Department of Systems Biology

Displaying 351 - 400 of 444CSV
Demichev, V., Szyrwiel, L., Yu, F., Teo, G. C., Rosenberger, G., Niewienda, A., Ludwig, D., Decker, J., Kaspar-Schoenefeld, S., Lilley, K. S., Mülleder, M., Nesvizhskii, A. I., & Ralser, M. (2022). dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-31492-0
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Domingo-Relloso, A., Makhani, K., Riffo-Campos, A. L., Tellez-Plaza, M., Klein, K. O., Subedi, P., Zhao, J., Moon, K. A., Bozack, A. K., Haack, K., Goessler, W., Umans, J. G., Best, L. G., Zhang, Y., Herreros-Martinez, M., Glabonjat, R. A., Schilling, K., Galvez-Fernandez, M., Kent, J. W., … Navas-Acien, A. (2022). Arsenic Exposure, Blood DNA Methylation, and Cardiovascular Disease. Circulation Research, 131(2). https://doi.org/10.1161/circresaha.122.320991
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Feng, S., Rastogi, C., Loker, R., Glassford, W. J., Tomas Rube, H., Bussemaker, H. J., & Mann, R. S. (2022). Transcription factor paralogs orchestrate alternative gene regulatory networks by context-dependent cooperation with multiple cofactors. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-31501-2
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Yang, C., Dawulieti, J., Zhang, K., Cheng, C., Zhao, Y., Hu, H., Li, M., Zhang, M., Chen, L., Leong, K. W., & Shao, D. (2022). An Injectable Antibiotic Hydrogel that Scavenges Proinflammatory Factors for the Treatment of Severe Abdominal Trauma. Advanced Functional Materials, 32(27). Portico. https://doi.org/10.1002/adfm.202111698
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Pérez-Torres, E. J., Utkina-Sosunova, I., Mishra, V., Barbuti, P., De Planell-Saguer, M., Dermentzaki, G., Geiger, H., Basile, A. O., Robine, N., Fagegaltier, D., Politi, K. A., Rinchetti, P., Jackson-Lewis, V., Harms, M., Phatnani, H., Lotti, F., Przedborski, S., Phatnani, H., … Traynor, B. J. (2022). Retromer dysfunction in amyotrophic lateral sclerosis. Proceedings of the National Academy of Sciences, 119(26). https://doi.org/10.1073/pnas.2118755119
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Kenchappa, R. S., Dovas, A., Argenziano, M. G., Meyer, C. T., Stopfer, L. E., Banu, M. A., Pereira, B., Griffith, J., Mohammad, A., Talele, S., Haddock, A., Zarco, N., Elmquist, W., White, F., Quaranta, V., Sims, P., Canoll, P., & Rosenfeld, S. S. (2022). Activation of STAT3 through combined SRC and EGFR signaling drives resistance to a mitotic kinesin inhibitor in glioblastoma. Cell Reports, 39(12), 110991. https://doi.org/10.1016/j.celrep.2022.110991
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Feng, S., & Mann, R. S. (2022). SpyChIP identifies cell type-specific transcription factor occupancy from complex tissues. Proceedings of the National Academy of Sciences, 119(25). https://doi.org/10.1073/pnas.2122900119
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Myer, P. A., Kim, H., Blümel, A. M., Finnegan, E., Kel, A., Thompson, T. V., Greally, J. M., Prehn, J. HM., O’Connor, D. P., Friedman, R. A., Floratos, A., & Das, S. (2022). Master Transcription Regulators and Transcription Factors Regulate Immune-Associated Differences Between Patients of African and European Ancestry With Colorectal Cancer. Gastro Hep Advances, 1(3), 328–341. https://doi.org/10.1016/j.gastha.2022.01.004
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Alvarez, S., da Silva Almeida, A. C., Albero, R., Biswas, M., Barreto-Galvez, A., Gunning, T. S., Shaikh, A., Aparicio, T., Wendorff, A., Piovan, E., Van Vlierberghe, P., Gygi, S., Gautier, J., Madireddy, A., & A. Ferrando, A. (2022). Functional mapping of PHF6 complexes in chromatin remodeling, replication dynamics, and DNA repair. Blood, 139(23), 3418–3429. https://doi.org/10.1182/blood.2021014103
