Department of Systems Biology

Displaying 151 - 200 of 444CSV
Weng, C., Yu, F., Yang, D., Poeschla, M., Liggett, L. A., Jones, M. G., Qiu, X., Wahlster, L., Caulier, A., Hussmann, J. A., Schnell, A., Yost, K. E., Koblan, L. W., Martin-Rufino, J. D., Min, J., Hammond, A., Ssozi, D., Bueno, R., Mallidi, H., … Sankaran, V. G. (2024). Deciphering cell states and genealogies of human haematopoiesis. Nature, 627(8003), 389–398. https://doi.org/10.1038/s41586-024-07066-z
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Galanti, M., Patiño-Galindo, J. A., Filip, I., Morita, H., Galianese, A., Youssef, M., Comito, D., Ligon, C., Lane, B., Matienzo, N., Ibrahim, S., Tagne, E., Shittu, A., Elliott, O., Perea-Chamblee, T., Natesan, S., Rosenbloom, D. S., Shaman, J., & Rabadan, R. (2024). Virome Data Explorer: A web resource to longitudinally explore respiratory viral infections, their interactions with other pathogens and host transcriptomic changes in over 100 people. PLOS Biology, 22(1), e3002089. https://doi.org/10.1371/journal.pbio.3002089
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Chunarkar-Patil, P., Kaleem, M., Mishra, R., Ray, S., Ahmad, A., Verma, D., Bhayye, S., Dubey, R., Singh, H., & Kumar, S. (2024). Anticancer Drug Discovery Based on Natural Products: From Computational Approaches to Clinical Studies. Biomedicines, 12(1), 201. https://doi.org/10.3390/biomedicines12010201
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Ehsan, N., Kotis, B. M., Castel, S. E., Song, E. J., Mancuso, N., & Mohammadi, P. (2024). Haplotype-aware modeling of cis-regulatory effects highlights the gaps remaining in eQTL data. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-44710-8
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Shih, B. B., Ma, C., Cortes, J. R., Reglero, C., Miller, H., Quinn, S. A., Albero, R., Laurent, A. P., Mackey, A., Ferrando, A. A., Geskin, L., & Palomero, T. (2024). Romidepsin and Afatinib Abrogate Jak–Signal Transducer and Activator of Transcription Signaling and Elicit Synergistic Antitumor Effects in Cutaneous T-Cell Lymphoma. Journal of Investigative Dermatology, 144(7), 1579-1589.e8. https://doi.org/10.1016/j.jid.2023.12.010
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Giacomini, G., Piquet, S., Chevallier, O., Dabin, J., Bai, S.-K., Kim, B., Siddaway, R., Raught, B., Coyaud, E., Shan, C.-M., Reid, R. J. D., Toda, T., Rothstein, R., Barra, V., Wilhelm, T., Hamadat, S., Bertin, C., Crane, A., Dubois, F., … Polo, S. E. (2024). Aberrant DNA repair reveals a vulnerability in histone H3.3-mutant brain tumors. Nucleic Acids Research, 52(5), 2372–2388. https://doi.org/10.1093/nar/gkad1257
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Kumar, D., Gurrapu, S., Wang, Y., Bae, S.-Y., Pandey, P. R., Chen, H., Mondal, J., Han, H., Wu, C.-J., Karaiskos, S., Yang, F., Sahin, A., Wistuba, I. I., Gao, J., Tripathy, D., Gao, H., Izar, B., & Giancotti, F. G. (2024). LncRNA Malat1 suppresses pyroptosis and T cell-mediated killing of incipient metastatic cells. Nature Cancer, 5(2), 262–282. https://doi.org/10.1038/s43018-023-00695-9
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Pakula, H., Omar, M., Carelli, R., Pederzoli, F., Fanelli, G. N., Pannellini, T., Socciarelli, F., Van Emmenis, L., Rodrigues, S., Fidalgo-Ribeiro, C., Nuzzo, P. V., Brady, N. J., Dinalankara, W., Jere, M., Valencia, I., Saladino, C., Stone, J., Unkenholz, C., Garner, R., … Loda, M. (2024). Distinct mesenchymal cell states mediate prostate cancer progression. Nature Communications, 15(1). https://doi.org/10.1038/s41467-023-44210-1
