isbscience.org/research/publications/2023
Aguilar, Boris, Kawther Abdilleh, and George K. Acquaah-Mensah. 2023. “Multi-Omics Inference of Differential Breast Cancer-Related Transcriptional Regulatory Network Gene Hubs between Young Black and White Patients.” Cancer Genetics 270–271: 1–11. https://doi.org/10.1016/j.cancergen.2022.11.001. Cite
Akhade, Ajay Suresh, and Naeha Subramanian. 2023. “Cytoplasmic Sensing in Innate Immunity.” In Encyclopedia of Cell Biology (Second Edition), edited by Ralph A. Bradshaw, Gerald W. Hart, and Philip D. Stahl, 624–43. Oxford: Academic Press. https://doi.org/10.1016/B978-0-12-821618-7.00012-2. Cite
Arrieta-Ortiz, Mario L., Min Pan, Amardeep Kaur, Evan Pepper-Tunick, Vivek Srinivas, Ananya Dash, Selva Rupa Christinal Immanuel, Aaron N. Brooks, Tyson R. Shepherd, and Nitin S. Baliga. 2023. “Disrupting the ArcA Regulatory Network Amplifies the Fitness Cost of Tetracycline Resistance in Escherichia Coli.” MSystems 8 (1): e0090422. https://doi.org/10.1128/msystems.00904-22. Cite Download
Bohmann, Nick, Tomasz Wilmanski, Lisa Levy, Johanna W. Lampe, Thomas Gurry, Noa Rappaport, Christian Diener, and Sean M. Gibbons. 2023. “Microbial Community-Scale Metabolic Modeling Predicts Personalized Short-Chain-Fatty-Acid Production Profiles in the Human Gut.” bioRxiv. https://doi.org/10.1101/2023.02.28.530516. Cite Download
Deutsch, Eric W, Nuno Bandeira, Yasset Perez-Riverol, Vagisha Sharma, Jeremy J Carver, Luis Mendoza, Deepti J Kundu, et al. 2023. “The ProteomeXchange Consortium at 10 Years: 2023 Update.” Nucleic Acids Research 51 (D1): D1539–48. https://doi.org/10.1093/nar/gkac1040. Cite Download
Deutsch, Eric W., Juan Antonio Vizcaíno, Andrew R. Jones, Pierre-Alain Binz, Henry Lam, Joshua Klein, Wout Bittremieux, et al. 2023. “Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work.” Journal of Proteome Research 22 (2): 287–301. https://doi.org/10.1021/acs.jproteome.2c00637. Cite Download
Deutsch, Eric W., Luis Mendoza, David D. Shteynberg, Michael R. Hoopmann, Zhi Sun, Jimmy K. Eng, and Robert L. Moritz. 2023. “Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite.” Journal of Proteome Research 22 (2): 615–24. https://doi.org/10.1021/acs.jproteome.2c00624. Cite
Diener, Christian, and Sean M. Gibbons. 2023. “More Is Different: Metabolic Modeling of Diverse Microbial Communities.” MSystems, e0127022. https://doi.org/10.1128/msystems.01270-22. Cite
Echlin, Moriah, Boris Aguilar, and Ilya Shmulevich. 2023. “Characterizing the Impact of Communication on Cellular and Collective Behavior Using a Three-Dimensional Multiscale Cellular Model.” Entropy (Basel, Switzerland) 25 (2): 319. https://doi.org/10.3390/e25020319. Cite Download
Glen, Amy K., Chunyu Ma, Luis Mendoza, Finn Womack, E. C. Wood, Meghamala Sinha, Liliana Acevedo, et al. 2023. “ARAX: A Graph-Based Modular Reasoning Tool for Translational Biomedicine.” Bioinformatics (Oxford, England) 39 (3): btad082. https://doi.org/10.1093/bioinformatics/btad082. Cite Download
Gorman, Chris, Davide Punzo, Igor Octaviano, Steven Pieper, William J. R. Longabaugh, David A. Clunie, Ron Kikinis, Andrey Y. Fedorov, and Markus D. Herrmann. 2023. “Interoperable Slide Microscopy Viewer and Annotation Tool for Imaging Data Science and Computational Pathology.” Nature Communications 14 (1): 1572. https://doi.org/10.1038/s41467-023-37224-2. Cite Download