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Chait, M., Yilmaz, M. M., Shakil, S., Ku, A. W., Dogra, P., Connors, T. J., Szabo, P. A., Gray, J. I., Wells, S. B., Kubota, M., Matsumoto, R., Poon, M. M. L., Snyder, M. E., Baldwin, M. R., Sims, P. A., Saqi, A., Farber, D. L., & Weisberg, S. P. (2022). Immune and epithelial determinants of age-related risk and alveolar injury in fatal COVID-19. JCI Insight, 7(11). https://doi.org/10.1172/jci.insight.157608
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Webster Carrion, A., Wei, H.-J., McQuillan, N., Tazhibi, M., Kokossis, D., Berg, X., Minns, H., Zhang, X., Zhang, Z., Wang, J., Fernandez, E. C., Jan, C.-I., Padilla, O., Gartrell, R. D., Becher, O., Jr, J. H. G., Pavisic, J., Szalontay, L., Konofagou, E. E., … Wu, C.-C. (2022). MODL-24. Focused ultrasound-mediated blood-brain barrier opening and panobinostat in a thalamic syngeneic murine DMG model is feasible and safe. Neuro-Oncology, 24(Supplement_1), i174–i174. https://doi.org/10.1093/neuonc/noac079.647
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Li, Z., Ji, B. W., Dixit, P. D., Tchourine, K., Lien, E. C., Hosios, A. M., Abbott, K. L., Rutter, J. C., Westermark, A. M., Gorodetsky, E. F., Sullivan, L. B., Vander Heiden, M. G., & Vitkup, D. (2022). Cancer cells depend on environmental lipids for proliferation when electron acceptors are limited. Nature Metabolism, 4(6), 711–723. https://doi.org/10.1038/s42255-022-00588-8
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Middelhoff, M., Valenti, G., Tomassoni, L., Ochiai, Y., Belin, B., Takahashi, R., Malagola, E., Nienhüser, H., Finlayson, M., Hayakawa, Y., Zamechek, L. B., Renz, B. W., Westphalen, C. B., Quante, M., Margolis, K. G., Sims, P. A., Laise, P., Califano, A., Rao, M., … Wang, T. C. (2022). Adult enteric Dclk1-positive glial and neuronal cells reveal distinct responses to acute intestinal injury. American Journal of Physiology-Gastrointestinal and Liver Physiology, 322(6), G583–G597. https://doi.org/10.1152/ajpgi.00244.2021
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Fernández, E. C., Wang, J., Griffin, A., Minns, H., Wei, H.-J., Zhang, X., Szalontay, L., Mundi, P., Wu, C.-C., Gartrell, R., Zacharoulis, S., Califano, A., & Pavisic, J. (2022). DIPG-57. A systems biology approach to defining and targeting master regulator dependencies from bulk and single-Cell RNA-seq in diffuse midline glioma (DMG). Neuro-Oncology, 24(Supplement_1), i31–i32. https://doi.org/10.1093/neuonc/noac079.114
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Obradovic, A., Graves, D., Korrer, M., Wang, Y., Roy, S., Naveed, A., Xu, Y., Luginbuhl, A., Curry, J., Gibson, M., Idrees, K., Hurley, P., Jiang, P., Liu, X. S., Uppaluri, R., Drake, C. G., Califano, A., & Kim, Y. J. (2022). Immunostimulatory Cancer-Associated Fibroblast Subpopulations Can Predict Immunotherapy Response in Head and Neck Cancer. Clinical Cancer Research, 28(10), 2094–2109. https://doi.org/10.1158/1078-0432.ccr-21-3570
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Domínguez Conde, C., Xu, C., Jarvis, L. B., Rainbow, D. B., Wells, S. B., Gomes, T., Howlett, S. K., Suchanek, O., Polanski, K., King, H. W., Mamanova, L., Huang, N., Szabo, P. A., Richardson, L., Bolt, L., Fasouli, E. S., Mahbubani, K. T., Prete, M., Tuck, L., … Teichmann, S. A. (2022). Cross-tissue immune cell analysis reveals tissue-specific features in humans. Science, 376(6594). https://doi.org/10.1126/science.abl5197
