Publications | Center for RNA Science and Medicine

Roger Abounader, MD. PhD.

Gibert, M., Saha, S., Zhang, Y., Marcinkiewicz, P. P., Chagari, B., Roig-Laboy, C., . . . Abounader, R. (2023). A FIRST COMPREHENSIVE ANALYSIS OF TRANSCRIBED ULTRA CONSERVED REGIONS UNCOVERS IMPORTANT REGULATORY FUNCTIONS OF NOVEL NON-CODING TRANSCRIPTS IN GLIOMAS. In NEURO-ONCOLOGY Vol. 25. Retrieved from https://www.webofscience.com/

Hudson, K., Mondia, M. W., Zhang, Y., Saha, S., Gibert Jr, M. K., Dube, C., . . . Abounader, R. (2024). The role of microRNAs in brain metastasis. JOURNAL OF NEURO-ONCOLOGY, 166(2), 231-241. doi:10.1007/s11060-023-04541-x

Zhang, Y., Hudson, K., & Abounader, R. (2024). Unraveling the hypoxic puzzle: LncRNA LUCAT1 drives glioblastoma in cooperation with HIF1α. NEURO-ONCOLOGY. doi:10.1093/neuonc/noae096

Dutta, A., Li, H., & Abounader, R. (2023). Cryptic lncRNA-encoded ORFs: A hidden source of regulatory proteins. JOURNAL OF CLINICAL INVESTIGATION, 133(5). doi:10.1172/JCI167271

Hanif, F., Zhang, Y., Dube, C., Gibert, M. K., Saha, S., Hudson, K., . . . Abounader, R. (2023). miR-3174 Is a New Tumor Suppressor MicroRNA That Inhibits Several Tumor-Promoting Genes in Glioblastoma. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 24(11). doi:10.3390/ijms24119326

Hudson, K., Gibert, M. K. J., Zhang, Y., Dube, C., Saha, S., Vernon, A., & Abounader, R. (2023). IDENTIFICATION AND CHARACTERIZATION OF NOVEL TRANSCRIBED ULTRACONSERVED REGIONS AS LONG NON-CODING RNAS IN MEDULLOBLASTOMA. In NEURO-ONCOLOGY Vol. 25. Retrieved from https://www.webofscience.com/

Li, Y., & Abounader, R. (2023). Editorial: GBM stem cells and the brain tumor microenvironment. FRONTIERS IN ONCOLOGY, 13. doi:10.3389/fonc.2023.1153803

Dube, C., Zhang, Y., Saha, S., Lai, M., Gibert, M., Escalante, M., . . . Abounader, R. (2022). T-TYPE CALCIUM CHANNELS DRIVE GLIOBLASTOMA GROWTH BY PROMOTING NEURONAL INTERACTIONS. In NEURO-ONCOLOGY Vol. 24 (pp. 24). Retrieved from https://www.webofscience.com/

Gibert, M. K. J., Sarkar, A., Chagari, B., Roig-Laboy, C., Saha, S., Bednarek, S., . . . Abounader, R. (2022). Transcribed Ultraconserved Regions in Cancer. CELLS, 11(10). doi:10.3390/cells11101684

Mulcahy, E. Q. X., Zhang, Y., Colon, R. R., Cain, S. R., Gibert, M. K. J., Dube, C. J., . . . Abounader, R. (2022). MicroRNA 3928 Suppresses Glioblastoma through Downregulation of Several Oncogenes and Upregulation of p53. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 23(7). doi:10.3390/ijms23073930

Zhang, Y., Yuan, F., Grello, C., Reon, B., Gibert, M., Dube, C., . . . Abounader, R. (2022). GAIN-OF-FUNCTION MUTANT P53 REGULATES LONG-NONCODING RNAS IN GLIOBLASTOMA. In NEURO-ONCOLOGY Vol. 24 (pp. 39-40). Retrieved from https://www.webofscience.com/

George S. Bloom, PhD.

2024:

Bloom GS, Baas PW. A half-century of tau. Cytoskeleton (Hoboken). 2024 Jan;81(1):7-9. doi: 10.1002/cm.21783. Epub 2023 Aug 28. PMID: 37638689; PMCID: PMC10840720.

Sun X, Eastman G, Shi Y, Saibaba S, Oliveira AK, Lukens JR, Norambuena A, Thompson JA, Purdy MD, Dryden K, Pardo E, Mandell JW, Bloom GS. Structural and functional damage to neuronal nuclei caused by extracellular tau oligomers. Alzheimers Dement. 2024 Mar;20(3):1656-1670. doi: 10.1002/alz.13535. Epub 2023 Dec 9. PMID: 38069673; PMCID: PMC10947977.

2023:

Bloom GS, Norambuena A. Dysregulation of mTOR by tau in Alzheimer's disease. Cytoskeleton (Hoboken). 2024 Jan;81(1):30-34. doi: 10.1002/cm.21782. Epub 2023 Aug 28. PMID: 37638691; PMCID: PMC10919542.

Post LA, Kulas JA, Milstein JL, Sebastian SVL, Hosseini-Barkooie S, Stevenson ME, Bloom GS, Ferris HA. Inceptor as a regulator of brain insulin sensitivity. Sci Rep. 2023 Jul 18;13(1):11582. doi: 10.1038/s41598-023-36248-4. PMID: 37463909; PMCID: PMC10354159.

Rajbanshi B, Guruacharya A, Mandell JW, Bloom GS. Localization, induction, and cellular effects of tau phosphorylated at threonine 217. Alzheimers Dement. 2023 Jul;19(7):2874-2887. doi: 10.1002/alz.12892. Epub 2023 Jan 12. PMID: 36633254; PMCID: PMC10336182.

Sun X, Eastman G, Shi Y, Saibaba S, Oliveira AK, Lukens JR, Norambuena A, Mandell JW, Bloom GS. Structural and functional damage to neuronal nuclei caused by extracellular tau oligomers. bioRxiv [Preprint]. 2023 May 8:2023.05.08.539873. doi: 10.1101/2023.05.08.539873. Update in: Alzheimers Dement. 2024 Mar;20(3):1656-1670. doi: 10.1002/alz.13535. PMID: 37214909; PMCID: PMC10197541.

2022:

Eastman G, Sharlow ER, Lazo JS, Bloom GS, Sotelo-Silveira JR. Transcriptome and Translatome Regulation of Pathogenesis in Alzheimer's Disease Model Mice. J Alzheimers Dis. 2022;86(1):365-386. doi: 10.3233/JAD-215357. PMID: 35034904.

Norambuena, A., Sun, X., Wallrabe, H., Cao, R., Sun, N., Pardo, E., . . . Bloom, G. S. (2022). SOD1 mediates lysosome-to-mitochondria communication and its dysregulation by amyloid-β oligomers. NEUROBIOLOGY OF DISEASE, 169. doi:10.1016/j.nbd.2022.105737.

Wu L, Wang Z, Lad S, Gilyazova N, Dougharty DT, Marcus M, Henderson F, Ray WK, Siedlak S, Li J, Helm RF, Zhu X, Bloom GS, Wang SJ, Zou WQ, Xu B. Selective Detection of Misfolded Tau From Postmortem Alzheimer's Disease Brains. Front Aging Neurosci. 2022 Jul 20;14:945875. doi: 10.3389/fnagi.2022.945875. PMID: 35936779; PMCID: PMC9352240.

Chuanxi Cai, PhD.

2024:

Speaks S, McFadden MI, Zani A, Solstad A, Leumi S, Roettger JE, Kenney AD, Bone H, Zhang L, Denz PJ, Eddy AC, Amer AO, Robinson RT, Cai C, Ma J, Hemann EA, Forero A, Yount JS. Gasdermin D promotes influenza virus-induced mortality through neutrophil amplification of inflammation. Nat Commun. 2024 Mar 29;15(1):2751. doi: 10.1038/s41467-024-47067-0. PMID: 38553499; PMCID: PMC10980740.

2023:

Li, H., Li, Z., Li, X., Cai, C., Zhao, S. L., Merritt, R. E., . . . Ma, J. (2023). MG53 Mitigates Nitrogen Mustard-Induced Skin Injury. CELLS, 12(14). doi:10.3390/cells12141915

Kaur, G., Wang, X., Li, X., Ong, H., He, X., & Cai, C. (2023). Overexpression of GREM1 Improves the Survival Capacity of Aged Cardiac Mesenchymal Progenitor Cells via Upregulation of the ERK/NRF2-Associated Antioxidant Signal Pathway. CELLS, 12(8). doi:10.3390/cells12081203

Speaks, S., Zani, A., Solstad, A., Kenney, A., McFadden, M. I., Zhang, L., . . . Yount, J. S. (2023). Gasdermin D promotes influenza virus-induced mortality through neutrophil amplification of inflammation.. bioRxiv. doi:10.1101/2023.03.08.531787

Kenney, A. D., Zani, A., Kawahara, J., Eddy, A. C., Wang, X. -L., Mahesh, K. C., . . . Yount, J. S. (2023). Interferon-induced transmembrane protein 3 (IFITM3) limits lethality of SARS-CoV-2 in mice. EMBO REPORTS, 24(4). doi:10.15252/embr.202256660

Liu, X., Chang, Y., Choi, S., Cai, C., Zhang, X., & Pan, Z. (2023). Blocking Store-Operated Ca2+ Entry to Protect HL-1 Cardiomyocytes from Epirubicin-Induced Cardiotoxicity. CELLS, 12(5). doi:10.3390/cells12050723

Zhou, X., Cho, J. H., Yi, J., Choi, K., Park, K. H., Zhu, H., . . . Ma, J. (2023). Quantification of autophagy flux in isolated mouse skeletal muscle fibers with overexpression of fluorescent protein mCherry-EGFP-LC3. STAR PROTOCOLS, 4(1). doi:10.1016/j.xpro.2022.101871

2022:

Jin, G., Ho, J. W., Keeney-Bonthrone, T. P., Ober, R. A., Liu, B., Chtraklin, K., . . . Alam, H. B. (2022). Recombinant human MG53 protein attenuates brain lesion size in a large animal model of traumatic brain injury. JOURNAL OF TRAUMA AND ACUTE CARE SURGERY, 93(5), 613-619. doi:10.1097/TA.0000000000003746

Li, X., Wang, X., He, P., Bennett, E., Haggard, E., Ma, J., & Cai, C. (2022). Mitochondrial Membrane Potential Identifies a Subpopulation of Mesenchymal Progenitor Cells to Promote Angiogenesis and Myocardial Repair. CELLS, 11(10). doi:10.3390/cells11101713

Kenney, A. D., Aron, S. L., Gilbert, C., Kumar, N., Chen, P., Eddy, A., . . . Yount, J. S. (2022). Influenza virus replication in cardiomyocytes drives heart dysfunction and fibrosis. SCIENCE ADVANCES, 8(19). doi:10.1126/sciadv.abm5371

Geng, B., Wang, X., Park, K. H., Lee, K. E., Kim, J., Chen, P., . . . Zhu, H. (2022). UCHL1 protects against ischemic heart injury via activating HIF-1a signal pathway. REDOX BIOLOGY, 52. doi:10.1016/j.redox.2022.102295

Li, H., Rosas, L., Li, Z., Bian, Z., Li, X., Choi, K., . . . Ma, J. (2022). MG53 attenuates nitrogen mustard-induced acute lung injury. JOURNAL OF CELLULAR AND MOLECULAR MEDICINE, 26(7), 1886-1895. doi:10.1111/jcmm.16917

Gupta, P., Li, H., Zhang, G. -N., Barbuti, A. M., Yang, Y., Lin, P. -H., . . . Chen, Z. -S. (2022). MG53 inhibits cellular proliferation and tumor progression in colorectal carcinoma. INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES, 18(14), 5221-5229. doi:10.7150/ijbs.67869

Mete Civelek, PhD.

