Alan M. Moses

32 papers A* 1B 1Misc 1Journal 28Unranked 1
YearRankTypeTitle / Venue / Authors
2025 — conf
Representation Learning Methods for Single-Cell Microscopy are Confounded by Background Cells.
MLCB
Arushi Gupta, Alan M. Moses, Alex Lu
2025 J jnl
Transformers and genome language models.
Nat. Mac. Intell.
Micaela E. Consens, Cameron Dufault, Michael Wainberg, Duncan Forster, Mehran Karimzadeh, Hani Goodarzi, Fabian J. Theis, Alan M. Moses, Bo Wang
2025 J jnl
Zero-shot segmentation using embeddings from a protein language model identifies functional regions in the human proteome.
PLoS Comput. Biol.
Ami G. Sangster, Cameron Dufault, Haoning Qu, Denise Le, Julie D. Forman-Kay, Alan M. Moses
2024 J jnl
Improving the performance of supervised deep learning for regulatory genomics using phylogenetic augmentation.
Bioinform.
Andrew G. Duncan, Jennifer A. Mitchell, Alan M. Moses
2023 J jnl
To Transformers and Beyond: Large Language Models for the Genome.
CoRR
Micaela E. Consens, Cameron Dufault, Michael Wainberg, Duncan Forster, Mehran Karimzadeh, Hani Goodarzi, Fabian J. Theis, Alan M. Moses, Bo Wang
2022 J jnl
Architect: A tool for aiding the reconstruction of high-quality metabolic models through improved enzyme annotation.
PLoS Comput. Biol.
Nirvana Nursimulu, Alan M. Moses, John Parkinson
2022 J jnl
Discovering molecular features of intrinsically disordered regions by using evolution for contrastive learning.
PLoS Comput. Biol.
Alex X. Lu, Amy X. Lu, Iva Pritisanac, Taraneh Zarin, Julie D. Forman-Kay, Alan M. Moses
2021 J jnl
CytoImageNet: A large-scale pretraining dataset for bioimage transfer learning.
CoRR
Stanley Bryan Z. Hua, Alex X. Lu, Alan M. Moses
2021 J jnl
Random Embeddings and Linear Regression can Predict Protein Function.
CoRR
Tianyu Lu, Alex X. Lu, Alan M. Moses
2020 J jnl
Evolution Is All You Need: Phylogenetic Augmentation for Contrastive Learning.
CoRR
Amy X. Lu, Alex X. Lu, Alan M. Moses
2020 J jnl
W-Cell-Net: Multi-frame Interpolation of Cellular Microscopy Videos.
CoRR
Rohit Saha, Abenezer Teklemariam, Ian Shenyen Hsu, Alan M. Moses
2019 J jnl
Entropy and Information within Intrinsically Disordered Protein Regions.
Entropy
Iva Pritisanac, Robert M. Vernon, Alan M. Moses, Julie D. Forman-Kay
2019 J jnl
Learning unsupervised feature representations for single cell microscopy images with paired cell inpainting.
PLoS Comput. Biol.
Alex X. Lu, Oren Z. Kraus, Sam Cooper, Alan M. Moses
2019 A* conf
The Cells Out of Sample (COOS) dataset and benchmarks for measuring out-of-sample generalization of image classifiers.
NeurIPS
Alex X. Lu, Amy X. Lu, Wiebke Schormann, Marzyeh Ghassemi, David W. Andrews, Alan M. Moses
2019 J jnl
The Cells Out of Sample (COOS) dataset and benchmarks for measuring out-of-sample generalization of image classifiers.
CoRR
Alex X. Lu, Amy X. Lu, Wiebke Schormann, David W. Andrews, Alan M. Moses
2019 J jnl
Variational infinite heterogeneous mixture model for semi-supervised clustering of heart enhancers.
Bioinform.
Tahmid F. Mehdi, Gurdeep Singh, Jennifer A. Mitchell, Alan M. Moses
2019 J jnl
YeastSpotter: accurate and parameter-free web segmentation for microscopy images of yeast cells.
