Dennis Shasha

About

Dennis Shasha is a professor whose research spans a diverse array of projects primarily focused on large data puzzles, pattern matching, and machine learning. His areas of interest include computational biology, particularly plant biology and biomedicine, time series analysis with applications such as correlation and burst detection, and pattern matching in trees and labeled graphs. He has collaborated on innovative devices like SnailGate for flood control, CorrectConsumer for medication adherence, and pedestrian alarm systems. Since 2013, Shasha has also engaged in millimeter wireless research in collaboration with NYU WIRELESS. His work on meta-algorithms includes the development of SafePredict, a framework that improves machine learning accuracy by selectively refusing uncertain predictions, co-advised with Elza Erkip and involving several collaborators. In biological computing, Shasha has contributed to molecular biology projects with plant biology labs, developing software for causality analysis in RNA expression, visualization tools like Sungear for intersecting experimental data, and combinatorial design software for experimental design. He has also worked on protein docking methods termed protein speed-dating. Shasha's research in graph algorithms addresses subgraph matching and pattern detection in labeled graphs, tackling NP-complete problems with heuristic approaches. He has contributed to debugging complex workflows by identifying root causes of failures and…

Research topics

• Machine Learning
• Artificial Intelligence
• Computer Science
• Genetics
• Pathology
• Psychology
• Botany
• Neuroscience
• Biology
• Medicine

Selected publications

• Cell-by-cell dissection of phloem development links a maturation gradient to cell specialization

  Science · 2021 · 115 citations

  root. PHLOEM EARLY DNA-BINDING-WITH-ONE-FINGER (PEAR) transcription factors mediate lineage bifurcation by activating guanosine triphosphatase signaling and prime a transcriptional differentiation program. This program is initially repressed by a meristem-wide gradient of PLETHORA transcription factors. Only the dissipation of PLETHORA gradient permits activation of the differentiation program that involves mutual inhibition of early versus late meristem regulators. Thus, for phloem development,…

  DOI

• Inexpensive, non-invasive biomarkers predict Alzheimer transition using machine learning analysis of the Alzheimer’s Disease Neuroimaging (ADNI) database

  PLoS ONE · 2020 · 48 citations

  The Alzheimer's Disease Neuroimaging (ADNI) database is an expansive undertaking by government, academia, and industry to pool resources and data on subjects at various stage of symptomatic severity due to Alzheimer's disease. As expected, magnetic resonance imaging is a major component of the project. Full brain images are obtained at every 6-month visit. A range of cognitive tests studying executive function and memory are employed less frequently. Two blood draws (baseline, 6 months) provide…

  DOI

• DietNerd: A Nutrition Question-Answering System That Summarizes and Evaluates Peer-Reviewed Scientific Articles

  Applied Sciences · 2024-10-06 · 3 citations

  articleOpen accessSenior authorCorresponding

  DietNerd is a large language model-based system designed to enhance public health education in diet and nutrition. The system responds to user questions with concise, evidence-based summaries and assesses the quality and potential biases of cited research. This paper describes the system’s workflow, back-end implementation, and the prompts used. Accuracy and quality-of-response results are presented based on an automated comparison against systematic surveys and against the responses of similar…

  PublisherOA PDFDOI

• Heuristic energy-based cyclic peptide design

  PLoS Computational Biology · 2025-04-30 · 2 citations

  articleOpen accessSenior author

  Rational computational design is crucial to the pursuit of novel drugs and therapeutic agents. Meso-scale cyclic peptides, which consist of 7-40 amino acid residues, are of particular interest due to their conformational rigidity, binding specificity, degradation resistance, and potential cell permeability. Because there are few natural cyclic peptides, de novo design involving non-canonical amino acids is a potentially useful goal. Here, we develop an efficient pipeline (CyclicChamp) for cyclic…

  PublisherDOI

• Machine Learning-Enhanced Pairs Trading

  Forecasting · 2024-06-11 · 2 citations

  articleOpen accessSenior authorCorresponding

  Forecasting returns in financial markets is notoriously challenging due to the resemblance of price changes to white noise. In this paper, we propose novel methods to address this challenge. Employing high-frequency Brazilian stock market data at one-minute granularity over a full year, we apply various statistical and machine learning algorithms, including Bidirectional Long Short-Term Memory (BiLSTM) with attention, Transformers, N-BEATS, N-HiTS, Convolutional Neural Networks (CNNs), and Tempo…

  PublisherOA PDFDOI

Recent grants

• Hit-and-Run transcription: The impact of transient interactions in dynamic gene regulatory networks that mediate rapid nutrient signaling

  NIH · $430k · 2020–2024

• Primitives for Online Time Series Analysis

  NSF · $360k · 2005–2009

• Hit-and-Run transcription: The impact of transient interactions in dynamic gene regulatory networks that mediate rapid nutrient signaling

  NIH · $1.3M · 2020–2026

Frequent coauthors

• Alfredo Pulvirenti

  University of Catania

  58 shared

• Rosalba Giugno

  University of Verona

  58 shared

• Alfredo Ferro

  53 shared

• Philippe Bonnet

  46 shared

• Kaizhong Zhang

  China University of Mining and Technology

  45 shared

• Bruce A. Shapiro

  National Cancer Institute

  37 shared

• Gloria M. Coruzzi

  New York University

  37 shared

• Patrick Valduriez

  Centre National de la Recherche Scientifique

  33 shared

Labs

• Dennis Shasha LabPI

Education

• B.S., Electrical Engineering

  Yale University

  1977

• M.S.

  Syracuse University

  1980

• Ph.D., applied mathematics

  Harvard University

  1984

Awards & honors

• U.S. National Academy of Inventors (2023)
• ACM SIGMOD Contributions Award (2020)
• Julius Silver Professor of Computer Science (2018)
• INRIA International Chair (2015)
• ACM Fellow (2014)

Similar researchers at New York University

• Rob Fergush-95
• Mehryar Mohrih-77
• Nasir Memonh-70