Publications

2022

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
Kwasniewski, Miroslaw, Urszula Korotko, Karolina Chwialkowska, Magdalena Niemira, Jerzy Jaroszewicz, Barbara Sobala-Szczygiel, Beata Puzanowska, et al. 2022. “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. https://doi.org/10.1111/all.15524. Cite
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
Piekos, Samantha N., Nathan D. Price, Leroy Hood, and Jennifer J. Hadlock. 2022. “The Impact of Maternal SARS-CoV-2 Infection and COVID-19 Vaccination on Maternal-Fetal Outcomes.” Reproductive Toxicology (Elmsford, N.Y.), S0890-6238(22)00153-8. https://doi.org/10.1016/j.reprotox.2022.10.003. Cite
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