Department of Systems Biology

Displaying 101 - 150 of 444CSV
Li, Y., Li, J., Li, W., Liang, S., Wei, W., Chu, J., Lai, J., Lin, Y., Chen, H., Su, J., Hu, X., Wang, G., Meng, J., Jiang, J., Ye, L., & An, S. (2024). Scm6A: A Fast and Low-cost Method for Quantifying m6A Modifications at the Single-cell Level. Genomics, Proteomics & Bioinformatics. https://doi.org/10.1093/gpbjnl/qzae039
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Malagola, E., Vasciaveo, A., Ochiai, Y., Kim, W., Zheng, B., Zanella, L., Wang, A. L. E., Middelhoff, M., Nienhüser, H., Deng, L., Wu, F., Waterbury, Q. T., Belin, B., LaBella, J., Zamechek, L. B., Wong, M. H., Li, L., Guha, C., Cheng, C.-W., … Wang, T. C. (2024). Isthmus progenitor cells contribute to homeostatic cellular turnover and support regeneration following intestinal injury. Cell, 187(12), 3056-3071.e17. https://doi.org/10.1016/j.cell.2024.05.004
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Regunath, K., Fomin, V., Liu, Z., Wang, P., Hoque, M., Tian, B., Rabadan, R., & Prives, C. (2024). Systematic Characterization of p53-Regulated Long Noncoding RNAs across Human Cancers Reveals Remarkable Heterogeneity among Different Tumor Types. Molecular Cancer Research, 22(6), 555–571. https://doi.org/10.1158/1541-7786.mcr-23-0295
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Buschur, K. L., Pottinger, T. D., Vogel-Claussen, J., Powell, C. A., Aguet, F., Allen, N. B., Ardlie, K., Bluemke, D. A., Durda, P., Hermann, E. A., Hoffman, E. A., Lima, J. A. C., Liu, Y., Malinsky, D., Manichaikul, A., Motahari, A., Post, W. S., Prince, M. R., Rich, S. S., … Barr, R. G. (2024). Peripheral Blood Mononuclear Cell Gene Expression Associated with Pulmonary Microvascular Perfusion: The Multi-Ethnic Study of Atherosclerosis Chronic Obstructive Pulmonary Disease. Annals of the American Thoracic Society, 21(6), 884–894. https://doi.org/10.1513/annalsats.202305-417oc
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Wright, J. R., Astrovskaya, I., Barns, S. D., Goler, A., Zhou, X., Shu, C., Snyder, L. G., Han, B., Aarrestad, A., Abbeduto, L., Aberbach, G., Aberle, S., Adegbite, A., Adeniji, D., Aguilar, M., Ahlers, K., Albright, C., Alessandri, M., Algaze, Z., … Chung, W. K. (2024). Return of genetic research results in 21,532 individuals with autism. Genetics in Medicine, 101202. https://doi.org/10.1016/j.gim.2024.101202
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Spisak, N., de Manuel, M., Milligan, W., Sella, G., & Przeworski, M. (2024). The clock-like accumulation of germline and somatic mutations can arise from the interplay of DNA damage and repair. PLOS Biology, 22(6), e3002678. https://doi.org/10.1371/journal.pbio.3002678
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Walsh, Z. H., Shah, P., Kothapalli, N., Shah, S. B., Nikolenyi, G., Brodtman, D. Z., Leuzzi, G., Rogava, M., Mu, M., Ho, P., Abuzaid, S., Vasan, N., AlQuraishi, M., Milner, J. D., Ciccia, A., Melms, J. C., & Izar, B. (2024). Mapping variant effects on anti-tumor hallmarks of primary human T cells with base-editing screens. Nature Biotechnology. https://doi.org/10.1038/s41587-024-02235-x
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Zhao, H., Petrey, D., Murray, D., & Honig, B. (2024). ZEPPI: Proteome-scale sequence-based evaluation of protein–protein interaction models. Proceedings of the National Academy of Sciences, 121(21). https://doi.org/10.1073/pnas.2400260121
