Phylogenetically and spatially conserved word pairs associated with gene expression changes in yeasts. - Derek Y. Chiang; Alan M. Moses; Manolis Kamvysselis; Eric S. Lander; Michael B. Eisen (RECOMB, 2003)

Phylogenetic Motif Detection by Expectation-Maximization on Evolutionary Mixtures. - Alan M. Moses; Derek Y. Chiang; Michael B. Eisen (Pacific Symposium on Biocomputing, 2004)

Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments. - Daniel A. Pollard; Alan M. Moses; Venky N. Iyer; Michael B. Eisen (BMC Bioinform., 2006)

Large-Scale Turnover of Functional Transcription Factor Binding Sites in Drosophila. - Alan M. Moses; Daniel A. Pollard; David A. Nix; Venky N. Iyer; Xiaoyong Li; Mark D. Biggin; Michael B. Eisen (PLoS Comput. Biol., 2006)

NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction. - Alex N. Nguyen Ba; Anastassia Pogoutse; Nicholas Provart; Alan M. Moses (BMC Bioinform., 2009)

Ranking insertion, deletion and nonsense mutations based on their effect on genetic information. - Amin Zia; Alan M. Moses (BMC Bioinform., 2011)

Modeling the evolution of a classic genetic switch. - Christos Josephides; Alan M. Moses (BMC Syst. Biol., 2011)

Predicting kinase substrates using conservation of local motif density. - Andy C. W. Lai; Alex N. Nguyen Ba; Alan M. Moses (Bioinform., 2012)

Towards a theoretical understanding of false positives in DNA motif finding. - Amin Zia; Alan M. Moses (BMC Bioinform., 2012)

Unsupervised Clustering of Subcellular Protein Expression Patterns in High-Throughput Microscopy Images Reveals Protein Complexes and Functional Relationships between Proteins. - Louis-François Handfield; Yolanda T. Chong; Jibril Simmons; Brenda J. Andrews; Alan M. Moses (PLoS Comput. Biol., 2013)

Detecting Functional Divergence after Gene Duplication through Evolutionary Changes in Posttranslational Regulatory Sequences. - Alex N. Nguyen Ba; Bob Strome; Jun Jie Hua; Jonathan Desmond; Isabelle Gagnon-Arsenault; Eric L. Weiss; Christian R. Landry; Alan M. Moses (PLoS Comput. Biol., 2014)

Local statistics allow quantification of cell-to-cell variability from high-throughput microscope images. - Louis-François Handfield; Bob Strome; Yolanda T. Chong; Alan M. Moses (Bioinform., 2015)

NoLogo: a new statistical model highlights the diversity and suggests new classes of Crm1-dependent nuclear export signals. - Muluye E. Liku; Elizabeth-Ann Legere; Alan M. Moses (BMC Bioinform., 2018)

Short linear motifs in intrinsically disordered regions modulate HOG signaling capacity. - Bob Strome; Ian Shenyen Hsu; Mitchell Li Cheong Man; Taraneh Zarin; Alex N. Nguyen Ba; Alan M. Moses (BMC Syst. Biol., 2018)

The Cells Out of Sample (COOS) dataset and benchmarks for measuring out-of-sample generalization of image classifiers. - Alex X. Lu; Amy X. Lu; Wiebke Schormann; Marzyeh Ghassemi; David W. Andrews; Alan M. Moses (NeurIPS, 2019)

YeastSpotter: accurate and parameter-free web segmentation for microscopy images of yeast cells. - Alex X. Lu; Taraneh Zarin; Ian Shenyen Hsu; Alan M. Moses (Bioinform., 2019)

Variational infinite heterogeneous mixture model for semi-supervised clustering of heart enhancers. - Tahmid F. Mehdi; Gurdeep Singh; Jennifer A Mitchell; Alan M. Moses (Bioinform., 2019)

The Cells Out of Sample (COOS) dataset and benchmarks for measuring out-of-sample generalization of image classifiers. - Alex X. Lu; Amy X. Lu; Wiebke Schormann; David W. Andrews; Alan M. Moses (CoRR, 2019)

Entropy and Information within Intrinsically Disordered Protein Regions. - Iva Pritisanac; Robert M. Vernon; Alan M. Moses; Julie D. Forman-Kay (Entropy, 2019)

Learning unsupervised feature representations for single cell microscopy images with paired cell inpainting. - Alex X. Lu; Oren Z. Kraus; Sam Cooper; Alan M. Moses (PLoS Comput. Biol., 2019)

W-Cell-Net: Multi-frame Interpolation of Cellular Microscopy Videos. - Rohit Saha; Abenezer Teklemariam; Ian Shenyen Hsu; Alan M. Moses (CoRR, 2020)

Evolution Is All You Need: Phylogenetic Augmentation for Contrastive Learning. - Amy X. Lu; Alex X. Lu; Alan M. Moses (CoRR, 2020)

Random Embeddings and Linear Regression can Predict Protein Function. - Tianyu Lu; Alex X. Lu; Alan M. Moses (CoRR, 2021)

CytoImageNet: A large-scale pretraining dataset for bioimage transfer learning. - Stanley Bryan Z. Hua; Alex X. Lu; Alan M. Moses (CoRR, 2021)

Discovering molecular features of intrinsically disordered regions by using evolution for contrastive learning. - Alex X. Lu; Amy X. Lu; Iva Pritisanac; Taraneh Zarin; Julie D. Forman-Kay; Alan M. Moses (PLoS Comput. Biol., 2022)

Architect: A tool for aiding the reconstruction of high-quality metabolic models through improved enzyme annotation. - Nirvana Nursimulu; Alan M. Moses; John Parkinson (PLoS Comput. Biol., 2022)