Hoopmann, Michael R., David D. Shteynberg, Alex Zelter, Michael Riffle, Andrew S. Lyon, David A. Agard, Qing Luan, et al. 2023. “Improved Analysis of Cross-Linking Mass Spectrometry Data with Kojak 2.0, Advanced by Integration into the Trans-Proteomic Pipeline.” Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.2c00670. Cite
Hughes, Laura D., Ginger Tsueng, Jack DiGiovanna, Thomas D. Horvath, Luke V. Rasmussen, Tor C. Savidge, Thomas Stoeger, et al. 2023. “Addressing Barriers in FAIR Data Practices for Biomedical Data.” Scientific Data 10 (1): 98. https://doi.org/10.1038/s41597-023-01969-8. Cite Download
Hwang, Yeon Mi, Ryan T. Roper, Samantha N. Piekos, Daniel A. Enquobahrie, Mary F. Hebert, Alison G. Paquette, Priyanka Baloni, Nathan D. Price, Leroy Hood, and Jennifer J. Hadlock. 2023. “Timing of Selective Serotonin Reuptake Inhibitor Use and Risk for Preterm Birth and Related Adverse Events.” medRxiv. https://doi.org/10.1101/2023.03.03.23286717. Cite Download
Johnson, James P., Christian Diener, Anne E. Levine, Tomasz Wilmanski, David L. Suskind, Alexandra Ralevski, Jennifer Hadlock, et al. 2023. “Generally-Healthy Individuals with Aberrant Bowel Movement Frequencies Show Enrichment for Microbially-Derived Blood Metabolites Associated with Impaired Kidney Function.” bioRxiv. https://doi.org/10.1101/2023.03.04.531100. Cite Download
Kertesz-Farkas, Attila, Frank Lawrence Nii Adoquaye Acquaye, Kishankumar Bhimani, Jimmy K. Eng, William E. Fondrie, Charles Grant, Michael R. Hoopmann, et al. 2023. “The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data.” Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.2c00615. Cite Download
Kwasniewski, Miroslaw, Urszula Korotko, Karolina Chwialkowska, Magdalena Niemira, Jerzy Jaroszewicz, Barbara Sobala-Szczygiel, Beata Puzanowska, et al. 2023. “Implementation of the Web-Based Calculator Estimating Odds Ratio of Severe COVID-19 for Unvaccinated Individuals in a Country with High Coronavirus-Related Death Toll.” Allergy 78 (1): 311–14. https://doi.org/10.1111/all.15524. Cite Download
Lorenzetti, Alan P. R., Ulrike Kusebauch, Lívia S. Zaramela, Wei-Ju Wu, João P. P. de Almeida, Serdar Turkarslan, Adrián L G de Lomana, et al. 2023. “A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon.” MSystems, e0081622. https://doi.org/10.1128/msystems.00816-22. Cite Download
Marcelino, Vanessa, Caitlin Welsh, Christian Diener, Emily Gulliver, Emily Rutten, Remy Young, Edward Giles, Sean Gibbons, Chris Greening, and Samuel Forster. 2023. “Disease-Specific Loss of Microbial Cross-Feeding Interactions in the Human Gu.” https://doi.org/10.1101/2023.02.17.528570. Cite Download
Midha, Mukul K., Charu Kapil, Michal Maes, David H. Baxter, Seamus R. Morrone, Timothy J. Prokop, and Robert L. Moritz. 2023. “Vacuum Insulated Probe Heated ElectroSpray Ionization Source (VIP-HESI) Enhances Micro Flow Rate Chromatography Signals in the Bruker TimsTOF Mass Spectrometer.” bioRxiv. https://doi.org/10.1101/2023.02.15.528699. Cite Download
Morris, John H., Karthik Soman, Rabia E. Akbas, Xiaoyuan Zhou, Brett Smith, Elaine C. Meng, Conrad C. Huang, et al. 2023. “The Scalable Precision Medicine Open Knowledge Engine (SPOKE): A Massive Knowledge Graph of Biomedical Information.” Bioinformatics (Oxford, England) 39 (2): btad080. https://doi.org/10.1093/bioinformatics/btad080. Cite Download
