CS
Claudia Solis-Lemus
Phylogenystat.APevolutionary biologyq-bio.PEhybridizationEvolution, Moleculargene flowstat.MEBiological Evolutioncs.LG
On Valency
published · living versionsW_kykeu3pp·v1 · currentpublished
Preprints & journals
58 papers in the corpus · 2015–2026Evolving View on Phylogenetic Networks.42424608 · Solís-Lemus, Claudia2026 · 0 citationsSystematic biology. 2026;75(6):1033-1048
Ancestral Sequences Cannot be Accurately Reconstructed via Interpolation in a Variational Autoencoder's Latent Space.42762397 · Gorstein, Evan, Tang, Mengze, Bruzzone, Hailey et al.2026 · 1 citationBulletin of mathematical biology. 2026;88(10)
MAST: Label-Efficient, Robust, and Generalizable Sound Detection for Biodiversity Monitoring via Masked Audio Pretraining and Self-Training2609.15221v1 · Tianyi Xu, Daniel Pimentel-Alarc'on, Zuzana Burivalov'a et al.2026 · 0 citationsarXiv
Generating the Unheard: Phylogeny-Guided Latent Generation for Ancestral Sound Reconstruction2609.15240v1 · Tianyi Xu, Shrinaath Narasimhan, Evan Gorstein et al.2026 · 0 citationsarXiv
Matrix representations and distance metrics for unlabeled ranked phylogenetic networks2606.08409v1 · Jiayang Wang, Julia A. Palacios, Claudia Sol'is-Lemus2026 · 0 citationsarXiv
SNaQ.jl: Improved scalability for level-1 phylogenetic network inference.42114082 · Kolbow, Nathan, Kong, Sungsik, Chafin, Tyler et al.2026 · 1 citationBioinformatics (Oxford, England). 2026;42(6)
tanggle: An R package for the visualization of phylogenetic networks.42343929 · Schliep, Klaus, Vidal-García, Marta, Biancani, Leann et al.2026 · 3 citationsApplications in plant sciences. 2026;14(3):e70060
Activity-Informed Network Analysis Reveals Keystone Microbes Shaping Freshwater Ecosystem Function.41853994 · Yang, Qiyao, Aghdam, Rosa, Tran, Patricia Q et al.2026 · 0 citationsEnvironmental microbiology reports. 2026;18(2):e70245
Bayesian chain graph models to characterize microbe-environment dynamics.41611306 · Shen, Yunyi, Solís-Lemus, Claudia2026 · 0 citationsMathematical biosciences and engineering : MBE. 2026;23(2):499-546
A hybrid framework for disease biomarker discovery in microbiome research combining Bayesian networks, machine learning, and network-based methods.41532068 · Aghdam, Rosa, Shan, Shan, Lankau, Richard et al.2026 · 5 citationsBiology methods & protocols. 2026;11(1):bpaf089
SNaQ.jl: Improved Scalability for Phylogenetic Network Inference10.1101/2025.11.17.688917v2 · Kolbow, N., Kong, S., Chafin, T. et al.2025 · 2 citationsbioRxiv
Sparse learning for scalable phylogenetic network inference10.1101/2025.11.16.688704v1 · Rosas-Puchuri, U., Kolbow, N., Solis-Lemus, C. et al.2025 · 0 citationsbioRxiv
Digging into the evolutionary history of the fungus-growing-ant symbiont, Escovopsis (Hypocreaceae).40931017 · Montoya, Quimi Vidaurre, Gerardo, Nicole Marie, Martiarena, Maria Jesus Sutta et al.2025 · 4 citationsCommunications biology. 2025;8(1):1340
Phylogenetic networks empower biodiversity research.40720655 · Kong, Sungsik, Solís-Lemus, Claudia, Tiley, George P2025 · 19 citationsProceedings of the National Academy of Sciences of the United States of America. 2025;122(31):e2410934122
Ancient reticulation, incomplete lineage sorting and the evolution of the pyrenoid at the dawn of hornwort diversification.39821234 · Peñaloza-Bojacá, Gabriel, Burleigh, J Gordon, Maciel-Silva, Adaíses et al.2025 · 14 citationsAnnals of botany. 2025;135(6):1199-1214
