Research output per year
Research output per year
- 1 - 50 out of 189 results
Search results
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2024
Intercellular communication atlas reveals Oprm1 as a neuroprotective factor for retinal ganglion cells
Qian, C., Xin, Y., Qi, C., Wang, H., Dong, B. C., Zack, D. J., Blackshaw, S., Hattar, S., Zhou, F. Q. & Qian, J., Dec 2024, In: Nature communications. 15, 1, 2206.Research output: Contribution to journal › Article › peer-review
Open Access -
Multimodal Phenomap of Stargardt Disease Integrating Structural, Psychophysical, and Electrophysiologic Measures of Retinal Degeneration
Abousy, M., Antonio-Aguirre, B., Aziz, K., Hu, M. W., Qian, J. & Singh, M. S., Jan 1 2024, In: Ophthalmology Science. 4, 1, 100327.Research output: Contribution to journal › Article › peer-review
Open Access -
2023
Astrocyte ensheathment of calyx-forming axons of the auditory brainstem precedes accelerated expression of myelin genes and myelination by oligodendrocytes
Heller, D. T., Kolson, D. R., Brandebura, A. N., Amick, E. M., Wan, J., Ramadan, J., Holcomb, P. S., Liu, S., Deerinck, T. J., Ellisman, M. H., Qian, J., Mathers, P. H. & Spirou, G. A., 2023, (Accepted/In press) In: Journal of Comparative Neurology.Research output: Contribution to journal › Article › peer-review
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CellAnn: a comprehensive, super-fast, and user-friendly single-cell annotation web server
Lyu, P., Zhai, Y., Li, T. & Qian, J., Sep 1 2023, In: Bioinformatics. 39, 9, btad521.Research output: Contribution to journal › Article › peer-review
Open Access -
Common and divergent gene regulatory networks control injury-induced and developmental neurogenesis in zebrafish retina
Lyu, P., Iribarne, M., Serjanov, D., Zhai, Y., Hoang, T., Campbell, L. J., Boyd, P., Palazzo, I., Nagashima, M., Silva, N. J., Hitchcock, P. F., Qian, J., Hyde, D. R. & Blackshaw, S., Dec 2023, In: Nature communications. 14, 1, 8477.Research output: Contribution to journal › Article › peer-review
Open Access -
Discovery and characterization of cross-reactive intrahepatic antibodies in severe alcoholic hepatitis
Ahmadi, A. R., Song, G., Gao, T., Ma, J., Han, X., Hu, M. W., Cameron, A. M., Wesson, R. N., Philosophe, B., Ottmann, S., King, E., Gurakar, A., Qi, L., Peiffer, B., Burdick, J., Anders, R., Zhou, Z., Lu, H., Feng, D., Chen, C. S., & 4 others, 2023, In: eLife. 12, RP86678.Research output: Contribution to journal › Article › peer-review
Open Access -
IKKβ Inhibition Attenuates Epithelial Mesenchymal Transition of Human Stem Cell-Derived Retinal Pigment Epithelium
Sripathi, S. R., Hu, M. W., Turaga, R. C., Mikeasky, R., Satyanarayana, G., Cheng, J., Duan, Y., Maruotti, J., Wahlin, K. J., Berlinicke, C. A., Qian, J., Esumi, N. & Zack, D. J., Apr 2023, In: Cells. 12, 8, 1155.Research output: Contribution to journal › Article › peer-review
Open Access -
Increased LCN2 (lipocalin 2) in the RPE decreases autophagy and activates inflammasome-ferroptosis processes in a mouse model of dry AMD
Gupta, U., Ghosh, S., Wallace, C. T., Shang, P., Xin, Y., Nair, A. P., Yazdankhah, M., Strizhakova, A., Ross, M. A., Liu, H., Hose, S., Stepicheva, N. A., Chowdhury, O., Nemani, M., Maddipatla, V., Grebe, R., Das, M., Lathrop, K. L., Sahel, J. A., Zigler, J. S., & 6 others, 2023, In: Autophagy. 19, 1, p. 92-111 20 p.Research output: Contribution to journal › Article › peer-review
