Publications

Baranzini, Sergio E., Katy Börner, John Morris, Charlotte A. Nelson, Karthik Soman, Erica Schleimer, Michael Keiser, et al. 2022. “A Biomedical Open Knowledge Network Harnesses the Power of AI to Understand Deep Human Biology.” AI Magazine 43 (1): 46–58. https://doi.org/10.1002/aaai.12037. Cite Download

Baumgartner, Andrew, Sevda Molani, Qi Wei, and Jennifer Hadlock. 2022. “Imputing Missing Observations with Time Sliced Synthetic Minority Oversampling Technique.” ArXiv:2201.05634 [Physics, q-Bio, Stat]. http://arxiv.org/abs/2201.05634. Cite Download

Cooper, Charlotte, Eliza J. R. Peterson, Rebeca Bailo, Min Pan, Albel Singh, Patrick Moynihan, Makoto Nakaya, Nagatoshi Fujiwara, Nitin Baliga, and Apoorva Bhatt. 2022. “MadR Mediates Acyl CoA-Dependent Regulation of Mycolic Acid Desaturation in Mycobacteria.” Proceedings of the National Academy of Sciences 119 (8): e2111059119. https://doi.org/10.1073/pnas.2111059119. Cite Download

Danileviciute, Egle, Ni Zeng, Christophe M. Capelle, Nicole Paczia, Mark A. Gillespie, Henry Kurniawan, Mohaned Benzarti, et al. 2022. “PARK7/DJ-1 Promotes Pyruvate Dehydrogenase Activity and Maintains Treg Homeostasis during Ageing.” Nature Metabolism 4 (5): 589–607. https://doi.org/10.1038/s42255-022-00576-y. Cite

Andrade, Kelvin César de, Elaine E. Lee, Elise M. Tookmanian, Chimene A. Kesserwan, James J. Manfredi, Jessica N. Hatton, Jennifer K. Loukissas, et al. 2022. “The TP53 Database: Transition from the International Agency for Research on Cancer to the US National Cancer Institute.” Cell Death and Differentiation. https://doi.org/10.1038/s41418-022-00976-3. Cite

Doty, Raymond T., Christopher G. Lausted, Adam D. Munday, Zhantao Yang, Xiaowei Yan, Changting Meng, Qiang Tian, and Janis L. Abkowitz. 2022. “The Transcriptomic Landscape of Normal and Ineffective Erythropoiesis at Single Cell Resolution.” medRxiv. https://doi.org/10.1101/2022.08.01.22278133. Cite Download

Fecho, Karamarie, Anne E. Thessen, Sergio E. Baranzini, Chris Bizon, Jennifer J. Hadlock, Sui Huang, Ryan T. Roper, et al. 2022. “Progress toward a Universal Biomedical Data Translator.” Clinical and Translational Science. https://doi.org/10.1111/cts.13301. Cite

Foo, Jasmine, David Basanta, Russell C. Rockne, Carly Strelez, Curran Shah, Kimya Ghaffarian, Shannon M. Mumenthaler, et al. 2022. “Roadmap on Plasticity and Epigenetics in Cancer.” Physical Biology. https://doi.org/10.1088/1478-3975/ac4ee2. Cite

Gautam, Shashyendra Singh, Raghwendra Pratap Singh, Kajal Karsauliya, Ashish Kumar Sonker, Panga Jaipal Reddy, Divya Mehrotra, Sameer Gupta, Sudhir Singh, Rashmi Kumar, and Sheelendra Pratap Singh. 2022. “Label-Free Plasma Proteomics for the Identification of the Putative Biomarkers of Oral Squamous Cell Carcinoma.” Journal of Proteomics 259: 104541. https://doi.org/10.1016/j.jprot.2022.104541. Cite

Gibbons, Sean M., Thomas Gurry, Johanna W. Lampe, Anirikh Chakrabarti, Veerle Dam, Amandine Everard, Almudena Goas, et al. 2022. “Perspective: Leveraging the Gut Microbiota to Predict Personalized Responses to Dietary, Prebiotic, and Probiotic Interventions.” Advances in Nutrition (Bethesda, Md.), nmac075. https://doi.org/10.1093/advances/nmac075. Cite

