I-LAMB The Illinois Laboratory for Animal Machine-learning and Bioinformatics

Lab Publications

Publications by members of the Robben Lab focus on new omics technologies including single cell RNA-seq and spatial transcriptomics in different aspects of animal and human biology research, including cancer immunology and autoimmune disease. Publications are a mix of preprint/in-submission, journal articles and conference publications.

Highlighted

In Submission

Single-cell RNA-seq reveals TCR clonal expansion and a high frequency of transcriptionally distinct double-negative T cells in NOD mice
Single-cell RNA-seq reveals TCR clonal expansion and a high frequency of transcriptionally distinct double-negative T cells in NOD mice
Md Zohorul Islam, Sam Zimmerman, Jon Weidanz, Jose Ordovas-Montanes, Michael Robben, Jacob M. Luber, Aleksandar D Kostic
Immunology   ·   25 Jul 2023   ·   https://doi.org/10.1101/2023.07.21.550036
scRNA-seq reveals novel genetic pathways and sex chromosome regulation in <i>Tribolium</i> spermatogenesis
scRNA-seq reveals novel genetic pathways and sex chromosome regulation in Tribolium spermatogenesis
Michael Robben, Balan Ramesh, Shana Pau, Demetra Meletis, Jacob Luber, Jeffery Demuth
Molecular Biology   ·   18 Jul 2023   ·   https://doi.org/10.1101/2023.07.18.549532

Journal Articles and Conference Papers

2024

scRNA-seq Reveals Novel Genetic Pathways and Sex Chromosome Regulation in <i>Tribolium</i> Spermatogenesis
scRNA-seq Reveals Novel Genetic Pathways and Sex Chromosome Regulation in Tribolium Spermatogenesis
Michael Robben, Balan Ramesh, Shana Pau, Demetra Meletis, Jacob Luber, Jeffery Demuth
Genome Biology and Evolution   ·   01 Mar 2024   ·   doi:10.1093/gbe/evae059
Single-cell RNA-seq reveals TCR clonal expansion and a high frequency of transcriptionally distinct double-negative T cells in NOD mice
Single-cell RNA-seq reveals TCR clonal expansion and a high frequency of transcriptionally distinct double-negative T cells in NOD mice
Michael Robben, Md ZOhorul Islam, Sam Zimmerman, Jon Weidanz, Jose Ordovas-Montanes, Aleksandar Kostic, Jacob Luber
Research Square Platform LLC   ·   16 Jan 2024   ·   doi:10.21203/rs.3.rs-3794984/v1
Clinically Relevant Latent Space Embedding of Cancer Histopathology Slides through Variational Autoencoder Based Image Compression
Clinically Relevant Latent Space Embedding of Cancer Histopathology Slides through Variational Autoencoder Based Image Compression
Mohammad Sadegh Nasr, Amir Hajighasemi, Paul Koomey, Parisa Boodaghi Malidarreh, Michael Robben, Jillur Rahman Saurav, Helen H. Shang, Manfred Huber, Jacob M. Luber
arXiv   ·   08 Jan 2024   ·   arXiv:2303.13332
A SSIM Guided cGAN Architecture For Clinically Driven Generative Image Synthesis of Multiplexed Spatial Proteomics Channels
A SSIM Guided cGAN Architecture For Clinically Driven Generative Image Synthesis of Multiplexed Spatial Proteomics Channels
Jillur Rahman Saurav, Mohammad Sadegh Nasr, Paul Koomey, Michael Robben, Manfred Huber, Jon Weidanz, Bríd Ryan, Eytan Ruppin, Peng Jiang, Jacob M. Luber
arXiv   ·   08 Jan 2024   ·   arXiv:2205.10373

