
• #### Unifying Büchi Complementation Constructions ﻿

(2013)
Complementation of B\"uchi automata, required for checking automata containment, is of major theoretical and practical interest in formal verification. We consider two recent approaches to complementation. The first is the ...
• #### Targeting the Src Homology 2 (SH2) Domain of Signal Transducer and Activator of Transcription 6 (STAT6) with Cell-Permeable, Phosphatase-Stable Phosphopeptide Mimics Potently Inhibits Tyr641 Phosphorylation and Transcriptional Activity ﻿

(2015)
Signal transducer and activator of transcription 6 (STAT6) transmits signals from cytokines IL-4 and IL-13 and is activated in allergic airway disease. We are developing phosphopeptide mimetics targeting the SH2 domain of ...
• #### Coarse-Grained Conformational Sampling of Protein Structure Improves the Fit to Experimental Hydrogen-Exchange Data ﻿

(2017)
Monitoring hydrogen/deuterium exchange (HDX) undergone by a protein in solution produces experimental data that translates into valuable information about the protein's structure. Data produced by HDX experiments is often ...
• #### Reasoning about Strategies: on the Satisfiability Problem ﻿

(2017)
Strategy Logic (SL, for short) has been introduced by Mogavero, Murano, and Vardi as a useful formalism for reasoning explicitly about strategies, as first-order objects, in multi-agent concurrent games. This logic turns ...
• #### Present but Unreachable: Reducing Persistentlatent Secrets in HotSpot JVM ﻿

(2017)
Applications that manage sensitive secrets, including cryptographic keys, are typically engineered to overwrite the secrets in memory once they’re no longer necessary, offering an important defense against forensic attacks ...
• #### Deep imaging in scattering media with selective plane illumination microscopy ﻿

(2016)
In most biological tissues, light scattering due to small differences in refractive index limits the depth of optical imaging systems. Two-photon microscopy (2PM), which significantly reduces the scattering of the excitation ...
• #### Inferring Atmospheric Particulate Matter Concentrations from Chinese Social Media Data ﻿

(2016)
Although studies have increasingly linked air pollution to specific health outcomes, less well understood is how public perceptions of air quality respond to changing pollutant levels. The growing availability of air ...
• #### Monovar: single-nucleotide variant detection in single cells ﻿

(2016)
Current variant callers are not suitable for single-cell DNA sequencing, as they do not account for allelic dropout, false-positive errors and coverage nonuniformity. We developed Monovar (https://bitbucket.org/hamimzafa ...
• #### Structure-guided selection of specificity determining positions in the human Kinome ﻿

(2016)
Abstract Background The human kinome contains many important drug targets. It is well-known that inhibitors of protein kinases bind with very different selectivity profiles. ...
• #### A maximum pseudo-likelihood approach for phylogenetic networks ﻿

(2015)
Abstract Background Several phylogenomic analyses have recently demonstrated the need to account simultaneously for incomplete lineage sorting (ILS) and hybridization when ...