Department of Systems Biology

Displaying 301 - 350 of 444CSV
Cohen, A. O., Woo, S.-H., Zhang, J., Cho, J., Ruiz, M. E., Gong, J., Du, R., Yarygina, O., Jafri, D. Z., Bachelor, M. A., Finlayson, M. O., Soni, R. K., Hayden, M. S., & Owens, D. M. (2022). Tbc1d10c is a selective, constitutive suppressor of the CD8 T-cell anti-tumor response. OncoImmunology, 11(1). https://doi.org/10.1080/2162402x.2022.2141011
Publication Date
Reglero, C., Dieck, C. L., Zask, A., Forouhar, F., Laurent, A. P., Lin, W.-H. W., Albero, R., Miller, H. I., Ma, C., Gastier-Foster, J. M., Loh, M. L., Tong, L., Stockwell, B. R., Palomero, T., & Ferrando, A. A. (2022). Pharmacologic Inhibition of NT5C2 Reverses Genetic and Nongenetic Drivers of 6-MP Resistance in Acute Lymphoblastic Leukemia. Cancer Discovery, 12(11), 2646–2665. https://doi.org/10.1158/2159-8290.cd-22-0010
Publication Date
Zhang, H., Xu, M. S., Fan, X., Chung, W. K., & Shen, Y. (2022). Predicting functional effect of missense variants using graph attention neural networks. Nature Machine Intelligence, 4(11), 1017–1028. https://doi.org/10.1038/s42256-022-00561-w
Publication Date
Li, T., Akinade, T., Zhou, J., Wang, H., Tong, Q., He, S., Rinebold, E., Valencia Salazar, L. E., Bhansali, D., Zhong, Y., Ruan, J., Du, J., Dalerba, P., & Leong, K. W. (2022). Therapeutic Nanocarriers Inhibit Chemotherapy‐Induced Breast Cancer Metastasis. Advanced Science, 9(33). Portico. https://doi.org/10.1002/advs.202203949
Publication Date
Coutinho, D. F., Mundi, P. S., Marks, L. J., Burke, C., Ortiz, M. V., Diolaiti, D., Bird, L., Vallance, K. L., Ibáñez, G., You, D., Long, M., Rosales, N., Grunn, A., Ndengu, A., Siddiquee, A., Gaviria, E. S., Rainey, A. R., Fazlollahi, L., Hosoi, H., … Dela Cruz, F. S. (2022). Validation of a non-oncogene encoded vulnerability to exportin 1 inhibition in pediatric renal tumors. Med, 3(11), 774-791.e7. https://doi.org/10.1016/j.medj.2022.09.002
Publication Date
Wendorff, A. A., Aidan Quinn, S., Alvarez, S., Brown, J. A., Biswas, M., Gunning, T., Palomero, T., & Ferrando, A. A. (2022). Epigenetic reversal of hematopoietic stem cell aging in Phf6-knockout mice. Nature Aging, 2(11), 1008–1023. https://doi.org/10.1038/s43587-022-00304-x
Publication Date
Chowdhury, R., Bouatta, N., Biswas, S., Floristean, C., Kharkar, A., Roy, K., Rochereau, C., Ahdritz, G., Zhang, J., Church, G. M., Sorger, P. K., & AlQuraishi, M. (2022). Single-sequence protein structure prediction using a language model and deep learning. Nature Biotechnology, 40(11), 1617–1623. https://doi.org/10.1038/s41587-022-01432-w
Publication Date
Hazra, R., Brine, L., Garcia, L., Benz, B., Chirathivat, N., Shen, M. M., Wilkinson, J. E., Lyons, S. K., & Spector, D. L. (2022). Platr4 is an early embryonic lncRNA that exerts its function downstream on cardiogenic mesodermal lineage commitment. Developmental Cell, 57(21), 2450-2468.e7. https://doi.org/10.1016/j.devcel.2022.10.002
Publication Date