MiNAA-WebApp: A Web-Based Tool for the Visualization and Analysis of Microbiome Networks2507.08822v1 · Qiyao Yang, Rosa Aghdam, Reed Nelson et al.2025 · 0 citationsarXiv
CMiNet: An R Package and User-Friendly Shiny App for Constructing Consensus Microbiome Networks10.1101/2025.05.09.653200v1 · Aghdam, R., Solis-Lemus, C.2025 · 3 citationsbioRxiv
A method for massively scalable phylogenetic network inference10.1101/2025.05.05.652278v5 · Kolbow, N., Kong, S., Solis-Lemus, C.2025 · 6 citationsbioRxiv
Leveraging Bayesian Networks for Consensus Network Construction and Multi-Method Feature Selection to Decode Disease Prediction10.1101/2025.04.07.647660v1 · Aghdam, R., Shan, S., Lankau, R. et al.2025 · 4 citationsbioRxiv
HighDimMixedModels.jl: Robust high-dimensional mixed-effects models across omics data.39804942 · Gorstein, Evan, Aghdam, Rosa, Solís-Lemus, Claudia2025 · 7 citationsPLoS computational biology. 2025;21(1):e1012143
Human limits in machine learning: prediction of potato yield and disease using soil microbiome data.39592933 · Aghdam, Rosa, Tang, Xudong, Shan, Shan et al.2024 · 21 citationsBMC bioinformatics. 2024;25(1):366
CMiNet: R package for learning the Consensus Microbiome Network2411.08309v1 · Rosa Aghdam, Claudia Solis-Lemus2024 · 0 citationsarXiv
Unraveling Keystone Taxa: Interactions Within Microbial Networks and Environmental Dynamics in Lake Mendota10.1101/2024.11.11.623027v1 · Yang, Q., Aghdam, R., Tran, P. Q. et al.2024 · 1 citationbioRxiv
Benefits and Limits of Phasing Alleles for Network Inference of Allopolyploid Complexes.38733563 · Tiley, George P, Crowl, Andrew A, Manos, Paul S et al.2024 · 22 citationsSystematic biology. 2024;73(4):666-682
Identifying microbial drivers in biological phenotypes with a Bayesian network regression model.38774136 · Ozminkowski, Samuel, Solís-Lemus, Claudia2026 · 2 citationsEcology and evolution. 2024;14(5):e11039
HighDimMixedModels.jl: Robust High Dimensional Mixed Models across Omics Data10.1101/2024.05.09.593305v1 · Gorstein, E., Aghdam, R., Solis-Lemus, C.2024 · 0 citationsbioRxiv
Novel symmetry-preserving neural network model for phylogenetic inference.38638281 · Tang, Xudong, Zepeda-Nuñez, Leonardo, Yang, Shengwen et al.2024 · 9 citationsBioinformatics advances. 2024;4(1):vbae022
Ultrafast learning of four-node hybridization cycles in phylogenetic networks using algebraic invariants.38384862 · Wu, Zhaoxing, Solís-Lemus, Claudia2024 · 6 citationsBioinformatics advances. 2024;4(1):vbae014
Unsupervised Learning of Phylogenetic Trees via Split-Weight Embedding2312.16074v2 · Yibo Kong, George P. Tiley, Claudia Solis-Lemus2023 · 1 citationarXiv
Machine learning identification of Pseudomonas aeruginosa strains from colony image data.38091365 · Rattray, Jennifer B, Lowhorn, Ryan J, Walden, Ryan et al.2023 · 20 citationsPLoS computational biology. 2023;19(12):e1011699
Non-linear phylogenetic regression using regularized kernels10.1101/2023.10.04.560983v1 · Rosas-Puchuri, U., Santaquiteria, A., Khanmohammadi, S. et al.2023 · 1 citationbioRxiv
Human Limits in Machine Learning: Prediction of Plant Phenotypes Using Soil Microbiome Data2306.11157v2 · Rosa Aghdam, Xudong Tang, Shan Shan et al.2023 · 2 citationsarXiv