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Kasela, S., Aguet, F., Kim-Hellmuth, S., Brown, B. C., Nachun, D. C., Tracy, R. P., Durda, P., Liu, Y., Taylor, K. D., Johnson, W. C., Van Den Berg, D., Gabriel, S., Gupta, N., Smith, J. D., Blackwell, T. W., Rotter, J. I., Ardlie, K. G., Manichaikul, A., Rich, S. S., … Lappalainen, T. (2024). Interaction molecular QTL mapping discovers cellular and environmental modifiers of genetic regulatory effects. The American Journal of Human Genetics, 111(1), 133–149. https://doi.org/10.1016/j.ajhg.2023.11.013
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Rashidi, A., Billingham, L. K., Zolp, A., Chia, T., Silvers, C., Katz, J. L., Park, C. H., Delay, S., Boland, L., Geng, Y., Markwell, S. M., Dmello, C., Arrieta, V. A., Zilinger, K., Jacob, I. M., Lopez-Rosas, A., Hou, D., Castro, B., Steffens, A. M., … Miska, J. (2024). Myeloid cell-derived creatine in the hypoxic niche promotes glioblastoma growth. Cell Metabolism, 36(1), 62-77.e8. https://doi.org/10.1016/j.cmet.2023.11.013
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Zhao, H., Wu, H., Guseman, A., Abeykoon, D., Camara, C. M., Dalal, Y., Fushman, D., & Papoian, G. A. (2024). The role of cryptic ancestral symmetry in histone folding mechanisms across Eukarya and Archaea. PLOS Computational Biology, 20(1), e1011721. https://doi.org/10.1371/journal.pcbi.1011721
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Chung, W., Ziegler, A., Koval-Burt, C., Kay, D., Suchy, S., Bergtrup, A., Langley, K., Amendola, L., Boyd, B., Bradley, J., Brandt, T., Cohen, L., Coffey, A., Devaney, J., Dygulska, B., Friedman, B., Fuleihan, R., Gyimah, A., Hernan, R., … Caggana, M. (2024). O35: Feasibility of expanded newborn screening using genome sequencing for early actionable conditions in a diverse city. Genetics in Medicine Open, 2, 101369. https://doi.org/10.1016/j.gimo.2024.101369
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Bhansali, D., Akinade, T., Li, T., Zhong, Y., Liu, F., Huang, H., Tu, Z., Devey, E. A., Zhu, Y., Jensen, D. D., & Leong, K. W. (2023). Comparative Analysis of Nucleic Acid-Binding Polymers as Potential Anti-Inflammatory Nanocarriers. Pharmaceutics, 16(1), 10. https://doi.org/10.3390/pharmaceutics16010010
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Altorki, N. K., Walsh, Z. H., Melms, J. C., Port, J. L., Lee, B. E., Nasar, A., Spinelli, C., Caprio, L., Rogava, M., Ho, P., Christos, P. J., Saxena, A., Elemento, O., Bhinder, B., Ager, C., Amin, A. D., Sanfilippo, N. J., Mittal, V., Borczuk, A. C., … McGraw, T. E. (2023). Neoadjuvant durvalumab plus radiation versus durvalumab alone in stages I–III non-small cell lung cancer: survival outcomes and molecular correlates of a randomized phase II trial. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-44195-x
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Su, J., Reynier, J.-B., Fu, X., Zhong, G., Jiang, J., Escalante, R. S., Wang, Y., Aparicio, L., Izar, B., Knowles, D. A., & Rabadan, R. (2023). Smoother: a unified and modular framework for incorporating structural dependency in spatial omics data. Genome Biology, 24(1). https://doi.org/10.1186/s13059-023-03138-x
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Melms, J. C., Ho, P., Rogava, M., & Izar, B. (2023). From patient tissue correlates to molecular mechanisms of cancer immune evasion: the emerging role of CD58 and PD-L1 co-regulation via CMTM6. Genes & Immunity, 25(1), 82–84. https://doi.org/10.1038/s41435-023-00224-9