Gunn, Sophia, Michael Wainberg, Zeyuan Song, Stacy Andersen, Robert Boudreau, Mary F. Feitosa, Qihua Tan, et al. 2022. “Distribution of 54 Polygenic Risk Scores for Common Diseases in Long Lived Individuals and Their Offspring.” GeroScience. https://doi.org/10.1007/s11357-022-00518-2. Cite Download

Hasin, Naushaba, Lace M. Riggs, Tatyana Shekhtman, Justin Ashworth, Robert Lease, Rediet T. Oshone, Elizabeth M. Humphries, et al. 2022. “Rare Variants Implicate NMDA Receptor Signaling and Cerebellar Gene Networks in Risk for Bipolar Disorder.” Molecular Psychiatry. https://doi.org/10.1038/s41380-022-01609-4. Cite

Heath, Laura, John C. Earls, Andrew T. Magis, Sergey A. Kornilov, Jennifer C. Lovejoy, Cory C. Funk, Noa Rappaport, et al. 2022. “Manifestations of Alzheimer’s Disease Genetic Risk in the Blood Are Evident in a Multiomic Analysis in Healthy Adults Aged 18 to 90.” Scientific Reports 12 (1): 6117. https://doi.org/10.1038/s41598-022-09825-2. Cite Download

Hoyt, Savannah J., Jessica M. Storer, Gabrielle A. Hartley, Patrick G. S. Grady, Ariel Gershman, Leonardo G. de Lima, Charles Limouse, et al. 2022. “From Telomere to Telomere: The Transcriptional and Epigenetic State of Human Repeat Elements.” Science 376 (6588): eabk3112. https://doi.org/10.1126/science.abk3112. Cite Download

Hua, Hui, Cem Meydan, Evan E. Afshin, Loukia N. Lili, Christopher R. D’Adamo, Nate Rickard, Joel T. Dudley, Nathan D. Price, Bodi Zhang, and Christopher E. Mason. 2022. “A Wipe-Based Stool Collection and Preservation Kit for Microbiome Community Profiling.” Frontiers in Immunology 13: 889702. https://doi.org/10.3389/fimmu.2022.889702. Cite Download

Hubley, Robert, Travis J. Wheeler, and Arian F. A. Smit. 2022. “Accuracy of Multiple Sequence Alignment Methods in the Reconstruction of Transposable Element Families.” NAR Genomics and Bioinformatics 4 (2): lqac040. https://doi.org/10.1093/nargab/lqac040. Cite Download

Kalyuzhnyy, Anton, Patrick A. Eyers, Claire E. Eyers, Emily Bowler-Barnett, Maria J. Martin, Zhi Sun, Eric W. Deutsch, and Andrew R. Jones. 2022. “Profiling the Human Phosphoproteome to Estimate the True Extent of Protein Phosphorylation.” Journal of Proteome Research 21 (6): 1510–24. https://doi.org/10.1021/acs.jproteome.2c00131. Cite Download

Kari, Sana, Kumar Subramanian, Ilenia Agata Altomonte, Akshaya Murugesan, Olli Yli-Harja, and Meenakshisundaram Kandhavelu. 2022. “Programmed Cell Death Detection Methods: A Systematic Review and a Categorical Comparison.” Apoptosis: An International Journal on Programmed Cell Death. https://doi.org/10.1007/s10495-022-01735-y. Cite Download

Kauffman, Stuart A. 2022. “Quantum Gravity If Non-Locality Is Fundamental.” Entropy (Basel, Switzerland) 24 (4): 554. https://doi.org/10.3390/e24040554. Cite Download

Kauffman, Stuart, and Sudip Patra. 2022. “A Testable Theory for the Emergence of the Classical World.” Entropy (Basel, Switzerland) 24 (6): 844. https://doi.org/10.3390/e24060844. Cite Download

