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Lawrence Shapiro

dblp:63/2884 · DBLP profile ↗
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2ranked-venue papers
0as first author
0since 2021 · last 2018
—ORCID · unresolved

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 2

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%
Artificial intelligence
1 paper
Image recognition and object detection · 100%

Topics — the 3 heaviest of 4, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › structural biology
cryo-electron microscopy
0.312018
Positive-Unlabeled Convolutional Neural Networks for Particle Picking in Cryo-electron Micrographs · RECOMB 2018
Bioinformatics and computational biology › bioimage informatics › single-particle analysis
particle picking
0.312018
Positive-Unlabeled Convolutional Neural Networks for Particle Picking in Cryo-electron Micrographs · RECOMB 2018
Bioinformatics and computational biology
structural biology
0.312018
Positive-Unlabeled Convolutional Neural Networks for Particle Picking in Cryo-electron Micrographs · RECOMB 2018

Methods — techniques the papers use, named apart from their topics

positive-unlabeled learning · 0.7convolutional neural network · 0.7
YearPublicationVenuePosition
2018 Positive-Unlabeled Convolutional Neural Networks for Particle Picking in Cryo-electron Micrographs
Tristan Bepler, Andrew Morin, Alex J. Noble, Julia Brasch, Lawrence Shapiro, Bonnie Berger
RECOMB5
2016 Effects of Darwinian Selection and Mutability on Rate of Broadly Neutralizing Antibody Evolution during HIV-1 Infection
abstract
Accumulation of somatic mutations in antibody variable regions is critical for antibody affinity maturation, with HIV-1 broadly neutralizing antibodies (bnAbs) generally requiring years to develop. We recently found that the rate at which mutations accumulate decreases over time, but the mechanism governing this slowing is unclear. In this study, we investigated whether natural selection and/or mutability of the antibody variable region contributed significantly to observed decrease in rate. We used longitudinally sampled sequences of immunoglobulin transcripts of single lineages from each of 3 donors, as determined by next generation sequencing. We estimated the evolutionary rates of the complementarity determining regions (CDRs), which are most significant for functional selection, and found they evolved about 1.5- to 2- fold faster than the framework regions. We also analyzed the presence of AID hotspots and coldspots at different points in lineage development and observed an average decrease in mutability of less than 10 percent over time. Altogether, the correlation between Darwinian selection strength and evolutionary rate trended toward significance, especially for CDRs, but cannot fully explain the observed changes in evolutionary rate. The mutability modulated by AID hotspots and coldspots changes correlated only weakly with evolutionary rates. The combined effects of Darwinian selection and mutability contribute substantially to, but do not fully explain, evolutionary rate change for HIV-1-targeting bnAb lineages.
Zizhang Sheng, Chaim A. Schramm, Mark Connors, Lynn Morris, John R. Mascola, Peter D. Kwong, Lawrence Shapiro
PLoS Comput. Biol.7