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Stokes, M. E., Vasciaveo, A., Small, J. C., Zask, A., Reznik, E., Smith, N., Wang, Q., Daniels, J., Forouhar, F., Rajbhandari, P., Califano, A., & Stockwell, B. R. (2024). Subtype-selective prenylated isoflavonoids disrupt regulatory drivers of MYCN-amplified cancers. Cell Chemical Biology, 31(4), 805-819.e9. https://doi.org/10.1016/j.chembiol.2023.11.007
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Smith, N., Reznik, E., Bisikirska, B., Polychronidou, V., Wang, Q., Zask, A., Forouhar, F., Califano, A., & Stockwell, B. R. (2023). Kinases Controlling Stability of the Oncogenic MYCN Protein. ACS Medicinal Chemistry Letters, 14(12), 1664–1672. https://doi.org/10.1021/acsmedchemlett.3c00274
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Morgado-Palacin, L., Brown, J. A., Martinez, T. F., Garcia-Pedrero, J. M., Forouhar, F., Quinn, S. A., Reglero, C., Vaughan, J., Heydary, Y. H., Donaldson, C., Rodriguez-Perales, S., Allonca, E., Granda-Diaz, R., Fernandez, A. F., Fraga, M. F., Kim, A. L., Santos-Juanes, J., Owens, D. M., Rodrigo, J. P., … Ferrando, A. A. (2023). The TINCR ubiquitin-like microprotein is a tumor suppressor in squamous cell carcinoma. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-36713-8
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Sturm, G., Karan, K. R., Monzel, A. S., Santhanam, B., Taivassalo, T., Bris, C., Ware, S. A., Cross, M., Towheed, A., Higgins-Chen, A., McManus, M. J., Cardenas, A., Lin, J., Epel, E. S., Rahman, S., Vissing, J., Grassi, B., Levine, M., Horvath, S., … Picard, M. (2023). OxPhos defects cause hypermetabolism and reduce lifespan in cells and in patients with mitochondrial diseases. Communications Biology, 6(1). https://doi.org/10.1038/s42003-022-04303-x
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Liao, J., Shenhav, L., Urban, J. A., Serrano, M., Zhu, B., Buck, G. A., & Korem, T. (2023). Microdiversity of the vaginal microbiome is associated with preterm birth. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-40719-7
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Shi, P., Murphy, M. R., Aparicio, A. O., Kesner, J. S., Fang, Z., Chen, Z., Trehan, A., Guo, Y., & Wu, X. (2023). Collateral activity of the CRISPR/RfxCas13d system in human cells. Communications Biology, 6(1). https://doi.org/10.1038/s42003-023-04708-2
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Austin, G. I., Park, H., Meydan, Y., Seeram, D., Sezin, T., Lou, Y. C., Firek, B. A., Morowitz, M. J., Banfield, J. F., Christiano, A. M., Pe’er, I., Uhlemann, A.-C., Shenhav, L., & Korem, T. (2023). Contamination source modeling with SCRuB improves cancer phenotype prediction from microbiome data. Nature Biotechnology, 41(12), 1820–1828. https://doi.org/10.1038/s41587-023-01696-w
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Buschur, K. L., Riley, C., Saferali, A., Castaldi, P., Zhang, G., Aguet, F., Ardlie, K. G., Durda, P., Craig Johnson, W., Kasela, S., Liu, Y., Manichaikul, A., Rich, S. S., Rotter, J. I., Smith, J., Taylor, K. D., Tracy, R. P., Lappalainen, T., Graham Barr, R., … Benos, P. V. (2023). Distinct COPD subtypes in former smokers revealed by gene network perturbation analysis. Respiratory Research, 24(1). https://doi.org/10.1186/s12931-023-02316-6
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Dmello, C., Zhao, J., Chen, L., Gould, A., Castro, B., Arrieta, V. A., Zhang, D. Y., Kim, K.-S., Kanojia, D., Zhang, P., Miska, J., Yeeravalli, R., Habashy, K., Saganty, R., Kang, S. J., Fares, J., Liu, C., Dunn, G., Bartom, E., … Sonabend, A. M. (2023). Checkpoint kinase 1/2 inhibition potentiates anti-tumoral immune response and sensitizes gliomas to immune checkpoint blockade. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-36878-2