2023

The state of applying artificial intelligence to tissue imaging for cancer research and early detection
The state of applying artificial intelligence to tissue imaging for cancer research and early detection
Michael Robben, Amir Hajighasemi, Mohammad Sadegh Nasr, Jai Prakesh Veerla, Anne Marie Alsup, ..., Kelli Fowlds, Parisa Boodaghi Malidarreh, Paul Koomey, Jillur Rahman Saurav, Jacob M. Luber
F1000Research   ·   06 Nov 2023   ·   doi:10.12688/f1000research.139210.1
A SSIM Guided cGAN Architecture For Clinically Driven Generative Image Synthesis of Multiplexed Spatial Proteomics Channels
A SSIM Guided cGAN Architecture For Clinically Driven Generative Image Synthesis of Multiplexed Spatial Proteomics Channels
Jillur Rahman Saurav, Mohammad Sadegh Nasr, Helen H Shang, Paul Koomey, Michael Robben, ..., Jon Weidanz, Bríd Ryan, Eytan Ruppin, Peng Jiang, Jacob M. Luber
2023 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)   ·   29 Aug 2023   ·   doi:10.1109/cibcb56990.2023.10264899
Analyzing Lack of Concordance Between the Proteome and Transcriptome in Paired scRNA-Seq and Multiplexed Spatial Proteomics
Analyzing Lack of Concordance Between the Proteome and Transcriptome in Paired scRNA-Seq and Multiplexed Spatial Proteomics
Jai Prakash Veerla, Jillur Rahman Saurav, Michael Robben, Jacob M Luber
arXiv   ·   04 Jul 2023   ·   arXiv:2307.00635
Comparison of the Strengths and Weaknesses of Machine Learning Algorithms and Feature Selection on KEGG Database Microbial Gene Pathway Annotation and Its Effects on Reconstructed Network Topology
Comparison of the Strengths and Weaknesses of Machine Learning Algorithms and Feature Selection on KEGG Database Microbial Gene Pathway Annotation and Its Effects on Reconstructed Network Topology
Michael Robben, Mohammad Sadegh Nasr, Avishek Das, Jai Prakash Veerla, Manfred Huber, Justyn Jaworski, Jon Weidanz, Jacob Luber
Journal of Computational Biology   ·   01 Jul 2023   ·   doi:10.1089/cmb.2022.0370
Multimodal Pathology Image Search Between H&E Slides and Multiplexed Immunofluorescent Images
Multimodal Pathology Image Search Between H&E Slides and Multiplexed Immunofluorescent Images
Amir Hajighasemi, MD Jillur Rahman Saurav, Mohammad S Nasr, Jai Prakash Veerla, Aarti Darji, Parisa Boodaghi Malidarreh, Michael Robben, Helen H Shang, Jacob M Luber
arXiv   ·   13 Jun 2023   ·   arXiv:2306.06780
Clinically Relevant Latent Space Embedding of Cancer Histopathology Slides Through Variational Autoencoder based Image Compression
Clinically Relevant Latent Space Embedding of Cancer Histopathology Slides Through Variational Autoencoder based Image Compression
Mohammad Sadegh Nasr, Amir Hajighasemi, Paul Koomey, Parisa Boodaghi Malidarreh, Michael Robben, Jillur Rahman Saurav, Helen H Shang, Manfred Huber, Jacob M. Luber
2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI)   ·   18 Apr 2023   ·   doi:10.1109/isbi53787.2023.10230343

2021

Integrative Analysis of Gene Expression and miRNAs Reveal Biological Pathways Associated with Bud Paradormancy and Endodormancy in Grapevine
Integrative Analysis of Gene Expression and miRNAs Reveal Biological Pathways Associated with Bud Paradormancy and Endodormancy in Grapevine
Shuchi Smita, Michael Robben, Anup Deuja, Monica Accerbi, Pamela J. Green, Senthil Subramanian, Anne Fennell
Plants   ·   31 Mar 2021   ·   doi:10.3390/plants10040669

2020

Draft genome of the Native American cold hardy grapevine Vitis riparia Michx. ‘Manitoba 37’
Draft genome of the Native American cold hardy grapevine Vitis riparia Michx. ‘Manitoba 37’
Sagar Patel, Michael Robben, Anne Fennell, Jason P. Londo, Dilmini Alahakoon, Roberto Villegas-Diaz, Padmapriya Swaminathan
Horticulture Research   ·   01 Jun 2020   ·   doi:10.1038/s41438-020-0316-2

2017

Transcriptome Analysis of the Heritable Salt Tolerance of Prairie Cordgrass (Spartina pectinata Link)
Transcriptome Analysis of the Heritable Salt Tolerance of Prairie Cordgrass (Spartina pectinata Link)
Michael Robben, Ethan Thibault, Michaellong Tran, Yajun Wu, Arvid Boe, Jose L. Gonzalez-Hernandez
BioEnergy Research   ·   23 Nov 2017   ·   doi:10.1007/s12155-017-9881-0