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Jaiswal, A., Verma, A., Dannenfelser, R., Melssen, M., Tirosh, I., Izar, B., Kim, T.-G., Nirschl, C. J., Devi, K. S. P., Olson, W. C., Slingluff, C. L., Engelhard, V. H., Garraway, L., Regev, A., Minkis, K., Yoon, C. H., Troyanskaya, O., Elemento, O., Suárez-Fariñas, M., & Anandasabapathy, N. (2022). An activation to memory differentiation trajectory of tumor-infiltrating lymphocytes informs metastatic melanoma outcomes. Cancer Cell, 40(5), 524-544.e5. https://doi.org/10.1016/j.ccell.2022.04.005
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Moy, R. H., Nguyen, A., Loo, J. M., Yamaguchi, N., Kajba, C. M., Santhanam, B., Ostendorf, B. N., Wu, Y. G., Tavazoie, S., & Tavazoie, S. F. (2022). Functional genetic screen identifies ITPR3/calcium/RELB axis as a driver of colorectal cancer metastatic liver colonization. Developmental Cell, 57(9), 1146-1159.e7. https://doi.org/10.1016/j.devcel.2022.04.010
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Hu, X., Qiao, D., Kim, W., Moll, M., Balte, P. P., Lange, L. A., Bartz, T. M., Kumar, R., Li, X., Yu, B., Cade, B. E., Laurie, C. A., Sofer, T., Ruczinski, I., Nickerson, D. A., Muzny, D. M., Metcalf, G. A., Doddapaneni, H., Gabriel, S., … Manichaikul, A. (2022). Polygenic transcriptome risk scores for COPD and lung function improve cross-ethnic portability of prediction in the NHLBI TOPMed program. The American Journal of Human Genetics, 109(5), 857–870. https://doi.org/10.1016/j.ajhg.2022.03.007
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Willcox, J. A. L., Geiger, J. T., Morton, S. U., McKean, D., Quiat, D., Gorham, J. M., Tai, A. C., DePalma, S., Bernstein, D., Brueckner, M., Chung, W. K., Giardini, A., Goldmuntz, E., Kaltman, J. R., Kim, R., Newburger, J. W., Shen, Y., Srivastava, D., Tristani-Firouzi, M., … Seidman, C. E. (2022). Neither cardiac mitochondrial DNA variation nor copy number contribute to congenital heart disease risk. The American Journal of Human Genetics, 109(5), 961–966. https://doi.org/10.1016/j.ajhg.2022.03.011
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Cambuli, F., Foletto, V., Alaimo, A., De Felice, D., Gandolfi, F., Palumbieri, M. D., Zaffagni, M., Genovesi, S., Lorenzoni, M., Celotti, M., Bertossio, E., Mazzero, G., Bertossi, A., Bisio, A., Berardinelli, F., Antoccia, A., Gaspari, M., Barbareschi, M., Fiorentino, M., … Lunardi, A. (2022). Intra‐epithelial non‐canonical Activin A signaling safeguards prostate progenitor quiescence. EMBO Reports, 23(5). Portico. https://doi.org/10.15252/embr.202154049
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Ronaldson-Bouchard, K., Teles, D., Yeager, K., Tavakol, D. N., Zhao, Y., Chramiec, A., Tagore, S., Summers, M., Stylianos, S., Tamargo, M., Lee, B. M., Halligan, S. P., Abaci, E. H., Guo, Z., Jacków, J., Pappalardo, A., Shih, J., Soni, R. K., Sonar, S., … Vunjak-Novakovic, G. (2022). A multi-organ chip with matured tissue niches linked by vascular flow. Nature Biomedical Engineering, 6(4), 351–371. https://doi.org/10.1038/s41551-022-00882-6
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Skok Gibbs, C., Jackson, C. A., Saldi, G.-A., Tjärnberg, A., Shah, A., Watters, A., De Veaux, N., Tchourine, K., Yi, R., Hamamsy, T., Castro, D. M., Carriero, N., Gorissen, B. L., Gresham, D., Miraldi, E. R., & Bonneau, R. (2022). High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0. Bioinformatics, 38(9), 2519–2528. https://doi.org/10.1093/bioinformatics/btac117
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Iketani, S., Liu, L., Guo, Y., Liu, L., Chan, J. F.-W., Huang, Y., Wang, M., Luo, Y., Yu, J., Chu, H., Chik, K. K.-H., Yuen, T. T.-T., Yin, M. T., Sobieszczyk, M. E., Huang, Y., Yuen, K.-Y., Wang, H. H., Sheng, Z., & Ho, D. D. (2022). Antibody evasion properties of SARS-CoV-2 Omicron sublineages. Nature, 604(7906), 553–556. https://doi.org/10.1038/s41586-022-04594-4