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Mitophagy initiates retrograde mitochondrial-nuclear signaling to guide retinal pigment cell heterogeneity
Datta, S., Cano, M., Satyanarayana, G., Liu, T., Wang, L., Wang, J., Cheng, J., Itoh, K., Sharma, A., Bhutto, I., Kannan, R., Qian, J., Sinha, D. & Handa, J. T., 2023, In: Autophagy. 19, 3, p. 966-983 18 p.Research output: Contribution to journal › Article › peer-review
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Neuronal Histone Methyltransferase EZH2 Regulates Neuronal Morphogenesis, Synaptic Plasticity, and Cognitive Behavior in Mice
Zhang, M., Zhang, Y., Xu, Q., Crawford, J., Qian, C., Wang, G. H., Qian, J., Dong, X. Z., Pletnikov, M. V., Liu, C. M. & Zhou, F. Q., Oct 2023, In: Neuroscience Bulletin. 39, 10, p. 1512-1532 21 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Single-cell transcriptome analysis of xenotransplanted human retinal organoids defines two migratory cell populations of nonretinal origin
Liu, Y. V., Santiago, C. P., Sogunro, A., Konar, G. J., Hu, M. W., McNally, M. M., Lu, Y. C., Flores-Bellver, M., Aparicio-Domingo, S., Li, K. V., Li, Z. L., Agakishiev, D., Hadyniak, S. E., Hussey, K. A., Creamer, T. J., Orzolek, L. D., Teng, D., Canto Soler, M., Qian, J., Jiang, Z., & 3 others, May 9 2023, In: Stem Cell Reports. 18, 5, p. 1138-1154 17 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Targeting hypoxia-inducible factors with 32-134D safely and effectively treats diabetic eye disease in mice
Zhang, J., Sharma, D., Dinabandhu, A., Sanchez, J., Applewhite, B., Jee, K., Deshpande, M., Flores-Bellver, M., Hu, M. W., Guo, C., Salman, S., Hwang, Y., Anders, N., Rudek, M., Qian, J., Canto Soler, M., Semenza, G. L., Montaner, S. & Sodhi, A., Jul 3 2023, In: Journal of Clinical Investigation. 133, 13, e163290.Research output: Contribution to journal › Article › peer-review
Open Access -
Transcriptomic comparison of two selective retinal cell ablation paradigms in zebrafish reveals shared and cell-specific regenerative responses
Emmerich, K., Walker, S. L., Wang, G., White, D. T., Ceisel, A., Wang, F., Teng, Y., Chunawala, Z., Graziano, G., Nimmagadda, S., Saxena, M. T., Qian, J. & Mumm, J. S., Oct 11 2023, In: PLoS genetics. 19, 10, e1010905.Research output: Contribution to journal › Article › peer-review
Open Access -
URINARY METABOLOMICS OF CENTRAL SEROUS CHORIORETINOPATHY
Meyerle, C. B., Lyu, P., Qian, J., Freund, K. B., Hafiz, G., Handa, J. T. & Semba, R. D., Mar 1 2023, In: Retina. 43, 3, p. 396-401 6 p.Research output: Contribution to journal › Article › peer-review
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2022
Aqueous proteins help predict the response of patients with neovascular age-related macular degeneration to anti-VEGF therapy
Cao, X., Sanchez, J. C., Dinabandhu, A., Guo, C., Patel, T. P., Yang, Z., Hu, M. W., Chen, L., Wang, Y., Malik, D., Jee, K., Daoud, Y. J., Handa, J. T., Zhang, H., Qian, J., Montaner, S. & Sodhi, A., Jan 18 2022, In: Journal of Clinical Investigation. 132, 2, 144469.Research output: Contribution to journal › Article › peer-review
Open Access -
Cell-specific cis-regulatory elements and mechanisms of non-coding genetic disease in human retina and retinal organoids
Thomas, E. D., Timms, A. E., Giles, S., Harkins-Perry, S., Lyu, P., Hoang, T., Qian, J., Jackson, V. E., Bahlo, M., Blackshaw, S., Friedlander, M., Eade, K. & Cherry, T. J., Mar 28 2022, In: Developmental Cell. 57, 6, p. 820-836.e6Research output: Contribution to journal › Article › peer-review