MiNAA: Microbiome Network Alignment Algorithm2212.05880v1 · Reed Nelson, Rosa Aghdam, Claudia Solis-Lemus2022 · 5 citationsarXiv
Ultrafast learning of 4-node hybridization cycles in phylogenetic networks using algebraic invariants2211.16647v3 · Zhaoxing Wu, Claudia Solis-Lemus2022 · 0 citationsarXiv
Detectability of Varied Hybridization Scenarios using Genome-Scale Hybrid Detection Methods2211.00712v2 · Marianne Bjorner, Erin K. Molloy, Colin N. Dewey et al.2022 · 15 citationsarXiv
SiPhyNetwork: An R package for Simulating Phylogenetic Networks10.1101/2022.10.26.513953v2 · Justison, J., Solis-Lemus, C., Heath, T. A.2022 · 19 citationsbioRxiv
BioKlustering: a web app for semi-supervised learning of maximally imbalanced genomic data2209.11730v3 · Samuel Ozminkowski, Yuke Wu, Hailey Bruzzone et al.2022 · 0 citationsarXiv
Estimating sparse direct effects in multivariate regression with the spike-and-slab LASSO2207.07020v3 · Yunyi Shen, Claudia Sol'is-Lemus, Sameer K. Deshpande2022 · 1 citationarXiv
Towards a robust out-of-the-box neural network model for genomic data.35397517 · Zhang, Zhaoyi, Cheng, Songyang, Solis-Lemus, Claudia2022 · 2 citationsBMC bioinformatics. 2022;23(1):125
Efficient estimation of indirect effects in case-control studies using a unified likelihood framework.35352841 · Satten, Glen A, Curtis, Sarah W, Solis-Lemus, Claudia et al.2022 · 8 citationsStatistics in medicine. 2022;41(15):2879-2893
Classification of animal sounds in a hyperdiverse rainforest using Convolutional Neural Networks2111.14971v2 · Yuren Sun, Tatiana Midori Maeda, Claudia Solis-Lemus et al.2021 · 0 citationsarXiv
A Kernel Method for Dissecting Genetic Signals in Tests of High-Dimensional Phenotypes10.1101/2021.07.29.454336v1 · Solis-Lemus, C., Holleman, A. M., Todor, A. et al.2021 · 0 citationsbioRxiv
CARlasso: An R package for the estimation of sparse microbial networks with predictors2107.13763v1 · Yunyi Shen, Claudia Solis-Lemus2021 · 3 citationsarXiv
Effect of genetic background on the evolution of Vancomycin-Intermediate Staphylococcus aureus (VISA).34306830 · Su, Michelle, Davis, Michelle H, Peterson, Jessica et al.2022 · 14 citationsPeerJ. 2021;9:e11764
The Effect of the Prior and the Experimental Design on the Inference of the Precision Matrix in Gaussian Chain Graph Models2107.01306v5 · Yunyi Shen, Claudia Solis-Lemus2021 · 2 citationsarXiv
Genes Influencing Phage Host Range in Staphylococcus aureus on a Species-Wide Scale.33441407 · Moller, Abraham G, Winston, Kyle, Ji, Shiyu et al.2021 · 52 citationsmSphere. 2021;6(1)
Bayesian Chain Graph LASSO Models to Learn Sparse Microbial Networks with Predictors2012.08397v6 · Yunyi Shen, Claudia Solis-Lemus2020 · 2 citationsarXiv
WI Fast Stats: a collection of web apps for the visualization and analysis of WI Fast Plants data2012.03290v1 · Yizhou Liu, Claudia Solis-Lemus2020 · 0 citationsarXiv
On the Identifiability of Phylogenetic Networks under a Pseudolikelihood model2010.01758v1 · Claudia Solis-Lemus, Arrigo Coen, Cecile Ane2020 · 5 citationsarXiv
Genomic analysis of variability in Delta-toxin levels between Staphylococcus aureus strains.32231873 · Su, Michelle, Lyles, James T, Petit Iii, Robert A et al.2024 · 27 citationsPeerJ. 2020;8:e8717
Career total: 87 works. 58 are in this corpus.Showing the 50 most recent.
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