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Cortes, J. R., Filip, I., Albero, R., Patiño-Galindo, J. A., Quinn, S. A., Lin, W.-H. W., Laurent, A. P., Shih, B. B., Brown, J. A., Cooke, A. J., Mackey, A., Einson, J., Zairis, S., Rivas-Delgado, A., Laginestra, M. A., Pileri, S., Campo, E., Bhagat, G., Ferrando, A. A., … Palomero, T. (2022). Oncogenic Vav1-Myo1f induces therapeutically targetable macrophage-rich tumor microenvironment in peripheral T cell lymphoma. Cell Reports, 39(3), 110695. https://doi.org/10.1016/j.celrep.2022.110695
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Mederacke, I., Filliol, A., Affo, S., Nair, A., Hernandez, C., Sun, Q., Hamberger, F., Brundu, F., Chen, Y., Ravichandra, A., Huebener, P., Anke, H., Shi, H., Martínez García de la Torre, R. A., Smith, J. R., Henderson, N. C., Vondran, F. W. R., Rothlin, C. V., Baehre, H., … Schwabe, R. F. (2022). The purinergic P2Y14 receptor links hepatocyte death to hepatic stellate cell activation and fibrogenesis in the liver. Science Translational Medicine, 14(639). https://doi.org/10.1126/scitranslmed.abe5795
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Snyder, M. E., Moghbeli, K., Bondonese, A., Craig, A., Popescu, I., Fan, L., Tabib, T., Lafyatis, R., Chen, K., Trejo Bittar, H. E., Lendermon, E., Pilewski, J., Johnson, B., Kilaru, S., Zhang, Y., Sanchez, P. G., Alder, J. K., Sims, P. A., & McDyer, J. F. (2022). Modulation of tissue resident memory T cells by glucocorticoids after acute cellular rejection in lung transplantation. Journal of Experimental Medicine, 219(4). https://doi.org/10.1084/jem.20212059
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Morton, S. U., Pereira, A. C., Quiat, D., Richter, F., Kitaygorodsky, A., Hagen, J., Bernstein, D., Brueckner, M., Goldmuntz, E., Kim, R. W., Lifton, R. P., Porter, G. A., Tristani-Firouzi, M., Chung, W. K., Roberts, A., Gelb, B. D., Shen, Y., Newburger, J. W., Seidman, J. G., & Seidman, C. E. (2022). Genome-Wide De Novo Variants in Congenital Heart Disease Are Not Associated With Maternal Diabetes or Obesity. Circulation: Genomic and Precision Medicine, 15(2). https://doi.org/10.1161/circgen.121.003500
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Garrido, A., Kim, E., Teijeiro, A., Sánchez Sánchez, P., Gallo, R., Nair, A., Matamala Montoya, M., Perna, C., Vicent, G. P., Muñoz, J., Campos-Olivas, R., Melms, J. C., Izar, B., Schwabe, R. F., & Djouder, N. (2022). Histone acetylation of bile acid transporter genes plays a critical role in cirrhosis. Journal of Hepatology, 76(4), 850–861. https://doi.org/10.1016/j.jhep.2021.12.019
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Galán-Díez, M., Borot, F., Ali, A. M., Zhao, J., Gil-Iturbe, E., Shan, X., Luo, N., Liu, Y., Huang, X.-P., Bisikirska, B., Labella, R., Kurland, I., Roth, B. L., Quick, M., Mukherjee, S., Rabadán, R., Carroll, M., Raza, A., & Kousteni, S. (2022). Subversion of Serotonin Receptor Signaling in Osteoblasts by Kynurenine Drives Acute Myeloid Leukemia. Cancer Discovery, 12(4), 1106–1127. https://doi.org/10.1158/2159-8290.cd-21-0692
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Xu, S., Sergeeva, A. P., Katsamba, P. S., Mannepalli, S., Bahna, F., Bimela, J., Zipursky, S. L., Shapiro, L., Honig, B., & Zinn, K. (2022). Affinity requirements for control of synaptic targeting and neuronal cell survival by heterophilic IgSF cell adhesion molecules. Cell Reports, 39(1), 110618. https://doi.org/10.1016/j.celrep.2022.110618
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McBee, R. M., Lucht, M., Mukhitov, N., Richardson, M., Srinivasan, T., Meng, D., Chen, H., Kaufman, A., Reitman, M., Munck, C., Schaak, D., Voigt, C., & Wang, H. H. (2021). Engineering living and regenerative fungal–bacterial biocomposite structures. Nature Materials, 21(4), 471–478. https://doi.org/10.1038/s41563-021-01123-y