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Rosenberger, G., Li, W., Turunen, M., He, J., Subramaniam, P. S., Pampou, S., Griffin, A. T., Karan, C., Kerwin, P., Murray, D., Honig, B., Liu, Y., & Califano, A. (2024). Network-based elucidation of colon cancer drug resistance mechanisms by phosphoproteomic time-series analysis. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-47957-3
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Recinos, Y., Ustianenko, D., Yeh, Y.-T., Wang, X., Jacko, M., Yesantharao, L. V., Wu, Q., & Zhang, C. (2024). CRISPR-dCas13d-based deep screening of proximal and distal splicing-regulatory elements. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-47140-8
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Riboldi, G. M., Faravelli, I., Rinchetti, P., & Lotti, F. (2023). SMN post-translational modifications in spinal muscular atrophy. Frontiers in Cellular Neuroscience, 17. https://doi.org/10.3389/fncel.2023.1092488
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Nakagawa, S., Carnevali, D., Tan, X., Alvarez, M. J., Parfitt, D.-E., Di Vicino, U., Arumugam, K., Shin, W., Aranda, S., Normanno, D., Sebastian-Perez, R., Cannatá, C., Cortes, P., Neguembor, M. V., Shen, M. M., Califano, A., & Cosma, M. P. (2024). The Wnt-dependent master regulator NKX1-2 controls mouse pre-implantation development. Stem Cell Reports, 19(5), 689–709. https://doi.org/10.1016/j.stemcr.2024.04.004
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Ho, C.-L. C., Gilbert, M. B., Urtecho, G., Lee, H., Drew, D. A., Klempner, S. J., Cho, J. S., Ryan, T. J., Rustgi, N., Lee, H., Lee, J., Caraballo, A., Magicheva-Gupta, M. V., Rios, C., Shin, A. E., Tseng, Y.-Y., Davis, J. L., Chung, D. C., Chan, A. T., … Ryeom, S. (2024). Stool Protein Mass Spectrometry Identifies Biomarkers for Early Detection of Diffuse-type Gastric Cancer. Cancer Prevention Research, OF1–OF16. https://doi.org/10.1158/1940-6207.capr-23-0449
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Schreidah, C. M., Gordon, E. R., Adeuyan, O., Chen, C., Lapolla, B. A., Kent, J. A., Reynolds, G. B., Fahmy, L. M., Weng, C., Tatonetti, N. P., Chase, H. S., Pe’er, I., & Geskin, L. J. (2024). Current status of artificial intelligence methods for skin cancer survival analysis: a scoping review. Frontiers in Medicine, 11. https://doi.org/10.3389/fmed.2024.1243659
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Cheng, Y. L., Banu, M. A., Zhao, W., Rosenfeld, S. S., Canoll, P., & Sims, P. A. (2024). Multiplexed single-cell lineage tracing of mitotic kinesin inhibitor resistance in glioblastoma. Cell Reports, 43(5), 114139. https://doi.org/10.1016/j.celrep.2024.114139
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Wu, L. W., Tao, J. J., McDonnell, D., & Izar, B. (2024). Pseudoprogression in a patient with metastatic melanoma treated with PD-1 and LAG-3 inhibition. Melanoma Research, 34(4), 382–385. https://doi.org/10.1097/cmr.0000000000000974
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Haq, I., Ngo, J. C., Roy, N., Pan, R. L., Nawsheen, N., Chiu, R., Zhang, Y., Fujita, M., Soni, R. K., Wu, X., Bennett, D. A., Menon, V., Olah, M., & Sher, F. (2024). An integrated toolkit for human microglia functional genomics. Stem Cell Research & Therapy, 15(1). https://doi.org/10.1186/s13287-024-03700-9