2024:

Reed, J. N., Huang, J., Li, Y., Ma, L., Banka, D., Wabitsch, M., . . . Civelek, M. (2024). Systems genetics analysis of human body fat distribution genes identifies adipocyte processes.. Life science alliance, 7(7), e202402603. doi:10.26508/lsa.202402603

Mocci, G., Sukhavasi, K., Örd, T., Bankier, S., Singha, P., Arasu, U. T., . . . Björkegren, J. L. M. (2024). Single-Cell Gene-Regulatory Networks of Advanced Symptomatic Atherosclerosis.. Circulation research, 134(11), 1405-1423. doi:10.1161/circresaha.123.323184

Benavente, E. D., Hartman, R. J. G., Sakkers, T. R., Wesseling, M., Sloots, Y., Slenders, L., . . . den Ruijter, H. M. (2024). Atherosclerotic Plaque Epigenetic Age Acceleration Predicts a Poor Prognosis and Is Associated With Endothelial-to-Mesenchymal Transition in Humans. ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY, 44(6), 1419-1431. doi:10.1161/ATVBAHA.123.320692

Rial, S. A., You, Z., Vivoli, A., Sean, D., Al-Khoury, A., Lavoie, G., . . . Lim, G. E. (2024). 14-3-3ζ regulates adipogenesis by modulating chromatin accessibility during the early stages of adipocyte differentiation.. bioRxiv. doi:10.1101/2024.03.18.585495

Aherrahrou, R., Baig, F., Theofilatos, K., Lue, D., Beele, A., Oerd, T., . . . Civelek, M. (2024). Secreted Protein Profiling of Human Aortic Smooth Muscle Cells Identifies Vascular Disease Associations. ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY, 44(4), 898-914. doi:10.1161/ATVBAHA.123.320274

2023:

Aherrahrou, R., Baig, F., Theofilatos, K., Lue, D., Beele, A., Örd, T., . . . Civelek, M. (2023). Secreted protein profiling of human aortic smooth muscle cells identifies vascular disease associations.. medRxiv. doi:10.1101/2023.11.10.23298351

Sakkers, T. R., Mokry, M., Civelek, M., Erdmann, J., Pasterkamp, G., Benavente, E. D., & den Ruijter, H. M. (2023). Sex differences in the genetic and molecular mechanisms of coronary artery disease. ATHEROSCLEROSIS, 384. doi:10.1016/j.atherosclerosis.2023.117279

Reed, J. N., Huang, J., Li, Y., Ma, L., Banka, D., Wabitsch, M., . . . Civelek, M. (2023). Systems genetics analysis of human body fat distribution genes identifies Wnt signaling and mitochondrial activity in adipocytes.. bioRxiv. doi:10.1101/2023.09.06.556534

Benavente, E. D., Karnewar, S., Buono, M., Mili, E., Hartman, R. J. G., Kapteijn, D., . . . den Ruijter, H. M. (2023). Female Gene Networks Are Expressed in Myofibroblast-Like Smooth Muscle Cells in Vulnerable Atherosclerotic Plaques. ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY, 43(10), 1836-1850. doi:10.1161/ATVBAHA.123.319325

Hu, P., Miller, A. E., Yeh, C. -R., Bingham, G. C., Civelek, M., & Barker, T. H. (2023). SEMA7a primes integrin α581 engagement instructing fibroblast mechanotransduction, phenotype and transcriptional programming. MATRIX BIOLOGY, 121, 179-193. doi:10.1016/j.matbio.2023.06.006

Perry, R. N., Albarracin, D., Aherrahrou, R., & Civelek, M. (2023). Network Preservation Analysis Reveals Dysregulated Metabolic Pathways in Human Vascular Smooth Muscle Cell Phenotypic Switching. CIRCULATION-GENOMIC AND PRECISION MEDICINE, 16(4), 372-381. doi:10.1161/CIRCGEN.122.003781

Aberra, Y. T., Ma, L., Bjorkegren, J. L. M., & Civelek, M. (2023). Predicting mechanisms of action at genetic loci associated with discordant effects on type 2 diabetes and abdominal fat accumulation. ELIFE, 12. doi:10.7554/eLife.79834

Wong, D., Auguste, G., Lino Cardenas, C. L., Turner, A. W., Chen, Y., Song, Y., . . . Miller, C. L. (2023). FHL5 Controls Vascular Disease-Associated Gene Programs in Smooth Muscle Cells. CIRCULATION RESEARCH, 132(9), 1144-1161. doi:10.1161/CIRCRESAHA.122.321692

Benavente, E. D., Karnewar, S., Buono, M., Mili, E., Hartman, R. J. G., Kapteijn, D., . . . den Ruijter, H. M. (2023). Female gene networks are expressed in myofibroblast-like smooth muscle cells in vulnerable atherosclerotic plaques.. bioRxiv. doi:10.1101/2023.02.08.527690

Xu, P., Wang, M., Sharma, N. K., Comeau, M. E., Wabitsch, M., Langefeld, C. D., . . . Das, S. K. (2023). Multi-omic integration reveals cell-type-specific regulatory networks of insulin resistance in distinct ancestry populations. CELL SYSTEMS, 14(1), 41-+. doi:10.1016/j.cels.2022.12.005

Aherrahrou, R., Lue, D., Perry, R. N., Aberra, Y. T., Khan, M. D., Soh, J. Y., . . . Civelek, M. (2023). Genetic Regulation of SMC Gene Expression and Splicing Predict Causal CAD Genes. CIRCULATION RESEARCH, 132(3), 323-338. doi:10.1161/CIRCRESAHA.122.321586

2022:

Mokry, M., Boltjes, A., Slenders, L., Bel-Bordes, G., Cui, K., Brouwer, E., . . . Pasterkamp, G. (2022). Transcriptomic-based clustering of human atherosclerotic plaques identifies subgroups with different underlying biology and clinical presentation. NATURE CARDIOVASCULAR RESEARCH, 1(12), 1140-+. doi:10.1038/s44161-022-00171-0

Aherrahrou, R., Lue, D., & Civelek, M. (2023). Genetic regulation of circular RNA expression in human aortic smooth muscle cells and vascular traits. HUMAN GENETICS AND GENOMICS ADVANCES, 4(1). doi:10.1016/j.xhgg.2022.100164

Civelek, M., Fogelman, A. M., Hedrick, C. C., Lusis, A. J., Romanoski, C. E., & Witztum, J. L. (2022). In memoriam: Judith A. Berliner, Ph.D.. JOURNAL OF LIPID RESEARCH, 63(4). doi:10.1016/j.jlr.2022.100180

Yang, Q., Hinkle, J., Reed, J. N., Aherrahrou, R., Xu, Z., Harris, T. E., . . . Civelek, M. (2022). Adipocyte-Specific Modulation of KLF14 Expression in Mice Leads to Sex-Dependent Impacts on Adiposity and Lipid Metabolism. DIABETES, 71(4), 677-693. doi:10.2337/db21-0674

Anna Cliffe, PhD.

2024:
Cuddy, S. R., Flores, M. E., Krakowiak, P. A., Whitford, A. L., Dochnal, S. A., Babnis, A., . . . Cliffe, A. R. (2024). Co-option of mitochondrial nucleic acid sensing pathways by HSV-1 UL12.5 for reactivation from latent Infection.. bioRxiv. doi:10.1101/2024.07.06.601241

Francois, A. K., Rohani, A., Loftus, M., Dochnal, S., Hrit, J., Mcfarlane, S., . . . Cliffe, A. R. (2024). Single-genome analysis reveals a heterogeneous association of the herpes simplex virus genome with H3K27me2 and the reader PHF20L1 following infection of human fibroblasts. MBIO, 15(4). doi:10.1128/mbio.03278-23

Rasmussen, A. L., Gronvall, G. K., Lowen, A. C., Goodrum, F., Alwine, J., Andersen, K. G., . . . Yurochko, A. (2024). Virology-the path forward (vol 98, e0179123, 2024). JOURNAL OF VIROLOGY, 98(3). doi:10.1128/jvi.00074-24

Dochnal, S. A., Whitford, A. L., Francois, A. K., Krakowiak, P. A., Cuddy, S., & Cliffe, A. R. (2024). c-Jun signaling during initial HSV-1 infection modulates latency to enhance later reactivation in addition to directly promoting the progression to full reactivation. JOURNAL OF VIROLOGY. doi:10.1128/jvi.01764-23

Rasmussen, A. L., Gronvall, G. K., Lowen, A. C., Goodrum, F., Alwine, J., Andersen, K. G., . . . Yurochko, A. (2024). Virology-the path forward. JOURNAL OF VIROLOGY, 98(1). doi:10.1128/jvi.01791-23

2023:
Francois, A. K., Rohani, A., Loftus, M., Dochnal, S., Hrit, J., McFarlane, S., . . . Cliffe, A. R. (2023). Single-genome analysis reveals heterogeneous association of the Herpes Simplex Virus genome with H3K27me2 and the reader PHF20L1 following infection of human fibroblasts.. bioRxiv. doi:10.1101/2023.12.03.569766

Dochnal, S. A., Whitford, A. L., Francois, A. K., Krakowiak, P. A., Cuddy, S., & Cliffe, A. R. (2023). c-Jun Signaling During Initial HSV-1 Infection Modulates Latency to Enhance Later Reactivation in addition to Directly Promoting the Progression to Full Reactivation.. bioRxiv. doi:10.1101/2023.11.10.566462

Cuddy, S. R., & Cliffe, A. R. (2023). The Intersection of Innate Immune Pathways with the Latent Herpes Simplex Virus Genome. JOURNAL OF VIROLOGY, 97(5). doi:10.1128/jvi.01352-22

Goodrum, F., Lowen, A., Lakdawala, S., Alwine, J., Casadevall, A., Imperiale, M., . . . Yurochko, A. (2023). Virology under the Microscope-a Call for Rational Discourse. JOURNAL OF VIROLOGY. doi:10.1128/jvi.00089-23

Goodrum, F., Lowen, A. C., Lakdawala, S., Alwine, J., Casadevall, A., Imperiale, M. J., . . . Yurochko, A. (2023). Virology under the Microscope-a Call for Rational Discourse. MSPHERE, 8(2). doi:10.1128/msphere.00034-23

Goodrum, F., Lowen, A., Lakdawala, S., Alwine, J., Casadevall, A., Imperiale, M., . . . Yurochko, A. (2023). Virology under the Microscope-a Call for Rational Discourse. MBIO. doi:10.1128/mbio.00188-23

2022:
Whitford, A. L., & Cliffe, A. R. (2022). Key questions on the epigenetics of herpes simplex virus latency. PLOS PATHOGENS, 18(6). doi:10.1371/journal.ppat.1010587

Dochnal, S., Merchant, H. Y., Schinlever, A. R., Babnis, A., Depledge, D. P., Wilson, A. C., & Cliffe, A. R. (2022). DLK-Dependent Biphasic Reactivation of Herpes Simplex Virus Latency Established in the Absence of Antivirals. JOURNAL OF VIROLOGY, 96(12). doi:10.1128/jvi.00508-22

Whitford, A. L., Clinton, C. A., Kennedy, E. B. L., Dochnal, S. A., Suzich, J. B., & Cliffe, A. R. (2022). Ex Vivo Herpes Simplex Virus Reactivation Involves a Dual Leucine Zipper Kinase-Dependent Wave of Lytic Gene Expression That Is Independent of Histone Demethylase Activity and Viral Genome Synthesis. JOURNAL OF VIROLOGY, 96(12). doi:10.1128/jvi.00475-22

Sarah Dremel, PhD.