Spinazzi, E. F., Argenziano, M. G., Upadhyayula, P. S., Banu, M. A., Neira, J. A., Higgins, D. M. O., Wu, P. B., Pereira, B., Mahajan, A., Humala, N., Al-Dalahmah, O., Zhao, W., Save, A. V., Gill, B. J. A., Boyett, D. M., Marie, T., Furnari, J. L., Sudhakar, T. D., Stopka, S. A., … Bruce, J. N. (2022). Chronic convection-enhanced delivery of topotecan for patients with recurrent glioblastoma: a first-in-patient, single-centre, single-arm, phase 1b trial. The Lancet Oncology, 23(11), 1409–1418. https://doi.org/10.1016/s1470-2045(22)00599-x
Publication Date
Filliol, A., Saito, Y., Nair, A., Dapito, D. H., Yu, L.-X., Ravichandra, A., Bhattacharjee, S., Affo, S., Fujiwara, N., Su, H., Sun, Q., Savage, T. M., Wilson-Kanamori, J. R., Caviglia, J. M., Chin, L., Chen, D., Wang, X., Caruso, S., Kang, J. K., … Schwabe, R. F. (2022). Opposing roles of hepatic stellate cell subpopulations in hepatocarcinogenesis. Nature, 610(7931), 356–365. https://doi.org/10.1038/s41586-022-05289-6
Publication Date
Hamerlynck, L. M., Bischoff, A. J., Rogers, J. R., Roberts, T. D., Dai, J., Geissler, P. L., Francis, M. B., & Ginsberg, N. S. (2022). Static Disorder has Dynamic Impact on Energy Transport in Biomimetic Light-Harvesting Complexes. The Journal of Physical Chemistry B, 126(40), 7981–7991. https://doi.org/10.1021/acs.jpcb.2c06614
Publication Date
Tabansky, I., Tanaka, A. J., Wang, J., Zhang, G., Dujmovic, I., Mader, S., Jeganathan, V., DeAngelis, T., Funaro, M., Harel, A., Messina, M., Shabbir, M., Nursey, V., DeGouvia, W., Laurent, M., Blitz, K., Jindra, P., Gudesblatt, M., … Stern, J. N. H. (2022). Rare variants and HLA haplotypes associated in patients with neuromyelitis optica spectrum disorders. Frontiers in Immunology, 13. https://doi.org/10.3389/fimmu.2022.900605
Publication Date
Shen, Y., Singh, J., Sah, B., Chen, Z., Ha, W., Henzler, C., Su, T., Xie, L., Deng, Y., Li, G., Guo, H., Hibshoosh, H., & Liu, L. (2022). The Histone Demethylase HR Suppresses Breast Cancer Development through Enhanced CELF2 Tumor Suppressor Activity. Cancers, 14(19), 4648. https://doi.org/10.3390/cancers14194648
Publication Date
Zhong, G., & Shen, Y. (2022). Statistical models of the genetic etiology of congenital heart disease. Current Opinion in Genetics & Development, 76, 101967. https://doi.org/10.1016/j.gde.2022.101967
Publication Date
Rube, H. T., Rastogi, C., Feng, S., Kribelbauer, J. F., Li, A., Becerra, B., Melo, L. A. N., Do, B. V., Li, X., Adam, H. H., Shah, N. H., Mann, R. S., & Bussemaker, H. J. (2022). Prediction of protein–ligand binding affinity from sequencing data with interpretable machine learning. Nature Biotechnology, 40(10), 1520–1527. https://doi.org/10.1038/s41587-022-01307-0
Publication Date
Blackett, J. W., Sun, Y., Purpura, L., Margolis, K. G., Elkind, M. S. V., O’Byrne, S., Wainberg, M., Abrams, J. A., Wang, H. H., Chang, L., & Freedberg, D. E. (2022). DECREASED GUT MICROBIOME TRYPTOPHAN METABOLISM AND SEROTONERGIC SIGNALING IN PATIENTS WITH PERSISTENT MENTAL HEALTH AND GASTROINTESTINAL SYMPTOMS AFTER COVID-19. Clinical and Translational Gastroenterology. https://doi.org/10.14309/ctg.0000000000000524
Publication Date
Lipman, A. R., Fan, X., Shen, Y., & Chung, W. K. (2022). Clinical and genetic characterization of CACNA1A‐related disease. Clinical Genetics, 102(4), 288–295. Portico. https://doi.org/10.1111/cge.14180
Publication Date
Ketcham, A., Freddolino, P. L., & Tavazoie, S. (2022). Intracellular acidification is a hallmark of thymineless death in E. coli. PLOS Genetics, 18(10), e1010456. https://doi.org/10.1371/journal.pgen.1010456