Open Access -
Corrigendum to “An Integrated Systems Biology Approach Identifies the Proteasome as A Critical Host Machinery for ZIKV and DENV Replication” [Genomics Proteomics Bioinformatics19 (1) (2021) 108–122, (S1672022921000255), (10.1016/j.gpb.2020.06.016)]
Song, G., Lee, E. M., Pan, J., Xu, M., Rho, H. S., Cheng, Y., Whitt, N., Yang, S., Kouznetsova, J., Klumpp-Thomas, C., Michael, S. G., Moore, C., Yun, K-J., Christian, K. M., Simeonov, A., Huang, W., Xia, M., Huang, R., Lal-Nag, M., Tang, H., & 5 others, Aug 2022, In: Genomics, Proteomics and Bioinformatics. 20, 4, p. 808-809 2 p.Research output: Contribution to journal › Comment/debate › peer-review
Open Access -
IReNA: Integrated regulatory network analysis of single-cell transcriptomes and chromatin accessibility profiles
Jiang, J., Lyu, P., Li, J., Huang, S., Tao, J., Blackshaw, S., Qian, J. & Wang, J., Nov 18 2022, In: iScience. 25, 11, 105359.Research output: Contribution to journal › Article › peer-review
Open Access -
LRLoop: a method to predict feedback loops in cell–cell communication
Xin, Y., Lyu, P., Jiang, J., Zhou, F., Wang, J., Blackshaw, S. & Qian, J., Sep 1 2022, In: Bioinformatics. 38, 17, p. 4117-4126 10 p.Research output: Contribution to journal › Article › peer-review
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Microglia–Neutrophil Interactions Drive Dry AMD-like Pathology in a Mouse Model
Boyce, M., Xin, Y., Chowdhury, O., Shang, P., Liu, H., Koontz, V., Strizhakova, A., Nemani, M., Hose, S., Zigler, J. S., Campbell, M., Sinha, D., Handa, J. T., Kaarniranta, K., Qian, J. & Ghosh, S., Nov 2022, In: Cells. 11, 22, 3535.Research output: Contribution to journal › Article › peer-review
Open Access -
ScEnhancer: A single-cell enhancer resource with annotation across hundreds of tissue/cell types in three species
Gao, T., Zheng, Z., Pan, Y., Zhu, C., Wei, F., Yuan, J., Sun, R., Fang, S., Wang, N., Zhou, Y. & Qian, J., Jan 7 2022, In: Nucleic acids research. 50, D1, p. D371-D379Research output: Contribution to journal › Article › peer-review
Open Access -
scRNA-sequencing reveals subtype-specific transcriptomic perturbationin DRG neurons of PirtEGFPf mice in neuropathic pain condition
Zhang, C., Hu, M. W., Wang, X. W., Cui, X., Liu, J., Huang, Q., Cao, X., Zhou, F. Q., Qian, J., He, S. Q. & Guan, Y., 2022, In: eLife. 11, e76063.Research output: Contribution to journal › Article › peer-review
Open Access -
2021
An all-to-all approach to the identification of sequence-specific readers for epigenetic DNA modifications on cytosine
Song, G., Wang, G., Luo, X., Cheng, Y., Song, Q., Wan, J., Moore, C., Song, H., Jin, P., Qian, J. & Zhu, H., Dec 1 2021, In: Nature communications. 12, 1, 795.Research output: Contribution to journal › Article › peer-review
Open Access -
An Integrated Systems Biology Approach Identifies the Proteasome as A Critical Host Machinery for ZIKV and DENV Replication
Song, G., Lee, E. M., Pan, J., Xu, M., Rho, H. S., Cheng, Y., Whitt, N., Yang, S., Kouznetsova, J., Klumpp-Thomas, C., Michael, S. G., Moore, C., Yoon, K. J., Christian, K. M., Simeonov, A., Huang, W., Xia, M., Huang, R., Lal-Nag, M., Tang, H., & 5 others, Feb 2021, In: Genomics, Proteomics and Bioinformatics. 19, 1, p. 108-122 15 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Author Correction: An all-to-all approach to the identification of sequence-specific readers for epigenetic DNA modifications on cytosine (Nature Communications, (2021), 12, 1, (795), 10.1038/s41467-021-20950-w)