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Wasko, U. N., Jiang, J., Dalton, T. C., Curiel-Garcia, A., Edwards, A. C., Wang, Y., Lee, B., Orlen, M., Tian, S., Stalnecker, C. A., Drizyte-Miller, K., Menard, M., Dilly, J., Sastra, S. A., Palermo, C. F., Hasselluhn, M. C., Decker-Farrell, A. R., Chang, S., Jiang, L., … Olive, K. P. (2024). Tumour-selective activity of RAS-GTP inhibition in pancreatic cancer. Nature, 629(8013), 927–936. https://doi.org/10.1038/s41586-024-07379-z
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Zhu, Y., Cai, S. S., Ma, J., Cheng, L., Wei, C., Aggarwal, A., Toh, W. H., Shin, C., Shen, R., Kong, J., Mao, S. A., Lao, Y.-H., Leong, K. W., & Mao, H.-Q. (2024). Optimization of lipid nanoparticles for gene editing of the liver via intraduodenal delivery. Biomaterials, 308, 122559. https://doi.org/10.1016/j.biomaterials.2024.122559
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Papachristodoulou, A., Heidegger, I., Virk, R. K., Di Bernardo, M., Kim, J. Y., Laplaca, C., Picech, F., Schäfer, G., De Castro, G. J., Hibshoosh, H., Loda, M., Klocker, H., Rubin, M. A., Zheng, T., Benson, M. C., McKiernan, J. M., Dutta, A., & Abate-Shen, C. (2024). Metformin Overcomes the Consequences of NKX3.1 Loss to Suppress Prostate Cancer Progression. European Urology, 85(4), 361–372. https://doi.org/10.1016/j.eururo.2023.07.016
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Liu, Z., Mela, A., Argenziano, M. G., Banu, M. A., Furnari, J., Kotidis, C., Sperring, C. P., Humala, N., Mahajan, A., Bruce, J. N., Canoll, P., & Sims, P. A. (2024). Single-cell analysis of 5-aminolevulinic acid intraoperative labeling specificity for glioblastoma. Journal of Neurosurgery, 140(4), 968–978. https://doi.org/10.3171/2023.7.jns23122
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Dermentzaki, G., Furlan, M., Tanaka, I., Leonardi, T., Rinchetti, P., Passos, P. M. S., Bastos, A., Ayala, Y. M., Hanna, J. H., Przedborski, S., Bonanomi, D., Pelizzola, M., & Lotti, F. (2024). Depletion of Mettl3 in cholinergic neurons causes adult-onset neuromuscular degeneration. Cell Reports, 43(4), 113999. https://doi.org/10.1016/j.celrep.2024.113999
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Kim, H. S., Xiao, Y., Chen, X., He, S., Im, J., Willner, M. J., Finlayson, M. O., Xu, C., Zhu, H., Choi, S. J., Mosharov, E. V., Kim, H., Xu, B., & Leong, K. W. (2024). Chronic Opioid Treatment Arrests Neurodevelopment and Alters Synaptic Activity in Human Midbrain Organoids. Advanced Science, 11(21). Portico. https://doi.org/10.1002/advs.202400847
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Ma, M., Ganapathi, M., Zheng, Y., Tan, K.-L., Kanca, O., Bove, K. E., Quintanilla, N., Sag, S. O., Temel, S. G., LeDuc, C. A., McPartland, A. J., Pereira, E. M., Shen, Y., Hagen, J., Thomas, C. P., Nguyen Galván, N. T., Pan, X., Lu, S., Rosenfeld, J. A., … Bellen, H. J. (2024). Homozygous missense variants in YKT6 result in loss of function and are associated with developmental delay, with or without severe infantile liver disease and risk for hepatocellular carcinoma. Genetics in Medicine, 26(7), 101125. https://doi.org/10.1016/j.gim.2024.101125
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Musini, A., Singh, H. N., Vulise, J., Pammi, S. S. S., & Archana Giri. (2024). Quercetin’s antibiofilm effectiveness against drug resistant Staphylococcus aureus and its validation by in silico modeling. Research in Microbiology, 175(3), 104091. https://doi.org/10.1016/j.resmic.2023.104091