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Tansey, W., Li, K., Zhang, H., Linderman, S. W., Rabadan, R., Blei, D. M., & Wiggins, C. H. (2021). Dose–response modeling in high-throughput cancer drug screenings: an end-to-end approach. Biostatistics, 23(2), 643–665. https://doi.org/10.1093/biostatistics/kxaa047
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Goodman, K. M., Katsamba, P. S., Rubinstein, R., Ahlsén, G., Bahna, F., Mannepalli, S., Dan, H., Sampogna, R. V., Shapiro, L., & Honig, B. (2022). How clustered protocadherin binding specificity is tuned for neuronal self-/nonself-recognition. ELife, 11. CLOCKSS. https://doi.org/10.7554/elife.72416
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Singh, H. N., Swarup, V., Dubey, N. K., Jha, N. K., Singh, A. K., Lo, W.-C., & Kumar, S. (2022). Differential Transcriptome Profiling Unveils Novel Deregulated Gene Signatures Involved in Pathogenesis of Alzheimer’s Disease. Biomedicines, 10(3), 611. https://doi.org/10.3390/biomedicines10030611
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Park, J., Foox, J., Hether, T., Danko, D. C., Warren, S., Kim, Y., Reeves, J., Butler, D. J., Mozsary, C., Rosiene, J., Shaiber, A., Afshin, E. E., MacKay, M., Rendeiro, A. F., Bram, Y., Chandar, V., Geiger, H., Craney, A., Velu, P., … Mason, C. E. (2022). System-wide transcriptome damage and tissue identity loss in COVID-19 patients. Cell Reports Medicine, 3(2), 100522. https://doi.org/10.1016/j.xcrm.2022.100522
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Cavassim, M. I. A., Baker, Z., Hoge, C., Schierup, M. H., Schumer, M., & Przeworski, M. (2022). PRDM9 losses in vertebrates are coupled to those of paralogs ZCWPW1 and ZCWPW2. Proceedings of the National Academy of Sciences, 119(9). https://doi.org/10.1073/pnas.2114401119
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Rashkovan, M., Albero, R., Gianni, F., Perez-Duran, P., Miller, H. I., Mackey, A. L., Paietta, E. M., Tallman, M. S., Rowe, J. M., Litzow, M. R., Wiernik, P. H., Luger, S., Sulis, M. L., Soni, R. K., & Ferrando, A. A. (2022). Intracellular Cholesterol Pools Regulate Oncogenic Signaling and Epigenetic Circuitries in Early T-cell Precursor Acute Lymphoblastic Leukemia. Cancer Discovery, 12(3), 856–871. https://doi.org/10.1158/2159-8290.cd-21-0551
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Shilo, S., Godneva, A., Rachmiel, M., Korem, T., Kolobkov, D., Karady, T., Bar, N., Wolf, B. C., Glantz-Gashai, Y., Cohen, M., Zuckerman Levin, N., Shehadeh, N., Gruber, N., Levran, N., Koren, S., Weinberger, A., Pinhas-Hamiel, O., & Segal, E. (2021). Prediction of Personal Glycemic Responses to Food for Individuals With Type 1 Diabetes Through Integration of Clinical and Microbial Data. Diabetes Care, 45(3), 502–511. https://doi.org/10.2337/dc21-1048
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Joseph, T. A., Chlenski, P., Litman, A., Korem, T., & Pe’er, I. (2022). Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reveals personalized growth rates. Genome Research, 32(3), 558–568. https://doi.org/10.1101/gr.275533.121
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Shilo, S., Godneva, A., Rachmiel, M., Korem, T., Bussi, Y., Kolobkov, D., Karady, T., Bar, N., Wolf, B. C., Glantz-Gashai, Y., Cohen, M., Levin, N. Z., Shehadeh, N., Gruber, N., Levran, N., Koren, S., Weinberger, A., Pinhas-Hamiel, O., & Segal, E. (2022). The Gut Microbiome of Adults With Type 1 Diabetes and Its Association With the Host Glycemic Control. Diabetes Care, 45(3), 555–563. https://doi.org/10.2337/dc21-1656
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