Layne, Scott P., Kathie-Anne Walters, John C. Kash, and Jeffery K. Taubenberger. 2022. “More Autopsy Studies Are Needed to Understand the Pathogenesis of Severe COVID-19.” Nature Medicine 28 (3): 427–28. https://doi.org/10.1038/s41591-022-01684-8. Cite Download

Le, Hien Thi Thu, Akshaya Murugesan, Nuno R. Candeias, Thiyagarajan Ramesh, Olli Yli-Harja, and Meenakshisundaram Kandhavelu. 2022. “P2Y1 Agonist HIC in Combination with Androgen Receptor Inhibitor Abiraterone Acetate Impairs Cell Growth of Prostate Cancer.” Apoptosis 27 (3): 283–95. https://doi.org/10.1007/s10495-022-01716-1. Cite Download

LeDuc, Richard D., Eric W. Deutsch, Pierre-Alain Binz, Ryan T. Fellers, Anthony J. Cesnik, Joshua A. Klein, Tim Van Den Bossche, et al. 2022. “Proteomics Standards Initiative’s ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms.” Journal of Proteome Research 21 (4): 1189–95. https://doi.org/10.1021/acs.jproteome.1c00771. Cite

Lee, Ming-Jen, Inyoul Lee, and Kai Wang. 2022. “Recent Advances in RNA Therapy and Its Carriers to Treat the Single-Gene Neurological Disorders.” Biomedicines 10 (1): 158. https://doi.org/10.3390/biomedicines10010158. Cite Download

Lee, Ming-Jen, Pi-Chen Lin, Ming-Hong Lin, Hsin-Ying Clair Chiou, Kai Wang, and Chiung-Wei Huang. 2022. “Kinetic Alterations in Resurgent Sodium Currents of Mutant Nav1.4 Channel in Two Patients Affected by Paramyotonia Congenita.” Biology 11 (4): 613. https://doi.org/10.3390/biology11040613. Cite Download

Leng, Trystan, Edward M. Hill, Alex Holmes, Emma Southall, Robin N. Thompson, Michael J. Tildesley, Matt J. Keeling, and Louise Dyson. 2022. “Quantifying Pupil-to-Pupil SARS-CoV-2 Transmission and the Impact of Lateral Flow Testing in English Secondary Schools.” Nature Communications 13 (1): 1106. https://doi.org/10.1038/s41467-022-28731-9. Cite Download

Li, Jing, Maxim Zaslavsky, Yapeng Su, Jing Guo, Michael J. Sikora, Vincent van Unen, Asbjørn Christophersen, et al. 2022. “KIR+CD8+ T Cells Suppress Pathogenic T Cells and Are Active in Autoimmune Diseases and COVID-19.” Science 0 (0): eabi9591. https://doi.org/10.1126/science.abi9591. Cite Download

Lindner, Scott E., Kristian E. Swearingen, Melanie J. Shears, Aswathy Sebastian, Michael P. Walker, Erin N. Vrana, Kevin J. Hart, et al. 2022. “Addendum: Transcriptomics and Proteomics Reveal Two Waves of Translational Repression during the Maturation of Malaria Parasite Sporozoites.” Nature Communications 13 (1): 283. https://doi.org/10.1038/s41467-021-27767-7. Cite Download

Luo, Xiyang, Wout Bittremieux, Johannes Griss, Eric W. Deutsch, Timo Sachsenberg, Lev I. Levitsky, Mark V. Ivanov, et al. 2022. “A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics.” Journal of Proteome Research 21 (6): 1566–74. https://doi.org/10.1021/acs.jproteome.2c00069. Cite Download

Manry, Jérémy, Paul Bastard, Adrian Gervais, Tom Le Voyer, Jérémie Rosain, Quentin Philippot, Eleftherios Michailidis, et al. 2022. “The Risk of COVID-19 Death Is Much Greater and Age Dependent with Type I IFN Autoantibodies.” Proceedings of the National Academy of Sciences of the United States of America 119 (21): e2200413119. https://doi.org/10.1073/pnas.2200413119. Cite Download