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Feng, H., Lu, X.-J., Maji, S., Liu, L., Ustianenko, D., Rudnick, N. D., & Zhang, C. (2024). Structure-based prediction and characterization of photo-crosslinking in native protein–RNA complexes. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-46429-y
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Einson, J., Minaeva, M., Rafi, F., & Lappalainen, T. (2024). The impact of genetically controlled splicing on exon inclusion and protein structure. PLOS ONE, 19(3), e0291960. https://doi.org/10.1371/journal.pone.0291960
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Arriaga, J. M., Ronaldson-Bouchard, K., Picech, F., Nunes de Almeida, F., Afari, S., Chhouri, H., Vunjak-Novakovic, G., & Abate-Shen, C. (2024). In vivo genome-wide CRISPR screening identifies CITED2 as a driver of prostate cancer bone metastasis. Oncogene, 43(17), 1303–1315. https://doi.org/10.1038/s41388-024-02995-5
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Fogarty, E. C., Schechter, M. S., Lolans, K., Sheahan, M. L., Veseli, I., Moore, R. M., Kiefl, E., Moody, T., Rice, P. A., Yu, M. K., Mimee, M., Chang, E. B., Ruscheweyh, H.-J., Sunagawa, S., Mclellan, S. L., Willis, A. D., Comstock, L. E., & Eren, A. M. (2024). A cryptic plasmid is among the most numerous genetic elements in the human gut. Cell, 187(5), 1206-1222.e16. https://doi.org/10.1016/j.cell.2024.01.039
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Solfisburg, Q. S., Baldini, F., Baldwin-Hunter, B., Austin, G. I., Lee, H. H., Park, H., Freedberg, D. E., Lightdale, C. J., Korem, T., & Abrams, J. A. (2023). The Salivary Microbiome and Predicted Metabolite Production Are Associated with Barrett’s Esophagus and High-Grade Dysplasia or Adenocarcinoma. Cancer Epidemiology, Biomarkers & Prevention, 33(3), 371–380. https://doi.org/10.1158/1055-9965.epi-23-0652
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Gelsinger, D. R., Vo, P. L. H., Klompe, S. E., Ronda, C., Wang, H. H., & Sternberg, S. H. (2024). Bacterial genome engineering using CRISPR-associated transposases. Nature Protocols, 19(3), 752–790. https://doi.org/10.1038/s41596-023-00927-3
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Hoge, C., de Manuel, M., Mahgoub, M., Okami, N., Fuller, Z., Banerjee, S., Baker, Z., McNulty, M., Andolfatto, P., Macfarlan, T. S., Schumer, M., Tzika, A. C., & Przeworski, M. (2024). Patterns of recombination in snakes reveal a tug-of-war between PRDM9 and promoter-like features. Science, 383(6685). https://doi.org/10.1126/science.adj7026
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Sepich-Poore, G. D., McDonald, D., Kopylova, E., Guccione, C., Zhu, Q., Austin, G., Carpenter, C., Fraraccio, S., Wandro, S., Kosciolek, T., Janssen, S., Metcalf, J. L., Song, S. J., Kanbar, J., Miller-Montgomery, S., Heaton, R., Mckay, R., Patel, S. P., Swafford, A. D., … Knight, R. (2024). Robustness of cancer microbiome signals over a broad range of methodological variation. Oncogene, 43(15), 1127–1148. https://doi.org/10.1038/s41388-024-02974-w
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Xiao, F., Zhang, X., Morton, S. U., Kim, S. W., Fan, Y., Gorham, J. M., Zhang, H., Berkson, P. J., Mazumdar, N., Cao, Y., Chen, J., Hagen, J., Liu, X., Zhou, P., Richter, F., Shen, Y., Ward, T., Gelb, B. D., Seidman, J. G., … Pu, W. T. (2024). Functional dissection of human cardiac enhancers and noncoding de novo variants in congenital heart disease. Nature Genetics, 56(3), 420–430. https://doi.org/10.1038/s41588-024-01669-y