2023:
Dremel, S. E., Tagawa, T., Koparde, V. N., Arbuckle, J. H., Kristie, T. M., Krug, L. T., & Ziegelbauer, J. M. (2023). Interferon induced circRNAs escape herpesvirus host shutoff and suppress lytic infection.. bioRxiv. doi:10.1101/2023.09.07.556698

Tagawa, T., Oh, D., Dremel, S., Mahesh, G., Koparde, V. N., Duncan, G., . . . Ziegelbauer, J. M. (2023). A virus-induced circular RNA maintains latent infection of Kaposi's sarcoma herpesvirus. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 120(6). doi:10.1073/pnas.2212864120

Dremel, S. E., Jimenez, A. R., & Tucker, J. M. (2023). ?Transfer? of power: The intersection of DNA virus infection and tRNA biology. SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY, 146, 31-39. doi:10.1016/j.semcdb.2023.01.011

2022:
Dremel, S. E., & Didychuk, A. L. (2023). Better late than never: A unique strategy for late gene transcription in the beta- and gammaherpesviruses. SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY, 146, 57-69. doi:10.1016/j.semcdb.2022.12.001

Dremel, S. E., Sivrich, F. L., Tucker, J., Glaunsinger, B. A., & DeLuca, N. A. (2022). Manipulation of RNA polymerase III by Herpes Simplex Virus-1. NATURE COMMUNICATIONS, 13(1). doi:10.1038/s41467-022-28144-8

Daniel A. Engel, PhD.

2024:

Cuddy SR, Flores ME, Krakowiak PA, Whitford AL, Dochnal SA, Babnis A, Miyake T, Tigano M, Engel DA, Cliffe AR. Co-option of mitochondrial nucleic acid sensing pathways by HSV-1 UL12.5 for reactivation from latent Infection. bioRxiv [Preprint]. 2024 Jul 9:2024.07.06.601241. doi: 10.1101/2024.07.06.601241. PMID: 39005440; PMCID: PMC11245091.

Charles R. Farber, PhD.

2024:
Abood, A., Mesner, L. D., Jeffery, E. D., Murali, M., Lehe, M. D., Saquing, J., . . . Sheynkman, G. M. (2024). Long-read proteogenomics to connect disease-associated sQTLs to the protein isoform effectors of disease.. American journal of human genetics, S0002-9297(24)00227-1. doi:10.1016/j.ajhg.2024.07.003

2023:
Allayee, H., Farber, C. R., Seldin, M. M., Williams, E. G., James, D. E., & Lusis, A. J. (2023). Systems genetics approaches for understanding complex traits with relevance for human disease. ELIFE, 12. doi:10.7554/eLife.91004

Dillard, L. J., Rosenow, W. T., Calabrese, G. M., Mesner, L. D., Al-Barghouthi, B. M., Abood, A., . . . Farber, C. R. (2023). Single-Cell Transcriptomics of Bone Marrow Stromal Cells in Diversity Outbred Mice: A Model for Population-Level scRNA-Seq Studies. JOURNAL OF BONE AND MINERAL RESEARCH, 38(9), 1350-1363. doi:10.1002/jbmr.4882

Friedman, M. A., Buettmann, E. G., Zeineddine, Y., Abraham, L. B., Hoppock, G. A., Meas, S. J., . . . Donahue, H. J. (2024). Genetic variation influences the skeletal response to hindlimb unloading in the eight founder strains of the diversity outbred mouse population. JOURNAL OF ORTHOPAEDIC RESEARCH, 42(1), 134-140. doi:10.1002/jor.25646

Migotsky, N., Surabhi Kumar., Shuster, J., Coulombe, J., Senwar, B., Gestos, A., . . . Silva, M. (2023). Multi-Scale Cortical Bone Traits Vary in Two Mouse Models of Genetic Diversity. doi:10.1101/2023.06.02.543484

Abood, A., Mesner, L., Jeffery, E., Murali, M., Lehe, M., Saquing, J., . . . Sheynkman, G. (2023). Long-read proteogenomics to connect disease-associated sQTLs to the protein isoform effectors of disease. doi:10.1101/2023.03.17.531557

2022:
Gonzalez, T. L., Schaub, A. M., Lee, B., Cui, J., Taylor, K. D., Dorfman, A. E., . . . Pisarska, M. D. (2023). Infertility and treatments used have minimal effects on first-trimester placental DNA methylation and gene expression. FERTILITY AND STERILITY, 119(2), 301-312. doi:10.1016/j.fertnstert.2022.11.010

Moran, M. M., Ko, F. C., Mesner, L. D., Calabrese, G. M., Al-Barghouthi, B. M., Farber, C. R., & Sumner, D. R. (2022). Intramembranous bone regeneration in diversity outbred mice is heritable. BONE, 164. doi:10.1016/j.bone.2022.116524

Castaldi, P. J., Abood, A., Farber, C. R., & Sheynkman, G. M. (2022). Bridging the splicing gap in human genetics with long-read RNA sequencing: finding the protein isoform drivers of disease. HUMAN MOLECULAR GENETICS, 31(R1), R123-R136. doi:10.1093/hmg/ddac196

Abood, A., Mesner, L., Rosenow, W., Al-Barghouthi, B. M., Horowitz, N., Morgan, E. F., . . . Farber, C. R. (2022). Identification of Known and Novel Long Noncoding RNAs Potentially Responsible for the Effects of Bone Mineral Density (BMD) Genomewide Association Study (GWAS) Loci. JOURNAL OF BONE AND MINERAL RESEARCH, 37(8), 1500-1510. doi:10.1002/jbmr.4622

Logan, J. G., Yun, S., Teachman, B. A., Bao, Y., Farber, E., & Farber, C. R. (2022). Genome-Wide mRNA Expression Analysis of Acute Psychological Stress Responses. MEDICC REVIEW, 24(2), 35-42. doi:10.37757/MR2022.V24.N2.6

Brent A. French, PhD.

2023:

Shah SA, Reagan CE, Bresticker JE, Wolpe AG, Good ME, Macal EH, Billcheck HO, Bradley LA, French BA, Isakson BE, Wolf MJ, Epstein FH. Obesity-Induced Coronary Microvascular Disease Is Prevented by iNOS Deletion and Reversed by iNOS Inhibition. JACC Basic Transl Sci. 2023 Feb 1;8(5):501-514. doi: 10.1016/j.jacbts.2022.11.005. PMID: 37325396; PMCID: PMC10264569.

2022:

Yu, G., Chakrabarti, S., Tischenko, M., Chen, A. -L., Wang, Z., Cho, H., . . . Wang, Q. K. (2022). Gene therapy targeting protein trafficking regulator MOG1 in mouse models of Brugada syndrome, arrhythmias, and mild cardiomyopathy. SCIENCE TRANSLATIONAL MEDICINE, 14(648). doi:10.1126/scitranslmed.abf3136

Becker, A. B., Chen, L., Ning, B., Hu, S., Hossack, J. A., Klibanov, A. L., . . . French, B. A. (2022). CONTRAST-ENHANCED ULTRASOUND REVEALS PARTIAL PERFUSION RECOVERY AFTER HINDLIMB ISCHEMIA AS OPPOSED TO FULL RECOVERY BY LASER DOPPLER PERFUSION IMAGING. ULTRASOUND IN MEDICINE AND BIOLOGY, 48(6), 1058-1069. doi:10.1016/j.ultrasmedbio.2022.02.002

Mariano Garcia-Blanco, MD. PhD.

2024:
Nagasawa, C. K., Bailey, A. O., Russell, W. K., & Garcia-Blanco, M. A. (2024). Inefficient recruitment of DDX39B impedes pre-spliceosome assembly on FOXP3 introns. RNA, 30(7), 824-838. doi:10.1261/rna.079933.123

Banerjee, S., Nagasawa, C. K., Widen, S. G., & Garcia-Blanco, M. A. (2024). Parsing the roles of DExD-box proteins DDX39A and DDX39B in alternative RNA splicing. NUCLEIC ACIDS RESEARCH. doi:10.1093/nar/gkae431

2023:
Banerjee, S., Galarza-Munoz, G., & Garcia-Blanco, M. A. (2023). Role of RNA Alternative Splicing in T Cell Function and Disease. GENES, 14(10). doi:10.3390/genes14101896

Nagasawa, C. K., & Garcia-Blanco, M. A. (2023). Early Splicing Complexes and Human Disease. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 24(14). doi:10.3390/ijms241411412

Hirano, M., Galarza-Munoz, G., Nagasawa, C., Schott, G., Wang, L., Antonia, A. L., . . . Garcia-Blanco, M. A. (2023). The RNA helicase DDX39B activates FOXP3 RNA splicing to control T regulatory cell fate. ELIFE, 12. doi:10.7554/eLife.76927

Yeh, S. -C., Strilets, T., Tan, W. -L., Castillo, D., Medkour, H., Rey-Cadilhac, F., . . . Garcia-Blanco, M. A. (2023). The anti-immune dengue subgenomic flaviviral RNA is present in vesicles in mosquito saliva and is associated with increased infectivity. PLOS PATHOGENS, 19(3). doi:10.1371/journal.ppat.1011224

2022:
Sehrawat, S., & Garcia-Blanco, M. A. (2023). RNA virus infections and their effect on host alternative splicing. ANTIVIRAL RESEARCH, 210. doi:10.1016/j.antiviral.2022.105503

Garcia-Blanco, M. A., Ooi, E. E., & Sessions, O. M. (2022). RNA Viruses, Pandemics and Anticipatory Preparedness. VIRUSES-BASEL, 14(10). doi:10.3390/v14102176

Galarza-Munoz, G., Kennedy-Boone, D., Schott, G., Bradrick, S. S., & Garcia-Blanco, M. A. (2022). Antisense modulation of IL7R splicing to control sIL7R expression in human CD4+ T cells. RNA, 28(8), 1058-1073. doi:10.1261/rna.079137.122

Fagg, W. S., Liu, N., Braunschweig, U., Pereira de Castro, K. L., Chen, X., Ditmars, F. S., . . . Garcia-Blanco, M. A. (2022). Definition of germ layer cell lineage alternative splicing programs reveals a critical role for Quaking in specifying cardiac cell fate. NUCLEIC ACIDS RESEARCH, 50(9), 5313-5334. doi:10.1093/nar/gkac327

Diosa-Toro, M., Kennedy, D. R., Chuo, V., Popov, V. L., Pompon, J., & Garcia-Blanco, M. A. (2022). Y-Box Binding Protein 1 Interacts with Dengue Virus Nucleocapsid and Mediates Viral Assembly. MBIO, 13(1). doi:10.1128/mbio.00196-22

Bradley Gelfand, PhD.