Publication Date
Masuda, I., Yamaki, Y., Detroja, R., Tagore, S., Moore, H., Maharjan, S., Nakano, Y., Christian, T., Matsubara, R., Lowe, T. M., Frenkel-Morgenstern, M., & Hou, Y.-M. (2022). tRNA methylation resolves codon usage bias at the limit of cell viability. Cell Reports, 41(4), 111539. https://doi.org/10.1016/j.celrep.2022.111539
Publication Date
Malina, S., Cizin, D., & Knowles, D. A. (2022). Deep mendelian randomization: Investigating the causal knowledge of genomic deep learning models. PLOS Computational Biology, 18(10), e1009880. https://doi.org/10.1371/journal.pcbi.1009880
Publication Date
Khan, S., Patel, S. P., Shoushtari, A. N., Ambrosini, G., Cremers, S., Lee, S., Franks, L., Singh-Kandah, S., Hernandez, S., Sender, N., Vuolo, K., Nesson, A., Mundi, P., Izar, B., Schwartz, G. K., & Carvajal, R. D. (2022). Intermittent MEK inhibition for the treatment of metastatic uveal melanoma. Frontiers in Oncology, 12. https://doi.org/10.3389/fonc.2022.975643
Publication Date
Huang, H., Fang, Y., Jiang, M., Zhang, Y., Biermann, J., Melms, J. C., Danielsson, J. A., Yang, Y., Qiang, L., Liu, J., Zhou, Y., Wang, M., Hu, Z., Wang, T. C., Saqi, A., Sun, J., Matsumoto, I., Cardoso, W. V., Emala, C. W., … Que, J. (2022). Contribution of Trp63CreERT2-labeled cells to alveolar regeneration is independent of tuft cells. ELife, 11. CLOCKSS. https://doi.org/10.7554/elife.78217
Publication Date
Kawano, Y., Edwards, M., Huang, Y., Bilate, A. M., Araujo, L. P., Tanoue, T., Atarashi, K., Ladinsky, M. S., Reiner, S. L., Wang, H. H., Mucida, D., Honda, K., & Ivanov, I. I. (2022). Microbiota imbalance induced by dietary sugar disrupts immune-mediated protection from metabolic syndrome. Cell, 185(19), 3501-3519.e20. https://doi.org/10.1016/j.cell.2022.08.005
Publication Date
Trolle, J., McBee, R. M., Kaufman, A., Pinglay, S., Berger, H., German, S., Liu, L., Shen, M. J., Guo, X., Martin, J. A., Pacold, M. E., Jones, D. R., Boeke, J. D., & Wang, H. H. (2022). Resurrecting essential amino acid biosynthesis in mammalian cells. ELife, 11. CLOCKSS. https://doi.org/10.7554/elife.72847
Publication Date
Zhou, X., Feliciano, P., Shu, C., Wang, T., Astrovskaya, I., Hall, J. B., Obiajulu, J. U., Wright, J. R., Murali, S. C., Xu, S. X., Brueggeman, L., Thomas, T. R., Marchenko, O., Fleisch, C., Barns, S. D., Snyder, L. G., Han, B., Chang, T. S., Turner, T. N., … Chung, W. K. (2022). Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes. Nature Genetics, 54(9), 1305–1319. https://doi.org/10.1038/s41588-022-01148-2
Publication Date
Peart, N. J., Johnson, T. A., Lee, S., Sears, M. J., Yang, F., Quesnel-Vallières, M., Feng, H., Recinos, Y., Barash, Y., Zhang, C., Hermann, B. P., Wang, P. J., Geyer, C. B., & Carstens, R. P. (2022). The germ cell-specific RNA binding protein RBM46 is essential for spermatogonial differentiation in mice. PLOS Genetics, 18(9), e1010416. https://doi.org/10.1371/journal.pgen.1010416
Publication Date