Song, G., Wang, G., Luo, X., Cheng, Y., Song, Q., Wan, J., Moore, C., Song, H., Jin, P., Qian, J. & Zhu, H., Dec 1 2021, In: Nature communications. 12, 1, 1371.Research output: Contribution to journal › Comment/debate › peer-review
Open Access -
Control of neurogenic competence in mammalian hypothalamic tanycytes
Yoo, S., Kim, J., Lyu, P., Hoang, T. V., Ma, A., Trinh, V., Dai, W., Jiang, L., Leavey, P., Duncan, L., Won, J. K., Park, S. H., Qian, J., Brown, S. P. & Blackshaw, S., May 2021, In: Science Advances. 7, 22, eabg3777.Research output: Contribution to journal › Article › peer-review
Open Access -
Erratum: Decomposing Cell Identity for Transfer Learning across Cellular Measurements, Platforms, Tissues, and Species (Cell Systems (2019) 8(5) (395–411.e8), (S2405471219301462), (10.1016/j.cels.2019.04.004))
Stein-O'Brien, G. L., Clark, B., Sherman, T., Zibetti, C., Hu, Q., Sealfon, R., Liu, S., Qian, J., Colantuoni, C., Blackshaw, S., Goff, L. A. & Fertig, E. J., Feb 17 2021, In: Cell Systems. 12, 2, p. 203 1 p.Research output: Contribution to journal › Comment/debate › peer-review
Open Access -
Factors Associated with a Patient's Decision to Select a Cost-effective vs the Most Effective Therapy for Their Own Eye Disease
Malik, D., Cao, X., Sanchez, J. C., Gao, T., Qian, J., Montaner, S. & Sodhi, A., Feb 22 2021, In: JAMA Network Open. 4, 2, p. E2037880Research output: Contribution to journal › Article › peer-review
Open Access -
Gene regulatory networks controlling temporal patterning, neurogenesis, and cell-fate specification in mammalian retina
Lyu, P., Hoang, T., Santiago, C. P., Thomas, E. D., Timms, A. E., Appel, H., Gimmen, M., Le, N., Jiang, L., Kim, D. W., Chen, S., Espinoza, D. F., Telger, A. E., Weir, K., Clark, B. S., Cherry, T. J., Qian, J. & Blackshaw, S., Nov 16 2021, In: Cell Reports. 37, 7, 109994.Research output: Contribution to journal › Article › peer-review
Open Access -
Human retinal organoids release extracellular vesicles that regulate gene expression in target human retinal progenitor cells
Zhou, J., Flores-Bellver, M., Pan, J., Benito-Martin, A., Shi, C., Onwumere, O., Mighty, J., Qian, J., Zhong, X., Hogue, T., Amponsah-Antwi, B., Einbond, L., Gharbaran, R., Wu, H., Chen, B. J., Zheng, Z., Tchaikovskaya, T., Zhang, X., Peinado, H., Canto-Soler, M. V., & 1 others, Dec 2021, In: Scientific reports. 11, 1, 21128.Research output: Contribution to journal › Article › peer-review
Open Access -
Identification of novel serological autoantibodies in takayasu arteritis patients using huprot arrays
Wen, X., Song, G., Hu, C., Pan, J., Wu, Z., Li, L., Liu, C., Tian, X., Zhang, F., Qian, J., Zhu, H. & Li, Y., 2021, In: Molecular and Cellular Proteomics. 20, 100036.Research output: Contribution to journal › Article › peer-review
Open Access -
Large-scale phenotypic drug screen identifies neuroprotectants in zebrafish and mouse models of retinitis pigmentosa
Zhang, L., Chen, C., Fu, J., Lilley, B., Berlinicke, C., Hansen, B., Ding, D., Wang, G., Wang, T., Shou, D., Ye, Y., Mulligan, T., Emmerich, K., Saxena, M. T., Hall, K. R., Sharrock, A. V., Brandon, C., Park, H., Kam, T. I., Dawson, V. L., & 10 others, Jun 2021, In: eLife. 10Research output: Contribution to journal › Article › peer-review
Open Access -
Primary angle closure glaucoma is characterized by altered extracellular matrix homeostasis in the iris