Bioinform.
Alex X. Lu, Taraneh Zarin, Ian Shenyen Hsu, Alan M. Moses
2018 J jnl
NoLogo: a new statistical model highlights the diversity and suggests new classes of Crm1-dependent nuclear export signals.
BMC Bioinform.
Muluye E. Liku, Elizabeth-Ann Legere, Alan M. Moses
2018 J jnl
Short linear motifs in intrinsically disordered regions modulate HOG signaling capacity.
BMC Syst. Biol.
Bob Strome, Ian Shenyen Hsu, Mitchell Li Cheong Man, Taraneh Zarin, Alex N. Nguyen Ba, Alan M. Moses
2015 J jnl
Local statistics allow quantification of cell-to-cell variability from high-throughput microscope images.
Bioinform.
Louis-François Handfield, Bob Strome, Yolanda T. Chong, Alan M. Moses
2014 J jnl
Detecting Functional Divergence after Gene Duplication through Evolutionary Changes in Posttranslational Regulatory Sequences.
PLoS Comput. Biol.
Alex N. Nguyen Ba, Bob Strome, Jun Jie Hua, Jonathan Desmond, Isabelle Gagnon-Arsenault, Eric L. Weiss, Christian R. Landry, Alan M. Moses
2013 J jnl
Unsupervised Clustering of Subcellular Protein Expression Patterns in High-Throughput Microscopy Images Reveals Protein Complexes and Functional Relationships between Proteins.
PLoS Comput. Biol.
Louis-François Handfield, Yolanda T. Chong, Jibril Simmons, Brenda J. Andrews, Alan M. Moses
2012 J jnl
Predicting kinase substrates using conservation of local motif density.
Bioinform.
Andy C. W. Lai, Alex N. Nguyen Ba, Alan M. Moses
2012 J jnl
Towards a theoretical understanding of false positives in DNA motif finding.
BMC Bioinform.
Amin Zia, Alan M. Moses
2011 J jnl
Modeling the evolution of a classic genetic switch.
BMC Syst. Biol.
Christos Josephides, Alan M. Moses
2011 J jnl
Ranking insertion, deletion and nonsense mutations based on their effect on genetic information.
BMC Bioinform.
Amin Zia, Alan M. Moses
2009 J jnl
NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction.
BMC Bioinform.
Alex N. Nguyen Ba, Anastassia Pogoutse, Nicholas Provart, Alan M. Moses
2008 J jnl
TreeFam: 2008 Update.
Nucleic Acids Res.
Jue Ruan, Heng Li, Zhongzhong Chen, Avril Coghlan, Lachlan James M. Coin, Yiran Guo, Jean-Karim Hériché, Yafeng Hu, Karsten Kristiansen, Ruiqiang Li, Tao Liu, Alan M. Moses, Junjie Qin, Søren Vang, Albert J. Vilella, Abel Ureta-Vidal, Lars Bolund, Jun Wang, Richard Durbin
2006 J jnl
Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments.
BMC Bioinform.
Daniel A. Pollard, Alan M. Moses, Venky N. Iyer, Michael B. Eisen
2006 J jnl
Large-Scale Turnover of Functional Transcription Factor Binding Sites in
PLoS Comput. Biol.
Alan M. Moses, Daniel A. Pollard, David A. Nix, Venky N. Iyer, Xiaoyong Li, Mark D. Biggin, Michael B. Eisen
2004 Misc conf
Phylogenetic Motif Detection by Expectation-Maximization on Evolutionary Mixtures.
Pacific Symposium on Biocomputing
Alan M. Moses, Derek Y. Chiang, Michael B. Eisen
2003 B conf
Phylogenetically and spatially conserved word pairs associated with gene expression changes in yeasts.
RECOMB
Derek Y. Chiang, Alan M. Moses, Manolis Kamvysselis, Eric S. Lander, Michael B. Eisen