Ganapathi, M., Friocourt, G., Gueguen, N., Friederich, M. W., Le Gac, G., Okur, V., Loaëc, N., Ludwig, T., Ka, C., Tanji, K., Marcorelles, P., Theodorou, E., Lignelli‐Dipple, A., Voisset, C., Walker, M. A., Briere, L. C., Bourhis, A., Blondel, M., LeDuc, C., … Chung, W. K. (2022). A homozygous splice variant in ATP5PO, disrupts mitochondrial complex V function and causes Leigh syndrome in two unrelated families. Journal of Inherited Metabolic Disease, 45(5), 996–1012. Portico. https://doi.org/10.1002/jimd.12526
Publication Date
Biswas, S., Shahriar, S., Giangreco, N. P., Arvanitis, P., Winkler, M., Tatonetti, N. P., Brunken, W. J., Cutforth, T., & Agalliu, D. (2022). Mural Wnt/β-catenin signaling regulates Lama2 expression to promote neurovascular unit maturation. Development, 149(17). https://doi.org/10.1242/dev.200610
Publication Date
Tu, Z., Zhu, Y., Xiao, Y., Chen, J., Shannon, S., Zhang, F., Li, Z., Zhou, J., Hu, H., Ho, T., Gao, W., Shao, D., & Leong, K. W. (2022). Scavenging Tumor‐Derived Small Extracellular Vesicles by Functionalized 2D Materials to Inhibit Tumor Regrowth and Metastasis Following Radiotherapy. Advanced Functional Materials, 32(39). Portico. https://doi.org/10.1002/adfm.202205663
Publication Date
Deng, Y., Bartosovic, M., Ma, S., Zhang, D., Kukanja, P., Xiao, Y., Su, G., Liu, Y., Qin, X., Rosoklija, G. B., Dwork, A. J., Mann, J. J., Xu, M. L., Halene, S., Craft, J. E., Leong, K. W., Boldrini, M., Castelo-Branco, G., & Fan, R. (2022). Spatial profiling of chromatin accessibility in mouse and human tissues. Nature, 609(7926), 375–383. https://doi.org/10.1038/s41586-022-05094-1
Publication Date
Fu, J., Wang, Z., Martinez, M., Jiao, W., Frangaj, K., Jones, R., Guo, X. V., Zhang, Y., Kuo, W.-I., Obradovic, A., Ma, W., Rogers, K., Kato, T., Shen, Y., & Sykes, M. (2022). 425.3: Single-Cell Immune Profiling of Human Intestinal Allografts Reveals Differential Phenotypes of Alloreactive T-Cell Clones in Quiescent vs Chronically Rejecting Allografts. Transplantation, 106(9S), S485–S485. https://doi.org/10.1097/01.tp.0000888048.23424.42
Publication Date
Boni, N., Shapiro, L., Honig, B., Wu, Y., & Rubinstein, R. (2022). On the formation of ordered protein assemblies in cell–cell interfaces. Proceedings of the National Academy of Sciences, 119(34). https://doi.org/10.1073/pnas.2206175119
Publication Date
Giangreco, N. P., & Tatonetti, N. P. (2022). A database of pediatric drug effects to evaluate ontogenic mechanisms from child growth and development. Med, 3(8), 579-595.e7. https://doi.org/10.1016/j.medj.2022.06.001
Publication Date
Ji, J. S., Liu, L., Shu, C., Yan, L. L., & Zeng, Y. (2021). Sex Difference and Interaction of SIRT1 and FOXO3 Candidate Longevity Genes on Life Expectancy: A 10-Year Prospective Longitudinal Cohort Study. The Journals of Gerontology: Series A, 77(8), 1557–1563. https://doi.org/10.1093/gerona/glab378
Publication Date
Glinos, D. A., Garborcauskas, G., Hoffman, P., Ehsan, N., Jiang, L., Gokden, A., Dai, X., Aguet, F., Brown, K. L., Garimella, K., Bowers, T., Costello, M., Ardlie, K., Jian, R., Tucker, N. R., Ellinor, P. T., Harrington, E. D., Tang, H., Snyder, M., … Cummings, B. B. (2022). Transcriptome variation in human tissues revealed by long-read sequencing. Nature, 608(7922), 353–359. https://doi.org/10.1038/s41586-022-05035-y
Publication Date