Semba, R. D., Zhang, P., Dufresne, C., Gao, T., Al-Jadaan, I., Craven, E. R., Qian, J., Edward, D. P. & Mahale, A., Nov 2021, In: Proteomics - Clinical Applications. 15, 6, 2000094.Research output: Contribution to journal › Article › peer-review
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Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma
Clinical Proteomic Tumor Analysis Consortium, Mar 8 2021, In: Cancer cell. 39, 3, p. 361-379.e16Research output: Contribution to journal › Article › peer-review
Open Access8 Scopus citations -
Proteome Landscape of Epithelial-to-Mesenchymal Transition (EMT) of Retinal Pigment Epithelium Shares Commonalities with Malignancy-Associated EMT
Sripathi, S. R., Hu, M. W., Turaga, R. C., Mertz, J., Liu, M. M., Wan, J., Maruotti, J., Wahlin, K. J., Berlinicke, C. A., Qian, J. & Zack, D. J., Aug 2021, In: Molecular and Cellular Proteomics. 20, 100131.Research output: Contribution to journal › Article › peer-review
Open Access -
Role of glia in optic nerve
Yazdankhah, M., Shang, P., Ghosh, S., Hose, S., Liu, H., Weiss, J., Fitting, C. S., Bhutto, I. A., Zigler, J. S., Qian, J., Sahel, J. A., Sinha, D. & Stepicheva, N. A., Mar 2021, In: Progress in Retinal and Eye Research. 81, 100886.Research output: Contribution to journal › Review article › peer-review
1 Scopus citations -
Temperature and species-dependent regulation of browning in retrobulbar fat
Rajaii, F., Kim, D. W., Pan, J., Mahoney, N. R., Eberhart, C. G., Qian, J. & Blackshaw, S., Dec 2021, In: Scientific reports. 11, 1, 3094.Research output: Contribution to journal › Article › peer-review
Open Access -
Transcriptome landscape of epithelial to mesenchymal transition of human stem cell–derived RPE
Sripathi, S. R., Hu, M. W., Liu, M. M., Wan, J., Cheng, J., Duan, Y., Mertz, J. L., Wahlin, K. J., Maruotti, J., Berlinicke, C. A., Qian, J. & Zack, D. J., Apr 2021, In: Investigative Ophthalmology and Visual Science. 62, 4, 1.Research output: Contribution to journal › Article › peer-review
Open Access -
βA1-crystallin regulates glucose metabolism and mitochondrial function in mouse retinal astrocytes by modulating PTP1B activity
Ghosh, S., Liu, H., Yazdankhah, M., Stepicheva, N., Shang, P., Vaidya, T., Hose, S., Gupta, U., Calderon, M. J., Hu, M. W., Nair, A. P., Weiss, J., Fitting, C. S., Bhutto, I. A., Gadde, S. G. K., Naik, N. K., Jaydev, C., Lutty, G. A., Handa, J. T., Jayagopal, A., & 9 others, Dec 2021, In: Communications biology. 4, 1, 248.Research output: Contribution to journal › Article › peer-review
Open Access -
βA3/A1-crystallin regulates apical polarity and EGFR endocytosis in retinal pigmented epithelial cells
Shang, P., Stepicheva, N., Teel, K., McCauley, A., Fitting, C. S., Hose, S., Grebe, R., Yazdankhah, M., Ghosh, S., Liu, H., Strizhakova, A., Weiss, J., Bhutto, I. A., Lutty, G. A., Jayagopal, A., Qian, J., Sahel, J. A., Samuel Zigler, J., Handa, J. T., Sergeev, Y., & 3 others, Dec 2021, In: Communications biology. 4, 1, 850.Research output: Contribution to journal › Article › peer-review
Open Access -
2020
EnhancerAtlas 2.0: An updated resource with enhancer annotation in 586 tissue/cell types across nine species
Gao, T. & Qian, J., Jan 1 2020, In: Nucleic acids research. 48, D1, p. D58-D64Research output: Contribution to journal › Article › peer-review
Open Access21 Scopus citations -
Erratum: Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma (Cell (2019) 179(4) (964–983.e31), (S0092867419311237), (10.1016/j.cell.2019.10.007))