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Yang, K., Alkhamis, O., Canoura, J., Bryant, A., Gong, E. M., Barbu, M., Taylor, S., Nikic, D., Banerjee, S., Xiao, Y., Stojanovic, M. N., & Landry, D. W. (2024). Exploring the Landscape of Aptamers: From Cross-Reactive to Selective to Specific, High-Affinity Receptors for Cocaine. JACS Au, 4(2), 760–770. https://doi.org/10.1021/jacsau.3c00781
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Hasselluhn, M. C., Decker-Farrell, A. R., Vlahos, L., Thomas, D. H., Curiel-Garcia, A., Maurer, H. C., Wasko, U. N., Tomassoni, L., Sastra, S. A., Palermo, C. F., Dalton, T. C., Ma, A., Li, F., Tolosa, E. J., Hibshoosh, H., Fernandez-Zapico, M. E., Muir, A., Califano, A., & Olive, K. P. (2023). Tumor Explants Elucidate a Cascade of Paracrine SHH, WNT, and VEGF Signals Driving Pancreatic Cancer Angiosuppression. Cancer Discovery, 14(2), 348–361. https://doi.org/10.1158/2159-8290.cd-23-0240
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Ricaurte, D., Huang, Y., Sheth, R. U., Gelsinger, D. R., Kaufman, A., & Wang, H. H. (2024). High-throughput transcriptomics of 409 bacteria–drug pairs reveals drivers of gut microbiota perturbation. Nature Microbiology, 9(2), 561–575. https://doi.org/10.1038/s41564-023-01581-x
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Leuzzi, G., Vasciaveo, A., Taglialatela, A., Chen, X., Firestone, T. M., Hickman, A. R., Mao, W., Thakar, T., Vaitsiankova, A., Huang, J.-W., Cuella-Martin, R., Hayward, S. B., Kesner, J. S., Ghasemzadeh, A., Nambiar, T. S., Ho, P., Rialdi, A., Hebrard, M., Li, Y., … Ciccia, A. (2024). SMARCAL1 is a dual regulator of innate immune signaling and PD-L1 expression that promotes tumor immune evasion. Cell, 187(4), 861-881.e32. https://doi.org/10.1016/j.cell.2024.01.008
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Stokes, G., Li, Z., Talaba, N., Genthe, W., Brix, M. B., Pham, B., Wienhold, M. D., Sandok, G., Hernan, R., Wynn, J., Tang, H., Tabima, D. M., Rodgers, A., Hacker, T. A., Chesler, N. C., Zhang, P., Murad, R., Yuan, J. X.-J., Shen, Y., … McCulley, D. J. (2024). Rescuing lung development through embryonic inhibition of histone acetylation. Science Translational Medicine, 16(732). https://doi.org/10.1126/scitranslmed.adc8930
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Chi, C.-W., Lao, Y.-H., Ahmed, A. H. R., He, S., Merghoub, T., Leong, K. W., & Wang, S. (2024). Enabling continuous immune cell recirculation on a microfluidic array to study immunotherapeutic interactions in a recapitulated tumour microenvironment. Lab on a Chip, 24(3), 396–407. https://doi.org/10.1039/d3lc00662j
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Rogava, M., Aprati, T. J., Chi, W.-Y., Melms, J. C., Hug, C., Davis, S. H., Earlie, E. M., Chung, C., Deshmukh, S. K., Wu, S., Sledge, G., Tang, S., Ho, P., Amin, A. D., Caprio, L., Gurjao, C., Tagore, S., Ngo, B., Lee, M. J., … Izar, B. (2024). Loss of Pip4k2c confers liver-metastatic organotropism through insulin-dependent PI3K-AKT pathway activation. Nature Cancer, 5(3), 433–447. https://doi.org/10.1038/s43018-023-00704-x
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