2024:

Ambati J, Gelfand BD. Response to 'Early Onset Drusen and RPE Dysfunction in a Patient with NLRP3-AID'. Ocul Immunol Inflamm. 2024 Jul;32(5):778. doi: 10.1080/09273948.2023.2191710. Epub 2023 Apr 12. PMID: 37043599; PMCID: PMC10567984.

2023:

An, S., Yu, H., Islam, M. D. M., Zhang, X., Zhan, Y., Olivieri, J. J., . . . Gelfand, B. D. (2023). Effects of donor-specific microvascular anatomy on hemodynamic perfusion in human choriocapillaris. SCIENTIFIC REPORTS, 13(1). doi:10.1038/s41598-023-48631-2

Gelfand, B. D., Argyle, D. A., Olivieri, J. J., & Ambati, J. (2023). Survey of commercial antibodies targeting Y chromosome-encoded genes.. MedComm - Future medicine, 2(4), e62. doi:10.1002/mef2.62

2022:
Huang, P., Narendran, S., Pereira, F., Fukuda, S., Nagasaka, Y., Apicella, I., . . . Ambati, J. (2022). Subretinal injection in mice to study retina physiology and disease. NATURE PROTOCOLS, 17(6), 1468-+. doi:10.1038/s41596-022-00689-4

Huang, P., Narendran, S., Pereira, F., Fukuda, S., Nagasaka, Y., Apicella, I., . . . Ambati, J. (2022). The Learning Curve of Murine Subretinal Injection Among Clinically Trained Ophthalmic Surgeons. TRANSLATIONAL VISION SCIENCE & TECHNOLOGY, 11(3). doi:10.1167/tvst.11.3.13

Palko, S. I., Saba, N. J., Mullane, E., Nicholas, B. D., Nagasaka, Y., Ambati, J., . . . Mohan, R. (2022). Compartmentalized citrullination in Muller glial endfeet during retinal degeneration. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 119(9). doi:10.1073/pnas.2121875119

Ropp, A., Frazier, A. A., Gelfand, B., & Jeudy, J. (2022). The Dean Effect: An Aortic Arch Flow Artifact Mimicking Dissection. RADIOLOGY-CARDIOTHORACIC IMAGING, 4(1). doi:10.1148/ryct.210229

Daniel Gioeli, PhD.

2024:
Scott, T. G., Sathyan, K. M., Gioeli, D., & Guertin, M. J. (2024). TRPS1 modulates chromatin accessibility to regulate estrogen receptor alpha (ER) binding and ER target gene expression in luminal breast cancer cells. PLOS GENETICS, 20(2). doi:10.1371/journal.pgen.1011159

2023:
Hasterok, S., Scott, T. G., Roller, D. G., Spencer, A., Dutta, A. B., Sathyan, K. M., . . . Gioeli, D. (2023). The Androgen Receptor Does Not Directly Regulate the Transcription of DNA Damage Response Genes. MOLECULAR CANCER RESEARCH, 21(12), 1329-1341. doi:10.1158/1541-7786.MCR-23-0358

Chow, P. I., Roller, D. G., Boukhechba, M., Shaffer, K. M., Ritterband, L. M., Reilley, M. J., . . . Gioeli, D. G. (2023). Mobile sensing to advance tumor modeling in cancer patients: A conceptual framework. INTERNET INTERVENTIONS-THE APPLICATION OF INFORMATION TECHNOLOGY IN MENTAL AND BEHAVIOURAL HEALTH, 34. doi:10.1016/j.invent.2023.100644

Scott, T. G., Sathyan, K. M., Gioeli, D., & Guertin, M. J. (2023). TRPS1 modulates chromatin accessibility to regulate estrogen receptor (ER) binding and ER target gene expression in luminal breast cancer cells.. bioRxiv. doi:10.1101/2023.07.03.547524

Li, J., Huang, T., Hua, J., Wang, Q., Su, Y., Chen, P., . . . He, J. (2023). CD46 targeted 212Pb alpha particle radioimmunotherapy for prostate cancer treatment. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH, 42(1). doi:10.1186/s13046-023-02636-x

Lian-Wang Guo, PhD.

2024:
Li, J., Shen, H., & Guo, L. -W. (2024). Transmembrane protein TMEM97 and epigenetic reader BAHCC1 constitute an axis that supports pro-inflammatory cytokine expression. CELLULAR SIGNALLING, 116. doi:10.1016/j.cellsig.2024.111069

2023:
Shirasu, T., Yodsanit, N., Li, J., Huang, Y., Xie, X., Tang, R., . . . Guo, L. -W. (2023). Neointima abating and endothelium preserving-An adventitia-localized nanoformulation to inhibit the epigenetic writer DOT1L. BIOMATERIALS, 301. doi:10.1016/j.biomaterials.2023.122245

Zhang, M., Li, J., Wang, Q., Urabe, G., Tang, R., Huang, Y., . . . Guo, L. -W. (2023). Gene-repressing epigenetic reader EED unexpectedly enhances cyclinD1 gene activation. MOLECULAR THERAPY-NUCLEIC ACIDS, 31. doi:10.1016/j.omtn.2023.02.024

Xie, X., Shirasu, T., Li, J., Guo, L. -W., & Kent, K. C. (2023). miR579-3p is an inhibitory modulator of neointimal hyperplasia and transcription factors c-MYB and KLF4. CELL DEATH DISCOVERY, 9(1). doi:10.1038/s41420-023-01364-7

Yodsanit, N., Shirasu, T., Huang, Y., Yin, L., Islam, Z. H., Gregg, A. C., . . . Wang, B. (2023). Targeted PERK inhibition with biomimetic nanoclusters confers preventative and interventional benefits to elastase-induced abdominal aortic aneurysms. BIOACTIVE MATERIALS, 26, 52-63. doi:10.1016/j.bioactmat.2023.02.009

Li, J., Satyshur, K. A., Guo, L. -W., & Ruoho, A. E. (2023). Sphingoid Bases Regulate the Sigma-1 Receptor-Sphingosine and N,N'-Dimethylsphingosine Are Endogenous Agonists. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 24(4). doi:10.3390/ijms24043103

2022:
Mavlyutov, T. A. A., Li, J., Liu, X., Shen, H., Yang, H., McCurdy, C. R. R., . . . Guo, L. -W. (2022). Retinal Photoreceptor Protection in an AMD-Related Mouse Model by Selective Sigma-1 or Sigma-2 Receptor Modulation. GENES, 13(12). doi:10.3390/genes13122386

Li, J., Felix-Soriano, E., Wright, K. R., Shen, H., Baer, L. A., Stanford, K. I., & Guo, L. -W. (2022). Differential Responses to Sigma-1 or Sigma-2 Receptor Ablation in Adiposity, Fat Oxidation, and Sexual Dimorphism. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 23(18). doi:10.3390/ijms231810846

Xie, X., Guo, L. -W., & Kent, C. K. (2022). miR548ai antagonism attenuates exosome-induced endothelial cell dysfunction (Oct, 10.1038/s41420-022-01178-z, 2021). CELL DEATH DISCOVERY, 8(1). doi:10.1038/s41420-022-01178-z

Li, J., Shen, H., Owens, G. K., & Guo, L. -W. (2022). SREBP1 regulates Lgals3 activation in response to cholesterol loading. MOLECULAR THERAPY-NUCLEIC ACIDS, 28, 892-909. doi:10.1016/j.omtn.2022.05.028

Zhang, M., Urabe, G., Ozer, H. G., Xie, X., Webb, A., Shirasu, T., . . . Guo, L. -W. (2022). Angioplasty induces epigenomic remodeling in injured arteries. LIFE SCIENCE ALLIANCE, 5(5). doi:10.26508/lsa.202101114

Marie-Louise Hammerskjold, PhD.

2024:

Jackson PEH, Dzhivhuho G, Huang J, Hammarskjold ML, Rekosh D. Measurement of HIV Rev-Rev Response Element Functional Activity. Methods Mol Biol. 2024;2807:175-194. doi: 10.1007/978-1-0716-3862-0_13. PMID: 38743229.

2023:
Jackson, P. E. H., Holsey, J., Turse, L., Hammarskjold, M. -L., & Rekosh, D. (2023). Rev-Rev Response Element Activity Selection Bias at the Human Immunodeficiency Virus Transmission Bottleneck. OPEN FORUM INFECTIOUS DISEASES, 10(10). doi:10.1093/ofid/ofad486

Jackson, P. E. H., Holsey, J., Turse, L., Marie-Louise, H., & Rekosh, D. (2023). Rev-Rev Response Element Activity Selection Bias at the HIV Transmission Bottleneck.. bioRxiv. doi:10.1101/2023.04.05.535732

2022:
Dzhivhuho, G., Holsey, J., Honeycutt, E., O'Farrell, H., Rekosh, D., Hammarskjold, M. -L., & Jackson, P. E. H. (2022). HIV-1 Rev-RRE functional activity in primary isolates is highly dependent on minimal context-dependent changes in Rev. SCIENTIFIC REPORTS, 12(1). doi:10.1038/s41598-022-21714-2

Cronk, J. M., Dziewulska, K. H., Puchalski, P., Crittenden, R. B., Hammarskjod, M. -L., & Brown, M. G. (2022). Altered-Self MHC Class I Sensing via Functionally Disparate Paired NK Cell Receptors Counters Murine Cytomegalovirus gp34-Mediated Immune Evasion. JOURNAL OF IMMUNOLOGY, 209(8), 1545-1554. doi:10.4049/jimmunol.2200441

Anuradha Illendula, PhD.

2022:

Doffo, J., Bamopoulos, S. A., Koese, H., Orben, F., Zang, C., Pons, M., . . . Wirth, M. (2022). NOXA expression drives synthetic lethality to RUNX1 inhibition in pancreatic cancer. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 119(9). doi:10.1073/pnas.2105691119

Qi, X., Wu, F., Kim, S. H., Kaifi, J. T., Kimchi, E. T., Snyder, H., . . . Li, G. (2022). Nanoliposome C6-Ceramide in combination with anti-CTLA4 antibody improves anti-tumor immunity in hepatocellular cancer. FASEB JOURNAL, 36(4). doi:10.1096/fj.202101707R

Salotto KE, Olson WC Jr, Pollack KE, Illendula A, Michel E, Henriques S, Fox T, Walker S, Dunlap-Brown M, Slingluff CL Jr, Kester M, Snyder HW. A nano-enhanced vaccine for metastatic melanoma immunotherapy. Cancer Drug Resist. 2022 Jul 7;5(3):829-845. doi: 10.20517/cdr.2021.132. PMID: 36176766; PMCID: PMC9511805.