Clinical Proteomic Tumor Analysis Consortium, Jan 9 2020, In: Cell. 180, 1, p. 207 1 p.Research output: Contribution to journal › Comment/debate › peer-review
Open Access7 Scopus citations -
Gene regulatory networks controlling vertebrate retinal regeneration
Hoang, T., Wang, J., Boyd, P., Wang, F., Santiago, C., Jiang, L., Yoo, S., Lahne, M., Todd, L. J., Jia, M., Saez, C., Keuthan, C., Palazzo, I., Squires, N., Campbell, W. A., Rajaii, F., Parayil, T., Trinh, V., Kim, D. W., Wang, G., & 6 others, Nov 20 2020, In: Science. 370, 6519, eabb8598.Research output: Contribution to journal › Article › peer-review
Open Access21 Scopus citations -
Glycoproteomics-based signatures for tumor subtyping and clinical outcome prediction of high-grade serous ovarian cancer
Pan, J., Hu, Y., Sun, S., Chen, L., Schnaubelt, M., Clark, D., Ao, M., Zhang, Z., Chan, D., Qian, J. & Zhang, H., Dec 2020, In: Nature communications. 11, 1, 6139.Research output: Contribution to journal › Article › peer-review
Open Access9 Scopus citations -
Integrated Proteomic and Glycoproteomic Characterization of Human High-Grade Serous Ovarian Carcinoma
Clinical Proteomic Tumor Analysis Consortium, Oct 20 2020, In: Cell Reports. 33, 3, 108276.Research output: Contribution to journal › Article › peer-review
Open Access7 Scopus citations -
Integration of IgA and IgG autoantigens improves performance of biomarker panels for early diagnosis of lung cancer
Pan, J., Yu, L., Wu, Q., Lin, X., Liu, S., Hu, S., Rosa, C., Eichinger, D., Pino, I., Zhu, H., Qian, J. & Huang, Y., 2020, In: Molecular and Cellular Proteomics. 19, 3, p. 490-500 11 p.Research output: Contribution to journal › Article › peer-review
Open Access5 Scopus citations -
Investigating cone photoreceptor development using patient-derived NRL null retinal organoids
Kallman, A., Capowski, E. E., Wang, J., Kaushik, A. M., Jansen, A. D., Edwards, K. L., Chen, L., Berlinicke, C. A., Joseph Phillips, M., Pierce, E. A., Qian, J., Wang, T. H., Gamm, D. M. & Zack, D. J., Feb 21 2020, In: Communications biology. 3, 1, p. 82 1 p.Research output: Contribution to journal › Article › peer-review
Open Access13 Scopus citations -
Knocking Out Non-muscle Myosin II in Retinal Ganglion Cells Promotes Long-Distance Optic Nerve Regeneration
Wang, X. W., Yang, S. G., Zhang, C., Hu, M. W., Qian, J., Ma, J. J., Zhang, Y., Yang, B. B., Weng, Y. L., Ming, G. L., Kosanam, A. R., Saijilafu & Zhou, F. Q., Apr 21 2020, In: Cell Reports. 31, 3, 107537.Research output: Contribution to journal › Article › peer-review
Open Access9 Scopus citations -
Retinal pigment epithelium transcriptome analysis in chronic smoking reveals a suppressed innate immune response and activation of differentiation pathways
Wang, L., Kaya, K. D., Kim, S., Brooks, M. J., Wang, J., Xin, Y., Qian, J., Swaroop, A. & Handa, J. T., Aug 20 2020, In: Free Radical Biology and Medicine. 156, p. 176-189 14 p.Research output: Contribution to journal › Article › peer-review
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2019
Decomposing Cell Identity for Transfer Learning across Cellular Measurements, Platforms, Tissues, and Species
Stein-O'Brien, G. L., Clark, B. S., Sherman, T., Zibetti, C., Hu, Q., Sealfon, R., Liu, S., Qian, J., Colantuoni, C., Blackshaw, S., Goff, L. A. & Fertig, E. J., May 22 2019, In: Cell Systems. 8, 5, p. 395-411.e8Research output: Contribution to journal › Article › peer-review
Open Access35 Scopus citations