Martyn, Gregory D., Gianluca Veggiani, Ulrike Kusebauch, Seamus R. Morrone, Bradley P. Yates, Alex U. Singer, Jiefei Tong, et al. 2022. “Engineered SH2 Domains for Targeted Phosphoproteomics.” ACS Chemical Biology 17 (6): 1472–84. https://doi.org/10.1021/acschembio.2c00051. Cite

Mastrogiorgio, Antonio, Teppo Felin, Stuart Kauffman, and Mariano Mastrogiorgio. 2022. “More Thumbs Than Rules: Is Rationality an Exaptation?” Frontiers in Psychology 13. https://www.frontiersin.org/article/10.3389/fpsyg.2022.805743. Cite Download

Molani, Sevda, Andrew M. Baumgartner, Yeon Mi Hwang, Venkata R. Duvvuri, Jason D. Goldman, and Jennifer J. Hadlock. 2022. “Time to Reinfection and Vaccine Breakthrough SARS-CoV-2 Infections: A Retrospective Cohort Study,” 2022.02.07.22270613. https://www.medrxiv.org/content/10.1101/2022.02.07.22270613v1. Cite Download

Molani, Sevda, Patricia V. Hernandez, Ryan T. Roper, Venkata R. Duvvuri, Andrew M. Baumgartner, Jason D. Goldman, Nilüfer Ertekin-Taner, et al. 2022. “Risk Factors for Severe COVID-19 Differ by Age for Hospitalized Adults.” Scientific Reports 12 (1): 6568. https://doi.org/10.1038/s41598-022-10344-3. Cite Download

Montaña-Lozano, Paula, Manuela Moreno-Carmona, Mauricio Ochoa-Capera, Natalia S. Medina, Jeffrey L. Boore, and Carlos F. Prada. 2022. “Comparative Genomic Analysis of Vertebrate Mitochondrial Reveals a Differential of Rearrangements Rate between Taxonomic Class.” Scientific Reports 12 (1): 5479. https://doi.org/10.1038/s41598-022-09512-2. Cite Download

Moser, Russell, Kay E. Gurley, Olga Nikolova, Guangrong Qin, Rashmi Joshi, Eduardo Mendez, Ilya Shmulevich, Amanda Ashley, Carla Grandori, and Christopher J. Kemp. 2022. “Synthetic Lethal Kinases in Ras/P53 Mutant Squamous Cell Carcinoma.” Oncogene. https://doi.org/10.1038/s41388-022-02330-w. Cite

Ng, Rachel H., Jihoon W. Lee, Priyanka Baloni, Christian Diener, James R. Heath, and Yapeng Su. 2022. “Constraint-Based Reconstruction and Analyses of Metabolic Models: Open-Source Python Tools and Applications to Cancer.” Frontiers in Oncology 12: 914594. https://doi.org/10.3389/fonc.2022.914594. Cite Download

Nguyen, Phung, Phuong Doan, Akshaya Murugesan, Thiyagarajan Ramesh, Tatu Rimpilainen, Nuno R. Candeias, Olli Yli-Harja, and Meenakshisundaram Kandhavelu. 2022. “GPR17 Signaling Activation by CHBC Agonist Induced Cell Death via Modulation of MAPK Pathway in Glioblastoma.” Life Sciences 291: 120307. https://doi.org/10.1016/j.lfs.2022.120307. Cite

Nissa, Mehar Un, Panga Jaipal Reddy, Nevil Pinto, Zhi Sun, Biplab Ghosh, Robert L. Moritz, Mukunda Goswami, and Sanjeeva Srivastava. 2022. “The PeptideAtlas of a Widely Cultivated Fish Labeo Rohita: A Resource for the Aquaculture Community.” Scientific Data 9 (1): 171. https://doi.org/10.1038/s41597-022-01259-9. Cite Download

Nurk, Sergey, Sergey Koren, Arang Rhie, Mikko Rautiainen, Andrey V. Bzikadze, Alla Mikheenko, Mitchell R. Vollger, et al. 2022. “The Complete Sequence of a Human Genome.” Science 376 (6588): 44–53. https://doi.org/10.1126/science.abj6987. Cite Download

