Publications

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

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

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

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

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

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

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

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, 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: A Retrospective Study of Hospitalized Adults,” 2022.02.02.22270287. https://www.medrxiv.org/content/10.1101/2022.02.02.22270287v1. 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

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, May. https://doi.org/10.1038/s41388-022-02330-w. Cite

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

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

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

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

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

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

Su, Yapeng, Dan Yuan, Daniel G. Chen, Rachel H. Ng, Kai Wang, Jongchan Choi, Sarah Li, et al. 2022. “Multiple Early Factors Anticipate Post-Acute COVID-19 Sequelae.” Cell 0 (0). https://doi.org/10.1016/j.cell.2022.01.014. Cite Download

Villani, Marco, Gianluca D’Addese, Stuart A. Kauffman, and Roberto Serra. 2022. “Attractor-Specific and Common Expression Values in Random Boolean Network Models (with a Preliminary Look at Single-Cell Data).” Entropy 24 (3): 311. https://doi.org/10.3390/e24030311. Cite Download

Xavier, Joao B., Jonathan M. Monk, Saugat Poudel, Charles J. Norsigian, Anand V. Sastry, Chen Liao, Jose Bento, et al. 2022. “Mathematical Models to Study the Biology of Pathogens and the Infectious Diseases They Cause.” IScience 25 (4). https://doi.org/10.1016/j.isci.2022.104079. Cite Download