Morrone, Seamus R., Michael R. Hoopmann, David D. Shteynberg, Ulrike Kusebauch, and Robert L. Moritz. 2023. “Optimization of Instrument Parameters for Efficient Phosphopeptide Identification and Localization by Data-Dependent Analysis Using Orbitrap Tribrid Mass Spectrometers.” ChemRxiv. https://doi.org/10.26434/chemrxiv-2023-qklh1-v2. Cite Download
Neely, Benjamin A., Viktoria Dorfer, Lennart Martens, Isabell Bludau, Robbin Bouwmeester, Sven Degroeve, Eric W. Deutsch, et al. 2023. “Toward an Integrated Machine Learning Model of a Proteomics Experiment.” Journal of Proteome Research 22 (3): 681–96. https://doi.org/10.1021/acs.jproteome.2c00711. Cite Download
Puig-Saus, Cristina, Barbara Sennino, Songming Peng, Clifford L. Wang, Zheng Pan, Benjamin Yuen, Bhamini Purandare, et al. 2023. “Neoantigen-Targeted CD8+ T Cell Responses with PD-1 Blockade Therapy.” Nature. https://doi.org/10.1038/s41586-023-05787-1. Cite
Rehfeldt, Tobias G., Ralf Gabriels, Robbin Bouwmeester, Siegfried Gessulat, Benjamin A. Neely, Magnus Palmblad, Yasset Perez-Riverol, Tobias Schmidt, Juan Antonio Vizcaíno, and Eric W. Deutsch. 2023. “ProteomicsML: An Online Platform for Community-Curated Data Sets and Tutorials for Machine Learning in Proteomics.” Journal of Proteome Research 22 (2): 632–36. https://doi.org/10.1021/acs.jproteome.2c00629. Cite Download
Sandmann, Clara-L., Jana F. Schulz, Jorge Ruiz-Orera, Marieluise Kirchner, Matthias Ziehm, Eleonora Adami, Maike Marczenke, et al. 2023. “Evolutionary Origins and Interactomes of Human, Young Microproteins and Small Peptides Translated from Short Open Reading Frames.” Molecular Cell 83 (6): 994-1011.e18. https://doi.org/10.1016/j.molcel.2023.01.023. Cite Download
Storer, Jessica M., Jerilyn A. Walker, Jasmine N. Baker, Shifat Hossain, Christian Roos, Travis J. Wheeler, and Mark A. Batzer. 2023. “Framework of the Alu Subfamily Evolution in the Platyrrhine Three-Family Clade of Cebidae, Callithrichidae, and Aotidae.” Genes 14 (2): 249. https://doi.org/10.3390/genes14020249. Cite Download
Wang, Janet, Jeanne Zheng, Elaine E. Lee, Boris Aguilar, John Phan, Kawther Abdilleh, Ronald C. Taylor, et al. 2023. “A Cloud-Based Resource for Genome Coordinate-Based Exploration and Large-Scale Analysis of Chromosome Aberrations and Gene Fusions in Cancer.” Genes, Chromosomes & Cancer. https://doi.org/10.1002/gcc.23128. Cite
Wang, Yaxi, Hannah E. Ledvina, Catherine A. Tower, Stanimir Kambarev, Elizabeth Liu, James C. Charity, Lieselotte S. M. Kreuk, et al. 2023. “Discovery of a Unique Pathway for Glutathione Utilization in Francisella.” bioRxiv. https://doi.org/10.1101/2023.02.02.526638. Cite Download
Watanabe, Kengo, Tomasz Wilmanski, Christian Diener, John C. Earls, Anat Zimmer, Briana Lincoln, Jennifer J. Hadlock, et al. 2023. “Multiomic Signatures of Body Mass Index Identify Heterogeneous Health Phenotypes and Responses to a Lifestyle Intervention.” Nature Medicine. https://doi.org/10.1038/s41591-023-02248-0. Cite
Zhang, Yu-Hang, Michael H. Cho, Jarrett D. Morrow, Peter J. Castaldi, Craig P. Hersh, Mukul K. Midha, Michael R. Hoopmann, Sharon M. Lutz, Robert L. Moritz, and Edwin K. Silverman. 2023. “Integrating Genetics, Transcriptomics, and Proteomics in Lung Tissue to Investigate COPD.” American Journal of Respiratory Cell and Molecular Biology. https://doi.org/10.1165/rcmb.2022-0302OC. Cite