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Al-Dalahmah, O., Argenziano, M. G., Kannan, A., Mahajan, A., Furnari, J., Paryani, F., Boyett, D., Save, A., Humala, N., Khan, F., Li, J., Lu, H., Sun, Y., Tuddenham, J. F., Goldberg, A. R., Dovas, A., Banu, M. A., Sudhakar, T., Bush, E., … Canoll, P. (2023). Re-convolving the compositional landscape of primary and recurrent glioblastoma reveals prognostic and targetable tissue states. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-38186-1
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Zhong, G., Choi, Y. A., & Shen, Y. (2023). VBASS enables integration of single cell gene expression data in Bayesian association analysis of rare variants. Communications Biology, 6(1). https://doi.org/10.1038/s42003-023-05155-9
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Kostyrko, K., Román, M., Lee, A. G., Simpson, D. R., Dinh, P. T., Leung, S. G., Marini, K. D., Kelly, M. R., Broyde, J., Califano, A., Jackson, P. K., & Sweet-Cordero, E. A. (2023). UHRF1 is a mediator of KRAS driven oncogenesis in lung adenocarcinoma. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-39591-2
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Brockmann, L., Tran, A., Huang, Y., Edwards, M., Ronda, C., Wang, H. H., & Ivanov, I. I. (2023). Intestinal microbiota-specific Th17 cells possess regulatory properties and suppress effector T cells via c-MAF and IL-10. Immunity, 56(12), 2719-2735.e7. https://doi.org/10.1016/j.immuni.2023.11.003
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Xiao, Y., Fang, H., Zhu, Y., Zhou, J., Dai, Z., Wang, H., Xia, Z., Tu, Z., & Leong, K. W. (2023). Multifunctional Cationic Hyperbranched Polyaminoglycosides that Target Multiple Mediators for Severe Abdominal Trauma Management. Advanced Science, 11(1). Portico. https://doi.org/10.1002/advs.202305273
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Wen, K., Dai, W., Meng, X., Lin, Q., Wei, J., Tong, L., Taylor, S. K., Rudchenko, S. A., Stojanovic, M. N., Kalantarov, G., & Trakht, I. (2024). Rapid isolation of anti-idiotype aptamers for quantification of human monoclonal antibodies against SARS-CoV-2 spike protein. Biosensors and Bioelectronics, 246, 115842. https://doi.org/10.1016/j.bios.2023.115842
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In, G. K., Ribeiro, J. R., Yin, J., Xiu, J., Bustos, M. A., Ito, F., Chow, F., Zada, G., Hwang, L., Salama, A. K. S., Park, S. J., Moser, J. C., Darabi, S., Domingo-Musibay, E., Ascierto, M. L., Margolin, K., Lutzky, J., Gibney, G. T., Atkins, M. B., … VanderWalde, A. M. (2023). Multi-omic profiling reveals discrepant immunogenic properties and a unique tumor microenvironment among melanoma brain metastases. Npj Precision Oncology, 7(1). https://doi.org/10.1038/s41698-023-00471-z
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Postler, T. S., Wang, A., Brundu, F. G., Wang, P., Wu, Z., Butler, K. E., Grinberg-Bleyer, Y., Krishnareddy, S., Lagana, S. M., Saqi, A., Oeckinghaus, A., Rabadan, R., & Ghosh, S. (2023). A pan-cancer analysis implicates human NKIRAS1 as a tumor-suppressor gene. Proceedings of the National Academy of Sciences, 120(46). https://doi.org/10.1073/pnas.2312595120
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Cherng, H.-J. J., Yang, X., Yancey, R., Gordillo, C. A., Piorczynski, T. B., Chan, H. T., Ofori, K. N., Bhagat, G., Califano, A., Pro, B., Booher, K., Amengual, J. E., Reshef, R., & Sina, A. A. I. (2023). Methylated Whole Genome Cell-Free DNA Sequencing before Chimeric Antigen Receptor T-Cell Therapy for Large B-Cell Lymphoma Predicts Treatment Outcomes. Blood, 142(Supplement 1), 4371–4371. https://doi.org/10.1182/blood-2023-178376