Wray JP, Deltcheva EM, Boiers C, Richardson SЕ, Chhetri JB, Brown J, Gagrica S, Guo Y, Illendula A, Martens JHA, Stunnenberg HG, Bushweller JH, Nimmo R, Enver T. Regulome analysis in B-acute lymphoblastic leukemia exposes Core Binding Factor addiction as a therapeutic vulnerability. Nat Commun. 2022 Nov 21;13(1):7124. doi: 10.1038/s41467-022-34653-3. PMID: 36411286; PMCID: PMC9678885.

Lulu Jiang, MD. PhD.

2024:
Jiang L, Roberts R, Wong M, Zhang L, Webber CJ, Libera J, Wang Z, Kilci A, Jenkins M, Ortiz AR, Dorrian L, Sun J, Sun G, Rashad S, Kornbrek C, Daley SA, Dedon PC, Nguyen B, Xia W, Saito T, Saido TC, Wolozin B. β-amyloid accumulation enhances microtubule associated protein tau pathology in an APPNL-G-F/MAPTP301S mouse model of Alzheimer's disease. Front Neurosci. 2024 Mar 20;18:1372297. doi: 10.3389/fnins.2024.1372297. PMID: 38572146; PMCID: PMC10987964.

2023:
Jiang, L., Roberts, R., Wong, M., Zhang, L., Webber, C. J., Kilci, A., . . . Wolozin, B. (2023). Accumulation of m6A exhibits stronger correlation with MAPT than β-amyloid pathology in an APPNL-G-F /MAPTP301S mouse model of Alzheimer's disease. doi:10.21203/rs.3.rs-2745852/v1

Jiang, L., Roberts, R., Wong, M., Zhang, L., Webber, C. J., Kilci, A., . . . Wolozin, B. (2023). Accumulation of m6A exhibits stronger correlation with MAPT than β-amyloid pathology in an APPNL-G-F/MAPTP301Smouse model of Alzheimer’s disease. doi:10.1101/2023.03.28.534515

Jiang, L., Chakraborty, P., Zhang, L., Wong, M., Hill, S. E., Webber, C. J., . . . Zweckstetter, M. (2023). Chaperoning of specific tau structure by immunophilin FKBP12 regulates the neuronal resilience to extracellular stress. SCIENCE ADVANCES, 9(5). doi:10.1126/sciadv.add9789

2022:
Rickner, H. D., Jiang, L., Hong, R., O'Neill, N. K., Mojica, C. A., Snyder, B. J., . . . Cheng, C. S. (2022). Single cell transcriptomic profiling of a neuron-astrocyte assembloid tauopathy model. NATURE COMMUNICATIONS, 13(1). doi:10.1038/s41467-022-34005-1

Hao Jiang, PhD.

2024:
Giudice, J., & Jiang, H. (2024). Splicing regulation through biomolecular condensates and membraneless organelles. NATURE REVIEWS MOLECULAR CELL BIOLOGY. doi:10.1038/s41580-024-00739-7

Jiang, H. (2024). Phase separation in nuclear biology. NUCLEUS, 15(1). doi:10.1080/19491034.2024.2310424

2023:
Banerjee, P. R., Holehouse, A. S., Kriwacki, R., Robustelli, P., Jiang, H., Sobolevsky, A. I., . . . Mendell, J. T. (2024). Dissecting the biophysics and biology of intrinsically disordered proteins. TRENDS IN BIOCHEMICAL SCIENCES, 49(2), 101-104. doi:10.1016/j.tibs.2023.10.002

Li, W., & Jiang, H. (2023). Analysis of Phase-Separated Biomolecular Condensates in Cancer.. Methods in molecular biology (Clifton, N.J.), 2660, 345-356. doi:10.1007/978-1-0716-3163-8_23

2022:
Zhao, Y., Hao, X., Li, Z., Feng, X., Katz, J., Michalek, S. M., . . . Zhang, P. (2022). Role of chromatin modulator Dpy30 in osteoclast differentiation and function. BONE, 159. doi:10.1016/j.bone.2022.116379

Ahmad Jomaa, PhD.

2023:
Gamerdinger, M., Jia, M., Schloemer, R., Rabl, L., Jaskolowski, M., Khakzar, K. M., . . . Deuerling, E. (2023). NAC controls cotranslational N-terminal methionine excision in eukaryotes. SCIENCE, 380(6651), 1238-1243. doi:10.1126/science.adg3297

Jaskolowski, M., Jomaa, A., Gamerdinger, M., Shrestha, S., Leibundgut, M., Deuerling, E., & Ban, N. (2023). Molecular basis of the TRAP complex function in ER protein biogenesis. NATURE STRUCTURAL & MOLECULAR BIOLOGY, 30(6), 770-+. doi:10.1038/s41594-023-00990-0

Fromm, S. A. A., O'Connor, K. M. M., Purdy, M., Bhatt, P. R. R., Loughran, G., Atkins, J. F. F., . . . Mattei, S. (2023). The translating bacterial ribosome at 1.55 Å resolution generated by cryo-EM imaging services. NATURE COMMUNICATIONS, 14(1). doi:10.1038/s41467-023-36742-3

2022:
Jomaa, A., Gamerdinger, M., Hsieh, H. -H., Wallisch, A., Chandrasekaran, V., Ulusoy, Z., . . . Deuerling, E. (2022). Mechanism of signal sequence handover from NAC to SRP on ribosomes during ER-protein targeting. SCIENCE, 375(6583), 839-+. doi:10.1126/science.abl6459

Kavalchuk, M., Jomaa, A., Mueller, A. U., & Weber-Ban, E. (2022). Structural basis of prokaryotic ubiquitin-like protein engagement and translocation by the mycobacterial Mpa-proteasome complex. NATURE COMMUNICATIONS, 13(1). doi:10.1038/s41467-021-27787-3

Melissa M. Kendell, PhD.

2024
Gonyar, L. A., Sauder, A. B., Mortensen, L., Willsey, G. G., & Kendall, M. M. (2024). The yad and yeh fimbrial loci influence gene expression and virulence in enterohemorrhagic Escherichia coli O157:H7. MSPHERE. doi:10.1128/msphere.00124-24

2022
Kreutzberger, M. A. B., Sobe, R. C., Sauder, A. B., Chatterjee, S., Pena, A., Wang, F., . . . Egelman, E. H. (2022). Flagellin outer domain dimerization modulates motility in pathogenic and soil bacteria from viscous environments. NATURE COMMUNICATIONS, 13(1). doi:10.1038/s41467-022-29069-y

Muge N. Kuyumcu-Martinez, PhD.

2024:
Verma, S. K., & Kuyumcu-Martinez, M. N. (2024). RNA binding proteins in cardiovascular development and disease.. Current topics in developmental biology, 156, 51-119. doi:10.1016/bs.ctdb.2024.01.007

2023:
Deberneh, H. M., Abdelrahman, D. R., Verma, S. K., Linares, J. J., Murton, A. J., Russell, W. K., . . . Sadygov, R. G. (2023). A large-scale LC-MS dataset of murine liver proteome from time course of heavy water metabolic labeling. SCIENTIFIC DATA, 10(1). doi:10.1038/s41597-023-02537-w

Mehlferber, M. M., Kuyumcu-Martinez, M., Miller, C. L., & Sheynkman, G. M. (2023). Transcription Factors and Splice Factors-Interconnected Regulators of Stem Cell Differentiation. CURRENT STEM CELL REPORTS, 9(2), 31-41. doi:10.1007/s40778-023-00227-2

Deberneh, H. M., Abdelrahman, D. R., Verma, S. K., Linares, J. J., Murton, A. J., Russell, W. K., . . . Sadygov, R. G. (2023). Quantifying label enrichment from two mass isotopomers increases proteome coverage for in vivo protein turnover using heavy water metabolic labeling. COMMUNICATIONS CHEMISTRY, 6(1). doi:10.1038/s42004-023-00873-x

Cao, J., & Kuyumcu-Martinez, M. N. (2023). Alternative polyadenylation regulation in cardiac development and cardiovascular disease. CARDIOVASCULAR RESEARCH, 119(6), 1324-1335. doi:10.1093/cvr/cvad014

2022:
Sotcheff, S. L., Chen, J. Y. -C., Elrod, N., Cao, J., Jaworski, E., Kuyumcu-Martinez, M. N., . . . Routh, A. L. (2022). Zika Virus Infection Alters Gene Expression and Poly-Adenylation Patterns in Placental Cells. PATHOGENS, 11(8). doi:10.3390/pathogens11080936

Cooper, A. M., Nutter, C. A., Kuyumcu-Martinez, M. N., & Wright, C. W. (2022). Alternative Splicing of the Aryl Hydrocarbon Receptor Nuclear Translocator (ARNT) Is Regulated by RBFOX2 in Lymphoid Malignancies. MOLECULAR AND CELLULAR BIOLOGY, 42(5). doi:10.1128/mcb.00503-21

Verma, S. K., Deshmukh, V., Thatcher, K., Belanger, K. K., Rhyner, A. M., Meng, S., . . . Kuyumcu-Martinez, M. N. (2022). RBFOX2 is required for establishing RNA regulatory networks essential for heart development. NUCLEIC ACIDS RESEARCH, 50(4), 2270-2286. doi:10.1093/nar/gkac055

Hui Li, PhD.