de Manuel, M., Wu, F. L., & Przeworski, M. (2022). A paternal bias in germline mutation is widespread in amniotes and can arise independently of cell division numbers. ELife, 11. CLOCKSS. https://doi.org/10.7554/elife.80008
Publication Date
Schoenfeld, D. A., Zhou, R., Zairis, S., Su, W., Steinbach, N., Mathur, D., Bansal, A., Zachem, A. L., Tavarez, B., Hasson, D., Bernstein, E., Rabadan, R., & Parsons, R. (2022). Loss of PBRM1 Alters Promoter Histone Modifications and Activates ALDH1A1 to Drive Renal Cell Carcinoma. Molecular Cancer Research, 20(8), 1193–1207. https://doi.org/10.1158/1541-7786.mcr-21-1039
Publication Date
Harimoto, T., Hahn, J., Chen, Y.-Y., Im, J., Zhang, J., Hou, N., Li, F., Coker, C., Gray, K., Harr, N., Chowdhury, S., Pu, K., Nimura, C., Arpaia, N., Leong, K. W., & Danino, T. (2022). A programmable encapsulation system improves delivery of therapeutic bacteria in mice. Nature Biotechnology, 40(8), 1259–1269. https://doi.org/10.1038/s41587-022-01244-y
Publication Date
Alvarez-Breckenridge, C., Markson, S. C., Stocking, J. H., Nayyar, N., Lastrapes, M., Strickland, M. R., Kim, A. E., de Sauvage, M., Dahal, A., Larson, J. M., Mora, J. L., Navia, A. W., Klein, R. H., Kuter, B. M., Gill, C. M., Bertalan, M., Shaw, B., Kaplan, A., Subramanian, M., … Carter, S. L. (2022). Microenvironmental Landscape of Human Melanoma Brain Metastases in Response to Immune Checkpoint Inhibition. Cancer Immunology Research, 10(8), 996–1012. https://doi.org/10.1158/2326-6066.cir-21-0870
Publication Date
Karn, V., Sandhya, S., Hsu, W., Parashar, D., Singh, H. N., Jha, N. K., Gupta, S., Dubey, N. K., & Kumar, S. (2022). CRISPR/Cas9 system in breast cancer therapy: advancement, limitations and future scope. Cancer Cell International, 22(1). https://doi.org/10.1186/s12935-022-02654-3
Publication Date
Chung, W. K., Berg, J. S., Botkin, J. R., Brenner, S. E., Brosco, J. P., Brothers, K. B., Currier, R. J., Gaviglio, A., Kowtoniuk, W. E., Olson, C., Lloyd‐Puryear, M., Saarinen, A., Sahin, M., Shen, Y., Sherr, E. H., Watson, M. S., & Hu, Z. (2022). Newborn screening for neurodevelopmental diseases: Are we there yet? American Journal of Medical Genetics Part C: Seminars in Medical Genetics, 190(2), 222–230. Portico. https://doi.org/10.1002/ajmg.c.31988
Publication Date
Zhong, G., Ahimaz, P., Edwards, N. A., Hagen, J. J., Faure, C., Lu, Q., Kingma, P., Middlesworth, W., Khlevner, J., El Fiky, M., Schindel, D., Fialkowski, E., Kashyap, A., Forlenza, S., Kenny, A. P., Zorn, A. M., Shen, Y., & Chung, W. K. (2022). Identification and validation of candidate risk genes in endocytic vesicular trafficking associated with esophageal atresia and tracheoesophageal fistulas. Human Genetics and Genomics Advances, 3(3), 100107. https://doi.org/10.1016/j.xhgg.2022.100107
Publication Date
Biermann, J., Melms, J. C., Amin, A. D., Wang, Y., Caprio, L. A., Karz, A., Tagore, S., Barrera, I., Ibarra-Arellano, M. A., Andreatta, M., Fullerton, B. T., Gretarsson, K. H., Sahu, V., Mangipudy, V. S., Nguyen, T. T. T., Nair, A., Rogava, M., Ho, P., Koch, P. D., … Izar, B. (2022). Dissecting the treatment-naive ecosystem of human melanoma brain metastasis. Cell, 185(14), 2591-2608.e30. https://doi.org/10.1016/j.cell.2022.06.007
Publication Date