Understanding the relationship between amino acid sequence and protein function is a long-
standing challenge with far-reaching scientific and translational implications. State-of-the-art …

Sequence alignment is a long standing problem in bioinformatics. The Basic Local
Alignment Search Tool (BLAST) is one of the most popular and fundamental alignment tools …

Computational biology in the 21st century: scaling with compressive algorithms Page 1 72
COMMUNICATIONS OF THE ACM | AUGUST 2016 | VOL. 59 | NO. 8 review articles DOI:10.1145/2957324 …

Large-scale genomics demands computational methods that scale sublinearly with the
growth of data. We review several data structures and sketching techniques that have been …

Levenshtein edit distance has played a central role-both past and present-in sequence
alignment in particular and biological database similarity search in general. We start our …

The amount of sequence information in public repositories is growing at a rapid rate.
Although these data are likely to contain clinically important information that has not yet …

Sequence-level searches on large collections of RNA sequencing experiments, such as the
NCBI Sequence Read Archive (SRA), would enable one to ask many questions about the …

The ever increasing growth of the production of high-throughput sequencing data poses a
serious challenge to the storage, processing and transmission of these data. As frequently …

The predominant model of the role of viruses in the marine trophic web is that of the “viral
shunt,” where viral infection funnels a substantial fraction of the microbial primary and …

Enormous databases of short-read RNA-seq experiments such as the NIH Sequencing
Read Archive are now available. These databases could answer many questions about …