2024:
Singh, S., Shi, X., Haddox, S., Elfman, J., Ahmad, S. B., Lynch, S., . . . Li, H. (2024). RTCpredictor: identification of read-through chimeric RNAs from RNA sequencing data. BRIEFINGS IN BIOINFORMATICS, 25(4). doi:10.1093/bib/bbae251

Elfman, J., Goins, L., Heller, T., Singh, S., Wang, Y. -H., & Li, H. (2024). Discovery of a polymorphic gene fusion via bottom-up chimeric RNA prediction. NUCLEIC ACIDS RESEARCH. doi:10.1093/nar/gkae258

Wang, Q., Cheng, B., Singh, S., Tao, Y., Xie, Z., Qin, F., . . . Huang, H. (2024). A protein-encoding CCDC7 circular RNA inhibits the progression of prostate cancer by up-regulating FLRT3. NPJ PRECISION ONCOLOGY, 8(1). doi:10.1038/s41698-024-00503-2

2023:
Chen, C., Qin, F., Singh, S., Tang, Y., & Li, H. (2023). CTNNBIP1-CLSTN1 functions as a housekeeping chimeric RNA and regulates cell proliferation through SERPINE2. CELL DEATH DISCOVERY, 9(1). doi:10.1038/s41420-023-01668-8

Cornelison, R., Marrah, L., Fierti, A., Piczak, C., Glowczyk, M., Tajammal, A., . . . Li, H. (2023). The Potential for Targeting AVIL and Other Actin-Binding Proteins in Rhabdomyosarcoma. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 24(18). doi:10.3390/ijms241814196

Li, H., & Wang, Q. (2023). Chimeric RNAs and their implication in prostate cancer.. Cancer pathogenesis and therapy, 1(3), 216-219. doi:10.1016/j.cpt.2023.04.003

Dutta, A., Li, H., & Abounader, R. (2023). Cryptic lncRNA-encoded ORFs: A hidden source of regulatory proteins. JOURNAL OF CLINICAL INVESTIGATION, 133(5). doi:10.1172/JCI167271

2022:
Lee, H. -Y., Jang, H. R., Li, H., Samuel, V. T., Dudek, K. D., Osipovich, A. B., . . . Shulmane, G. I. (2022). Deletion of Jazf 1 gene causes early growth retardation and insulin resistance in mice. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 119(49). doi:10.1073/pnas.2213628119

Elagib, K. E., Brock, A., Clementelli, C. M., Mosoyan, G., Delehanty, L. L., Sahu, R. K., . . . Goldfarb, A. N. (2022). Relieving DYRK1A repression of MKL1 confers an adult- like phenotype to human infantile megakaryocytes. JOURNAL OF CLINICAL INVESTIGATION, 132(19). doi:10.1172/JCI154839

Wang, Q., Chen, J., Singh, S., Xie, Z., Qin, F., Shi, X., . . . Huang, H. (2022). Profile of chimeric RNAs and TMPRSS2-ERG e2e4 isoform in neuroendocrine prostate cancer. CELL AND BIOSCIENCE, 12(1). doi:10.1186/s13578-022-00893-5

Xie, Z., Janczyk, P. L., Shi, X., Wang, Q., Singh, S., Cornelison, R., . . . Li, H. (2022). Rhabdomyosarcomas are oncogene addicted to the activation of AVIL. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 119(24). doi:10.1073/pnas.2118048119

Sun, Y., & Li, H. (2022). Chimeric RNAs Discovered by RNA Sequencing and Their Roles in Cancer and Rare Genetic Diseases. GENES, 13(5). doi:10.3390/genes13050741

Mani S. Mahadevan, MD.

2023:
Alam, S. R., Mahadevan, M. S., & Periasamy, A. (2023). Detecting RNA-Protein Interactions With EGFP-Cy3 FRET by Acceptor Photobleaching.. Current protocols, 3(2), e689. doi:10.1002/cpz1.689

Manoj Patel, PhD.

2023:
Miralles, R., & Patel, M. K. (2024). Unspooling the Thread: VIP Interneurons Linked With Autism Spectrum Disorder Behaviors but Not Seizures in Dravet Syndrome. EPILEPSY CURRENTS, 24(1), 62-64. doi:10.1177/15357597231218876

Wenker, I. C., & Patel, M. K. (2023). A Water Nymph's Curse and the Serotonergic Mechanism of Postictal Breathing Dysfunction. EPILEPSY CURRENTS, 23(6), 369-371. doi:10.1177/15357597231199340

Wenker, I. C., & Patel, M. K. (2023). Waiting to Inhale: Preventing Fatality From Seizure-Induced Apnea. EPILEPSY CURRENTS, 23(3), 185-187. doi:10.1177/15357597231159466

2022:
Wenker, I. C., Wagley, P. K., Boscia, A. R., Lewis, C., & Patel, M. K. (2022). Opto- and Chemogenetic Dissection of Ictal Apnea Neural Circuitry.. FASEB journal : official publication of the Federation of American Societies for Experimental Biology, 36 Suppl 1. doi:10.1096/fasebj.2022.36.s1.r2354

Thompson, J. A., Miralles, R. M., Wengert, E. R., Wagley, P. K., Yu, W., Wenker, I. C., & Patel, M. K. (2022). Astrocyte reactivity in a mouse model of SCN8A epileptic encephalopathy. EPILEPSIA OPEN, 7(2), 280-292. doi:10.1002/epi4.12564

Miralles, R., & Patel, M. K. (2022). That's a Wrap: Could Controlling Activity-Regulated Myelination Prevent Absence Seizures?. EPILEPSY CURRENTS, 22(6), 395-397. doi:10.1177/15357597221123898

Wenker, I. C., Boscia, A. R., Lewis, C., Tariq, A., Miralles, R., Hanflink, J. C., . . . Patel, M. K. (2022). Forebrain epileptiform activity is not required for seizure-induced apnea in a mouse model of Scn8a epilepsy. FRONTIERS IN NEURAL CIRCUITS, 16. doi:10.3389/fncir.2022.1002013

John H. Platig, PhD.

2024:
Stone, K., Platig, J., Quackenbush, J., & Fagny, M. (2024). Complex Traits Heritability is Highly Clustered in the eQTL Bipartite Network.. bioRxiv. doi:10.1101/2024.02.27.582063

2023:
Ben Guebila, M., Wang, T., Lopes-Ramos, C. M. M., Fanfani, V., Weighill, D., Burkholz, R., . . . Quackenbush, J. (2023). The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks. GENOME BIOLOGY, 24(1). doi:10.1186/s13059-023-02877-1

2022:
Gaynor, S. M., Fagny, M., Lin, X., Platig, J., & Quackenbush, J. (2022). Connectivity in eQTL networks dictates reproducibility and genomic properties. CELL REPORTS METHODS, 2(5). doi:10.1016/j.crmeth.2022.100218

Ben Guebila, M., Weighill, D., Lopes-Ramos, C. M., Burkholz, R., Pop, R. T., Palepu, K., . . . Quackenbush, J. (2022). An online notebook resource for reproducible inference, analysis and publication of gene regulatory networks. NATURE METHODS, 19(5), 511-513. doi:10.1038/s41592-022-01479-2

Weighill, D., Ben Guebila, M., Glass, K., Quackenbush, J., & Platig, J. (2022). Predicting genotype-specific gene regulatory networks. GENOME RESEARCH, 32(3), 524-533. doi:10.1101/gr.275107.120

David Rekosh, PhD.

2024:

Stephen S. Rich, PhD.

2024:
Lim, S. S., Semnani-Azad, Z., Morieri, M. L., Ng, A. H., Ahmad, A., Fitipaldi, H., . . . Franks, P. W. (2024). Reporting guidelines for precision medicine research of clinical relevance: the BePRECISE checklist.. Nature medicine, 30(7), 1874-1881. doi:10.1038/s41591-024-03033-3

Phillip, M., Achenbach, P., Addala, A., Albanese-O'Neill, A., Battelino, T., Bell, K. J., . . . DiMeglio, L. A. (2024). Consensus guidance for monitoring individuals with islet autoantibody-positive pre-stage 3 type 1 diabetes. DIABETOLOGIA. doi:10.1007/s00125-024-06205-5

Phillip, M., Achenbach, P., Addala, A., Albanese-O'Neill, A., Battelino, T., Bell, K. J., . . . DiMeglio, L. A. (2024). Consensus Guidance for Monitoring Individuals With Islet Autoantibody-Positive Pre-Stage 3 Type 1 Diabetes.. Diabetes care, dci240042. doi:10.2337/dci24-0042

Mack, T. M., Raddatz, M. A., Pershad, Y., Nachun, D. C., Taylor, K. D., Guo, X., . . . Bick, A. G. (2024). Epigenetic and proteomic signatures associate with clonal hematopoiesis expansion rate. NATURE AGING. doi:10.1038/s43587-024-00647-7

Keener, R., Chhetri, S. B., Connelly, C. J., Taub, M. A., Conomos, M. P., Weinstock, J., . . . Battle, A. (2024). Validation of human telomere length multi-ancestry meta-analysis association signals identifies POP5 and KBTBD6 as human telomere length regulation genes.. Nature communications, 15(1), 4417. doi:10.1038/s41467-024-48394-y

Chen, Z., Satake, E., Pezzolesi, M. G., Md Dom, Z. I., Stucki, D., Kobayashi, H., . . . Natarajan, R. (2024). Integrated analysis of blood DNA methylation, genetic variants, circulating proteins, microRNAs, and kidney failure in type 1 diabetes. SCIENCE TRANSLATIONAL MEDICINE, 16(748). doi:10.1126/scitranslmed.adj3385

Triolo, T. M., Parikh, H. M., Tosur, M., Ferrat, L. A., You, L., Gottlieb, P. A., . . . Redondo, M. J. (2024). Genetic Associations With C-peptide Levels Before Type 1 Diabetes Diagnosis in At-risk Relatives. JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM. doi:10.1210/clinem/dgae349

Pershad, Y., Mack, T., Poisner, H., Jakubek, Y. A., Stilp, A. M., Mitchell, B. D., . . . Bick, A. G. (2024). Determinants of mosaic chromosomal alteration fitness. NATURE COMMUNICATIONS, 15(1). doi:10.1038/s41467-024-48190-8

Lincoln, M. R., Connally, N., Axisa, P. -P., Gasperi, C., Mitrovic, M., van Heel, D., . . . Cotsapas, C. (2024). Genetic mapping across autoimmune diseases reveals shared associations and mechanisms. NATURE GENETICS. doi:10.1038/s41588-024-01732-8

Keaton, J. M., Kamali, Z., Xie, T., Vaez, A., Williams, A., Goleva, S. B., . . . Warren, H. R. (2024). Genome-wide analysis in over 1 million individuals of European ancestry yields improved polygenic risk scores for blood pressure traits.. Nature genetics, 56(5), 778-791. doi:10.1038/s41588-024-01714-w

Kwak, S. H., Hernandez-Cancela, R. B., DiCorpo, D. A., Condon, D. E., Merino, J., Wu, P., . . . Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium. (2024). Time-to-Event Genome-Wide Association Study for Incident Cardiovascular Disease in People With Type 2 Diabetes.. Diabetes care, 47(6), 1042-1047. doi:10.2337/dc23-2274

Felton, J. L., Redondo, M. J., Oram, R. A., Speake, C., Long, S. A., Onengut-Gumuscu, S., . . . Franks, P. W. (2024). Islet autoantibodies as precision diagnostic tools to characterize heterogeneity in type 1 diabetes: a systematic review. COMMUNICATIONS MEDICINE, 4(1). doi:10.1038/s43856-024-00478-y

Lundin, J. I., Peters, U., Hu, Y., Ammous, F., Avery, C. L., Benjamin, E. J., . . . Kooperberg, C. (2024). Methylation patterns associated with C-reactive protein in racially and ethnically diverse populations. EPIGENETICS, 19(1). doi:10.1080/15592294.2024.2333668

Xiao, S., Li, V. L., Lyu, X., Chen, X., Wei, W., Abbasi, F., . . . Long, J. Z. (2024). Lac-Phe mediates the effects of metformin on food intake and body weight. NATURE METABOLISM, 6(4). doi:10.1038/s42255-024-00999-9

Michalek, D. A., Tern, C., Zhou, W., Robertson, C. C., Farber, E., Campolieto, P., . . . Rich, S. S. (2024). A multi-ancestry genome-wide association study in type 1 diabetes. HUMAN MOLECULAR GENETICS, 33(11), 958-968. doi:10.1093/hmg/ddae024

