Resolving the structure of phage–bacteria interactions in the context of natural diversity

KM Kauffman, WK Chang, JM Brown… - Nature …, 2022 - nature.com
Microbial communities are shaped by viral predators. Yet, resolving which viruses (phages)
and bacteria are interacting is a major challenge in the context of natural levels of microbial …

The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera

V Ahola, R Lehtonen, P Somervuo, L Salmela… - Nature …, 2014 - nature.com
Previous studies have reported that chromosome synteny in Lepidoptera has been well
conserved, yet the number of haploid chromosomes varies widely from 5 to 223. Here we …

[PDF][PDF] Software reflexion models: Bridging the gap between source and high-level models

GC Murphy, D Notkin, K Sullivan - Proceedings of the 3rd ACM SIGSOFT …, 1995 - dl.acm.org
Software engineers often use high-level models(for instance, box and arrow sketches) to
reason and communicate about an existing software system. One problem with high-level …

Software reflexion models: Bridging the gap between design and implementation

GC Murphy, D Notkin, KJ Sullivan - IEEE Transactions on …, 2001 - ieeexplore.ieee.org
The artifacts constituting a software system often drift apart over time. We have developed
the software reflexion model technique to help engineers perform various software …

Notable design patterns for domain-specific languages

D Spinellis - Journal of systems and software, 2001 - Elsevier
The realisation of domain-specific languages (dsls) differs in fundamental ways from that of
traditional programming languages. We describe eight recurring patterns that we have …

An empirical study of static call graph extractors

GC Murphy, D Notkin, WG Griswold… - ACM Transactions on …, 1998 - dl.acm.org
Informally, a call graph represents calls between entities in a given program. The call graphs
that compilers compute to determine the applicability of an optimization must typically be …

DDM1-mediated gene body DNA methylation is associated with inducible activation of defense-related genes in Arabidopsis

S Lee, J Choi, J Park, CP Hong, D Choi, S Han, K Choi… - Genome Biology, 2023 - Springer
Background Plants memorize previous pathogen attacks and are “primed” to produce a
faster and stronger defense response, which is critical for defense against pathogens. In …

The chromatin landscape of pathogenic transcriptional cell states in rheumatoid arthritis

K Weinand, S Sakaue, A Nathan, AH Jonsson… - Nature …, 2024 - nature.com
Synovial tissue inflammation is a hallmark of rheumatoid arthritis (RA). Recent work has
identified prominent pathogenic cell states in inflamed RA synovial tissue, such as T …

Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family

PJG Malé, L Bardon, G Besnard… - Molecular ecology …, 2014 - Wiley Online Library
Whole genome sequencing is helping generate robust phylogenetic hypotheses for a range
of taxonomic groups that were previously recalcitrant to classical molecular phylogenetic …

AWK and GNU octave programming languages integrated with generic mapping tools for geomorphological analysis

P Lemenkova - GeoScience Engineering, 2019 - papers.ssrn.com
The paper presents a sequential use of the AWK and GNU Octave programming languages
integrated with Generic Mapping Tools (GMT) for geospatial data analysis. The geographic …