Omenn, Gilbert S., Andrew T. Magis, Nathan D. Price, and Leroy Hood. 2022. “Personal Dense Dynamic Data Clouds Connect Systems Biomedicine to Scientific Wellness.” Methods in Molecular Biology (Clifton, N.J.) 2486: 315–34. https://doi.org/10.1007/978-1-0716-2265-0_15. Cite

Ouyang, Jian, Guangrong Qin, Zhenhao Liu, Xingxing Jian, Tieliu Shi, and Lu Xie. 2022. “ToPP: Tumor Online Prognostic Analysis Platform for Prognostic Feature Selection and Clinical Patient Subgroup Selection.” IScience 25 (5): 104190. https://doi.org/10.1016/j.isci.2022.104190. Cite Download

Piekos, Samantha N., Ryan T. Roper, Yeon Mi Hwang, Tanya Sorensen, Nathan D. Price, Leroy Hood, and Jennifer J. Hadlock. 2022. “The Effect of Maternal SARS-CoV-2 Infection Timing on Birth Outcomes: A Retrospective Multicentre Cohort Study.” The Lancet. Digital Health 4 (2): e95–104. https://doi.org/10.1016/S2589-7500(21)00250-8. Cite Download

Plaugher, Daniel, Boris Aguilar, and David Murrugarra. 2022. “Uncovering Potential Interventions for Pancreatic Cancer Patients via Mathematical Modeling.” Journal of Theoretical Biology 548: 111197. https://doi.org/10.1016/j.jtbi.2022.111197. Cite Download

Qin, Guangrong, Theo A. Knijnenburg, David L. Gibbs, Russell Moser, Raymond J. Monnat, Christopher J. Kemp, and Ilya Shmulevich. 2022. “A Functional Module States Framework Reveals Transcriptional States for Drug and Target Prediction.” Cell Reports 38 (3): 110269. https://doi.org/10.1016/j.celrep.2021.110269. Cite Download

Ramsbottom, Kerry A., Ananth Prakash, Yasset Perez Riverol, Oscar Martin Camacho, Maria-Jesus Martin, Juan Antonio Vizcaíno, Eric W. Deutsch, and Andrew R. Jones. 2022. “Method for Independent Estimation of the False Localization Rate for Phosphoproteomics.” Journal of Proteome Research 21 (7): 1603–15. https://doi.org/10.1021/acs.jproteome.1c00827. Cite

Riffle, Michael, Michael R. Hoopmann, Daniel Jaschob, Guo Zhong, Robert L. Moritz, Michael J. MacCoss, Trisha N. Davis, Nina Isoherranen, and Alex Zelter. 2022. “Discovery and Visualization of Uncharacterized Drug–Protein Adducts Using Mass Spectrometry.” Analytical Chemistry 94 (8): 3501–9. https://doi.org/10.1021/acs.analchem.1c04101. Cite Download

Roach, Jared C., John F. Hodes, Cory C. Funk, William R Shankle, David A. Merrill, Leroy Hood, and Jennifer Bramen. 2022. “Dense Data Enables 21th Century Clinical Trials.” Alzheimer’s & Dementia: Translational Research & Clinical Interventions 8 (1): e12297. https://doi.org/10.1002/trc2.12297. Cite Download

Schapiro, Denis, Clarence Yapp, Artem Sokolov, Sheila M. Reynolds, Yu-An Chen, Damir Sudar, Yubin Xie, et al. 2022. “MITI Minimum Information Guidelines for Highly Multiplexed Tissue Images.” Nature Methods 19 (3): 262–67. https://doi.org/10.1038/s41592-022-01415-4. Cite Download

Sherif, Shimaa, Jessica Roelands, William Mifsud, Eiman I. Ahmed, Christophe M. Raynaud, Darawan Rinchai, Abbirami Sathappan, et al. 2022. “The Immune Landscape of Solid Pediatric Tumors.” Journal of Experimental & Clinical Cancer Research: CR 41 (1): 199. https://doi.org/10.1186/s13046-022-02397-z. Cite