Shetty, N. S., Pampana, A., Patel, N., Yerabolu, K., Patel, G., Irvin, M. R., . . . Arora, P. (2024). Sex Differences in the Association of Multiethnic Genome-Wide Blood Pressure Polygenic Risk Score With Population-Level Systolic Blood Pressure Trajectories. CIRCULATION-GENOMIC AND PRECISION MEDICINE, 17(2). doi:10.1161/CIRCGEN.123.004515

Peterson, T. E., Hahn, V. S., Moaddel, R., Zhu, M., Haberlen, S. A., Palella, F. J., . . . Post, W. S. (2024). Proteomic Signature of HIV-Associated Subclinical Left Atrial Remodeling and Incident Heart Failure.. medRxiv. doi:10.1101/2024.02.13.24302797

Guertin, K. A., Repaske, D. R., Taylor, J. F., Williams, E. S., Onengut-Gumuscu, S., Chen, W. -M., . . . Rich, S. S. (2024). Implementation of type 1 diabetes genetic risk screening in children in diverse communities: the Virginia PrIMeD project. GENOME MEDICINE, 16(1). doi:10.1186/s13073-024-01305-8

Higbee, D. H., Lirio, A., Hamilton, F., Granell, R., Wyss, A. B., London, S. J., . . . Dodd, J. W. (2024). Genome-wide association study of preserved ratio impaired spirometry (PRISm). EUROPEAN RESPIRATORY JOURNAL, 63(1). doi:10.1183/13993003.00337-2023

2023:
de Vries, P. S., Conomos, M. P., Singh, K., Nicholson, C. J., Jain, D., Hasbani, N. R., . . . Malhotra, R. (2023). Whole-genome sequencing uncovers two loci for coronary artery calcification and identifies ARSE as a regulator of vascular calcification. NATURE CARDIOVASCULAR RESEARCH, 2(12), 1159-+. doi:10.1038/s44161-023-00375-y

Hasbani, N. R., Westerman, K. E., Kwak, S. H., Chen, H., Li, X., Di Corpo, D., . . . de Vries, P. S. (2023). Type 2 Diabetes Modifies the Association of CAD Genomic Risk Variants With Subclinical Atherosclerosis. CIRCULATION-GENOMIC AND PRECISION MEDICINE, 16(6). doi:10.1161/CIRCGEN.123.004176

Tin, A., Fohner, A. E., Yang, Q., Brody, J. A., Davies, G., Yao, J., . . . Fornage, M. (2023). Identification of circulating proteins associated with general cognitive function among middle-aged and older adults. COMMUNICATIONS BIOLOGY, 6(1). doi:10.1038/s42003-023-05454-1

Jakubek, Y. A., Zhou, Y., Stilp, A., Bacon, J., Wong, J. W., Ozcan, Z., . . . Auer, P. L. (2023). Mosaic chromosomal alterations in blood across ancestries using whole-genome sequencing. NATURE GENETICS, 55(11), 1912-+. doi:10.1038/s41588-023-01553-1

Pershad, Y., Mack, T., Poisner, H., Jakubek, Y. A., Stilp, A. M., Mitchell, B. D., . . . Bick, A. G. (2023). Determinants of mosaic chromosomal alteration fitness.. medRxiv. doi:10.1101/2023.10.20.23297280

Liu, X., Sun, X., Zhang, Y., Jiang, W., Lai, M., Wiggins, K. L., . . . Liu, C. (2023). Association Between Whole Blood-Derived Mitochondrial DNA Copy Number, Low-Density Lipoprotein Cholesterol, and Cardiovascular Disease Risk. JOURNAL OF THE AMERICAN HEART ASSOCIATION, 12(20). doi:10.1161/JAHA.122.029090

2022:
Li, X., Quick, C., Zhou, H., Gaynor, S. M., Liu, Y., Chen, H., . . . Lin, X. (2023). Powerful, scalable and resource-efficient meta-analysis of rare variant associations in large whole genome sequencing studies. NATURE GENETICS, 55(1), 154-+. doi:10.1038/s41588-022-01225-6

Wheeler, M. M., Stilp, A. M., Rao, S., Halldorsson, B. V., Beyter, D., Wen, J., . . . Reiner, A. P. (2022). Whole genome sequencing identifies structural variants contributing to hematologic traits in the NHLBI TOPMed program. NATURE COMMUNICATIONS, 13(1). doi:10.1038/s41467-022-35354-7

Liang, J., Wang, H., Cade, B. E., Kurniansyah, N., He, K. Y., Lee, J., . . . Zhu, X. (2022). Targeted Genome Sequencing Identifies Multiple Rare Variants in Caveolin-1 Associated with Obstructive Sleep Apnea. AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, 206(10), 1271-1280. doi:10.1164/rccm.202203-0618OC

Mishra, A., Malik, R., Hachiya, T., Jürgenson, T., Namba, S., Posner, D. C., . . . Debette, S. (2022). Publisher Correction: Stroke genetics informs drug discovery and risk prediction across ancestries.. Nature, 612(7938), E7. doi:10.1038/s41586-022-05492-5

Parcha, V., Pampana, A., Shetty, N. S. S., Irvin, M. R. R., Natarajan, P., Lin, H. J. J., . . . Arora, P. (2022). Association of a Multiancestry Genome-Wide Blood Pressure Polygenic Risk Score With Adverse Cardiovascular Events. CIRCULATION-GENOMIC AND PRECISION MEDICINE, 15(6), 580-593. doi:10.1161/CIRCGEN.122.003946

Li, Z., Li, X., Zhou, H., Gaynor, S. M., Selvaraj, M. S., Arapoglou, T., . . . Lin, X. (2022). A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies. NATURE METHODS, 19(12), 1599-+. doi:10.1038/s41592-022-01640-x

Evan A. Scott

2024:
Du F, Rische S, Li Y, Vincent M, Krier-Burris R, Qian Y, Yuk S, Almunif S, Bochner B, Qiao B, Scott EA. Controlled adsorption of multiple bioactive proteins enables targeted mast cell nanotherapy. Nat. Nanotechnol. (2024). DOI: 10.1038/s41565-023-01584-z.

Klug N, Burke J, Scott EA. Rational Engineering of Islet Tolerance via Biomaterial-Mediated Immune Modulation. J. Immunol. 15 January 2024; 212 (2): 216–224. DOI:10.4049/jimmunol.2300527.
2023:
Morgun E, Zhu J, Almunif S, Bobbala S, Aguilar MS, Wang J, Conner K, Cui Y, Cao L, Seshadri C, Scott EA‡, Wang C-R‡. Vaccination with mycobacterial lipid loaded nanoparticle leads to lipid antigen persistence and memory differentiation of antigen-specific T cells. eLife. 12:RP87431, 2023. DOI: 10.7554/eLife.87431.2. ‡Corresponding authors.

Pagendarm HM, Stone PT, Kimmel BR, Baljon JJ, Aziz MH, Pastora LE, Hubert L, Roth EW, Almunif S, Scott EA, Wilson JT. Engineering endosomolytic nanocarriers of diverse morphologies using confined impingement jet mixing. Nanoscale. 2023;15(39):16016-29. DOI:10.1039/ D3NR02874G.

Boaz B, Sharma S, Scott EA. Nanomedicine in kidney disease. Current Opinion in Nephrology and Hypertension 32(4):p 366-376, July 2023. DOI: 10.1097/MNH.0000000000000897. Download Here

Rische CH, Thames AH, Krier-Burris RA, Bochner BS, Scott EA. Drug Delivery Targets, Strategies, and Formulations to Address Mast Cell Diseases. Expert Opin. Drug Deliv. 20:2, 205-222, DOI: 10.1080/17425247.2023.2166926.

Lescott C, Bobbala S, Modak M, Reis R, Scott EA, Dravid VP. Multimodal Investigation of Damage Processes in Self-Assembled Polymers using Scanning Transmission Electron Microscopy. Microsc. Microanal. Volume 29, Issue 1, February 2023, Pages 16–26, DOI: 10.1093/micmic/ozac023.

2022:
Scott EA, Mooney DJ. A combination microparticle strategy for achieving antigen-specific tolerance. PNAS. 119 (52) e2216976119. DOI: 10.1073/pnas.2216976119.

Scariot DB, Staneviciute A, Scott EA, Engman DM. Leishmaniasis and Chagas disease: Is there hope in nanotechnology to fight neglected tropical diseases? Front. Cell. Infect. Microbiol. 16 September, 2022; DOI: 10.3389/fcimb.2022.1000972. Download Here

Ankeny CJ, Dunton C, Virk R, Scott EA, Kamat N. Development of a Low-Cost, Easy-to-Adopt Diversity, Equity, and Inclusion Program During Crisis. Biomedical Engineering Education. 2022;2(2):175-81. DOI: 10.1007/s43683-022-00072-5.

Bhushan N, Stack T, Scott EA, Shull K, Mathew B; Bijukumar D., In vitro assessment of varying peptide surface density on the suppression of angiogenesis by micelles displaying αvβ3 blocking peptides, J. Biomed. Mater. Res. Part B Appl. Biomater. 2022. DOI:10.1002/jbm.b.35154.

Barman S, Borriello F, Brook B, Pietrasanta C, DeLeon M, Sweitzer C, Menon M, Van Haren S, Soni D, Saito Y, Nanishi E, Yi S, Bobbala S, Ofer L, Scott E, Dowling D. Shaping neonatal immunization by tuning delivery of synergistic adjuvants via nanocarriers. ACS Chem. Biol. 2022; DOI: 10.1021/acschembio.2c00497.

Yi S, Kim SY, Vincent MP, Yuk SA, Bobbala S, Du F, Scott EA. Dendritic peptide-conjugated polymeric nanovectors for nontoxic delivery of plasmid DNA and enhanced non-viral transfection of immune cells. iScience. 25, 104555, July 15, 2022. DOI:10.1016/j.isci.2022.104555.

Plumblee L, Jaishankar D, Scott EA, Atkinson C, Tietjen GT, Nadig SN. Nanotherapeutics in Transplantation: how do we get to clinical implementation? Am J Transplant. 2022; 00: 1– 6. DOI:10.1111/ajt.17012.

Vincent MP, Navidzadeh JO, Bobbala S, Scott EA. Leveraging self-assembled nanobiomaterials for improved cancer immunotherapy. Cancer Cell. 2022. DOI: 10.1016/j.ccell.2022.01.006.

Burke JA, Zhang X, Bobbala S, Frey MA, Furentes CB, Haddad HF, Allen SD, Richardson R, Ameer GA, Scott EA. Subcutaneous nanotherapy repurposes the immunosuppressive mechanism of rapamycin to enhance allogeneic islet graft viability. Nat. Nanotechnol. (2022). DOI: 10.1038/s41565-021-01048-2.

Gloria M. Sheynkman, PhD.