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Lin, W.-H. W., Rodriguez Cortes, J., Aitken, M., Reglero, C., Laurent, A., Cooke, A., Belver, L., Bhagat, G., Rabadan, R., Ferrando, A. A., & Palomero, T. (2023). Role of the S1P Signaling Pathway in the Pathogenesis of Angioimmunoblastic T-Cell Lymphoma. Blood, 142(Supplement 1), 526–526. https://doi.org/10.1182/blood-2023-174090
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Schreidah, C. M., DeStephano, D. M., Pan, S. S., Wang, S., Shen, H., Ta, C. N., Reynolds, G. B., Fahmy, L. M., Gordon, E. R., Adeuyan, O., Kwinta, B. D., Stonesifer, C. J., Chan, W. H., Choi, J., Duvic, M., Gallardo, F., Girardi, M., Guitart, J., Kim, Y. H., … Geskin, L. J. (2023). Machine Learning-Based Survival Analysis Reveals Prognostic Clinical and Genetic Insights for Patients with Cutaneous T-Cell Lymphoma. Blood, 142(Supplement 1), 1715–1715. https://doi.org/10.1182/blood-2023-190775
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Chernak, B., Galan-Diez, M., Ali, A. M., Cuesta-Dominguez, A., Chen, Z., Koehnke, T., Majeti, R., Carroll, M., Raza, A., & Kousteni, S. (2023). Serum Amyloid A1 (SAA1) Secreted By the Stromal Microenvironment Drives Malignant Clonal Proliferation in Myelodysplastic Syndromes (MDS) and Acute Myeloid Leukemia (AML). Blood, 142(Supplement 1), 4118–4118. https://doi.org/10.1182/blood-2023-174485
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Hawley, J. E., Obradovic, A. Z., Dallos, M. C., Lim, E. A., Runcie, K., Ager, C. R., McKiernan, J., Anderson, C. B., Decastro, G. J., Weintraub, J., Virk, R., Lowy, I., Hu, J., Chaimowitz, M. G., Guo, X. V., Zhang, Y., Haffner, M. C., Worley, J., Stein, M. N., … Drake, C. G. (2023). Anti-PD-1 immunotherapy with androgen deprivation therapy induces robust immune infiltration in metastatic castration-sensitive prostate cancer. Cancer Cell, 41(11), 1972-1988.e5. https://doi.org/10.1016/j.ccell.2023.10.006
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Angelini, E. D., Yang, J., Balte, P. P., Hoffman, E. A., Manichaikul, A. W., Sun, Y., Shen, W., Austin, J. H. M., Allen, N. B., Bleecker, E. R., Bowler, R., Cho, M. H., Cooper, C. S., Couper, D., Dransfield, M. T., Garcia, C. K., Han, M. K., Hansel, N. N., Hughes, E., … Barr, R. G. (2023). Pulmonary emphysema subtypes defined by unsupervised machine learning on CT scans. Thorax, 78(11), 1067–1079. https://doi.org/10.1136/thorax-2022-219158
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Wang, Q., Guo, Y., Liu, L., Schwanz, L. T., Li, Z., Nair, M. S., Ho, J., Zhang, R. M., Iketani, S., Yu, J., Huang, Y., Qu, Y., Valdez, R., Lauring, A. S., Huang, Y., Gordon, A., Wang, H. H., Liu, L., & Ho, D. D. (2023). Antigenicity and receptor affinity of SARS-CoV-2 BA.2.86 spike. Nature, 624(7992), 639–644. https://doi.org/10.1038/s41586-023-06750-w
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Li, T., Ferraro, N., Strober, B. J., Aguet, F., Kasela, S., Arvanitis, M., Ni, B., Wiel, L., Hershberg, E., Ardlie, K., Arking, D. E., Beer, R. L., Brody, J., Blackwell, T. W., Clish, C., Gabriel, S., Gerszten, R., Guo, X., Gupta, N., … Montgomery, S. B. (2023). The functional impact of rare variation across the regulatory cascade. Cell Genomics, 3(10), 100401. https://doi.org/10.1016/j.xgen.2023.100401
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