2024:
Korchak, J. A., Jeffery, E. D., Bandyopadhyay, S., Jordan, B. T., Lehe, M. D., Watts, E. F., . . . Sheynkman, G. M. (2024). IS-PRM-Based Peptide Targeting Informed by Long-Read Sequencing for Alternative Proteome Detection.. Journal of the American Society for Mass Spectrometry. doi:10.1021/jasms.4c00119

Pardo-Palacios, F. J., Wang, D., Reese, F., Diekhans, M., Carbonell-Sala, S., Williams, B., . . . Brooks, A. N. (2024). Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. NATURE METHODS. doi:10.1038/s41592-024-02298-3

Joglekar, A., Hu, W., Zhang, B., Narykov, O., Diekhans, M., Marrocco, J., . . . Tilgner, H. U. (2024). Single-cell long-read sequencing-based mapping reveals specialized splicing patterns in developing and adult mouse and human brain. NATURE NEUROSCIENCE, 27(6). doi:10.1038/s41593-024-01616-4

Korchak, J. A., Jeffery, E. D., Bandyopadhyay, S., Jordan, B. T., Lehe, M., Watts, E. F., . . . Sheynkman, G. M. (2024). IS-PRM-based peptide targeting informed by long-read sequencing for alternative proteome detection.. bioRxiv. doi:10.1101/2024.04.01.587549

2023:
Pardo-Palacios, F. J., Wang, D., Reese, F., Diekhans, M., Carbonell-Sala, S., Williams, B., . . . Brooks, A. N. (2023). Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.. bioRxiv. doi:10.1101/2023.07.25.550582

Acharya, B. R., Fang, J. S., Jeffery, E., Chavkin, N. W., Genet, G., Vasavada, H., . . . Hirschi, K. K. (2023). Connexin 37 sequestering of activated-ERK in the cytoplasm promotes p27-mediated endothelial cell cycle arrest. LIFE SCIENCE ALLIANCE, 6(8). doi:10.26508/lsa.202201685

de Souza, V. B. C., Jordan, B. T. T., Tseng, E., Nelson, E. A. A., Hirschi, K. K. K., Sheynkman, G., & Robinson, M. D. D. (2023). Transformation of alignment files improves performance of variant callers for long-read RNA sequencing data. GENOME BIOLOGY, 24(1). doi:10.1186/s13059-023-02923-y

Joglekar, A., Hu, W., Zhang, B., Narykov, O., Diekhans, M., Balacco, J., . . . Tilgner, H. U. (2023). Single-cell long-read mRNA isoform regulation is pervasive across mammalian brain regions, cell types, and development.. bioRxiv. doi:10.1101/2023.04.02.535281

Pan, X., Akdemir, Z. H. C., Gao, R., Jiang, X., Sheynkman, G. M., Wu, E., . . . Yi, S. S. (2023). AD-Syn-Net: systematic identification of Alzheimer's disease-associated mutation and co-mutation vulnerabilities via deep learning. BRIEFINGS IN BIOINFORMATICS, 24(2). doi:10.1093/bib/bbad030

Li, M. M., Awasthi, S., Ghosh, S., Bisht, D., Coban Akdemir, Z. H., Sheynkman, G. M., . . . Yi, S. S. (2023). Gain-of-Function Variomics and Multi-omics Network Biology for Precision Medicine.. Methods in molecular biology (Clifton, N.J.), 2660, 357-372. doi:10.1007/978-1-0716-3163-8_24

2022:

Chavkin, N. W., Genet, G., Poulet, M., Jeffery, E. D., Marziano, C., Genet, N., . . . Hirschi, K. K. (2022). Endothelial cell cycle state determines propensity for arterial-venous fate. NATURE COMMUNICATIONS, 13(1). doi:10.1038/s41467-022-33324-7

de Crecy-Lagard, V., de Hegedus, R. A., Arighi, C., Babor, J., Bateman, A., Blaby, I., . . . Xu, J. (2022). A roadmap for the functional annotation of protein families: a community perspective. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2022. doi:10.1093/database/baac062

Miller, R. M., Jordan, B. T., Mehlferber, M. M., Jeffery, E. D., Chatzipantsiou, C., Kaur, S., . . . Sheynkman, G. M. (2022). Enhanced protein isoform characterization through long-read proteogenomics. GENOME BIOLOGY, 23(1). doi:10.1186/s13059-022-02624-y

Mehlferber, M. M., Jeffery, E. D., Saquing, J., Jordan, B. T., Sheynkman, L., Murali, M., . . . Sheynkman, G. M. (2022). Characterization of protein isoform diversity in human umbilical vein endothelial cells via long-read proteogenomics. RNA BIOLOGY, 19(1), 1228-1243. doi:10.1080/15476286.2022.2141938

Jung-Bum Shin, PhD.

2023:
Wagner, E. L., Im, J. -S., Sala, S., Nakahata, M. I., Imbery, T. E., Li, S., . . . Shin, J. -B. (2023). Repair of noise-induced damage to stereocilia F-actin cores is facilitated by XIRP2 and its novel mechanosensor domain. ELIFE, 12. doi:10.7554/eLife.72681

2022:
Rivet-Noor, C. R., Merchak, A. R., Li, S., Beiter, R. M., Lee, S., Thomas, J. A., . . . Gaultier, A. (2022). Stress-induced despair behavior develops independently of the Ahr-RORγt axis in CD4+cells. SCIENTIFIC REPORTS, 12(1). doi:10.1038/s41598-022-12464-2

Katia Sol-Church, PhD.

2022:

Turner AW, Hu SS, Mosquera JV, Ma WF, Hodonsky CJ, Wong D, Auguste G, Song Y, Sol-Church K, Farber E, Kundu S, Kundaje A, Lopez NG, Ma L, Ghosh SKB, Onengut-Gumuscu S, Ashley EA, Quertermous T, Finn AV, Leeper NJ, Kovacic JC, Björkegren JLM, Zang C, Miller CL. Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk Nat Genet. 2022 Jun;54(6):804-816. doi: 10.1038/s41588-022-01069-0. Epub 2022 May 19. PMID: 35590109

P. Todd Stukenberg, PhD.

2024:
Bryan, N. W., Ali, A., Niedzialkowska, E., Mayne, L., Stukenberg, P. T., & Black, B. E. (2024). Structural basis for the phase separation of the chromosome passenger complex. ELIFE, 13. doi:10.7554/eLife.92709

Niedzialkowska, E., Truong, T. M., Eldredge, L. A., Ali, A., Redemann, S., & Stukenberg, P. T. (2024). Chromosomal passenger complex condensates generate parallel microtubule bundles in vitro.. The Journal of biological chemistry, 300(3), 105669. doi:10.1016/j.jbc.2024.105669

2023:
Ali, A., & Stukenberg, P. T. (2023). Aurora kinases: Generators of spatial control during mitosis. FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY, 11. doi:10.3389/fcell.2023.1139367

2022:
Janczyk, P. L., Zylkiewicz, E., De Hoyos, H., West, T., Matson, D. R., Choi, W. -C., . . . Stukenberg, P. T. (2023). Aurora A phosphorylates Ndel1 to reduce the levels of Mad1 and NuMA at spindle poles. MOLECULAR BIOLOGY OF THE CELL, 34(1). doi:10.1091/mbc.E21-09-0438

Morris, B. B., Smith, J. P., Zhang, Q., Jiang, Z., Hampton, O. A., Churchman, M. L., . . . Mayo, M. W. (2022). Replicative Instability Drives Cancer Progression. BIOMOLECULES, 12(11). doi:10.3390/biom12111570

Niedzialkowska, E., Liu, L., Kuscu, C., Mayo, Z., Minor, W., Strahl, B. D., . . . Stukenberg, P. T. (2022). Tip60 acetylation of histone H3K4 temporally controls chromosome passenger complex localization.. Molecular biology of the cell, 33(9), br15. doi:10.1091/mbc.e21-06-0283

Jie Sun, PhD.

2024:
Li, C., Qian, W., Wei, X., Narasimhan, H., Wu, Y., Arish, M., . . . Sun, J. (2024). Comparative single-cell analysis reveals IFN-γ as a driver of respiratory sequelae after acute COVID-19.. Science translational medicine, 16(756), eadn0136. doi:10.1126/scitranslmed.adn0136

Nguyen, C., Kudek, M., Zander, R., Niu, H., Shen, J., Bauer, A., . . . Cui, W. (2024). Bhlhe40 Promotes CD4+ T Helper 1 Cell and Suppresses T Follicular Helper Cell Differentiation during Viral Infection.. Journal of immunology (Baltimore, Md. : 1950), 212(11), 1829-1842. doi:10.4049/jimmunol.2300355

Canderan, G., Muehling, L. M., Kadl, A., Ladd, S., Bonham, C., Cross, C. E., . . . Woodfolk, J. A. (2024). Distinct Type 1 Immune Networks Underlie the Severity of Restrictive Lung Disease after COVID-19.. bioRxiv. doi:10.1101/2024.04.03.587929

Zhu, X., Wu, Y., Li, Y., Zhou, X., Watzlawik, J. O., Chen, Y. M., . . . Zeng, H. (2024). Rag-GTPase-TFEB/TFE3 axis controls B cell mitochondrial fitness and humoral immunity independent of mTORC1.. Res Sq. doi:10.21203/rs.3.rs-3957355/v1

Zhu, X., Wu, Y., Li, Y., Zhou, X., Watzlawik, J. O., Chen, Y. M., . . . Zeng, H. (2024). The nutrient-sensing Rag-GTPase complex in B cells controls humoral immunity via TFEB/TFE3-dependent mitochondrial fitness.. bioRxiv. doi:10.1101/2024.02.26.582122

Ge, J., Shao, H., Ding, H., Huang, Y., Wu, X., Sun, J., & Que, J. (2024). Single Cell Analysis of Lung Lymphatic Endothelial Cells and Lymphatic Responses during Influenza Infection.. Journal of respiratory biology and translational medicine, 1(1), 10003. doi:10.35534/jrbtm.2024.10003

Son, Y. M., Cheon, I. S., Li, C., & Sun, J. (2024). Persistent B Cell-Derived MHC Class II Signaling Is Required for the Optimal Maintenance of Tissue-Resident Helper T Cells.. ImmunoHorizons, 8(2), 163-171. doi:10.4049/immunohorizons.2300093

Guo, K., Yombo, D. J. K., Wang, Z., Navaeiseddighi, Z., Xu, J., Schmit, T., . . . Khan, N. (2024). The chemokine receptor CXCR3 promotes CD8+ T cell-dependent lung pathology during influenza pathogenesis. SCIENCE ADVANCES, 10(1). doi:10.1126/sciadv.adj1120

2023:
Jie, S., Narasimhan, H., Cheon, I. S., Qian, W., Hu, S., Parimon, T., . . . Chen, P. (2023). Proximal immune-epithelial progenitor interactions drive chronic tissue sequelae post COVID-19. doi:10.21203/rs.3.rs-3587418/v1

Narasimhan, H., Cheon, I. S., Qian, W., Hu, S., Parimon, T., Li, C., . . . Sun, J. (2023). Proximal immune-epithelial progenitor interactions drive chronic tissue sequelae post COVID-19.. bioRxiv. doi:10.1101/2023.09.13.557622

Kasmani, M. Y., Topchyan, P., Brown, A. K., Brown, R. J., Wu, X., Chen, Y., . . . Cui, W. (2023). A spatial sequencing atlas of age-induced changes in the lung during influenza infection. NATURE COMMUNICATIONS, 14(1). doi:10.1038/s41467-023-42021-y

Monroe, J. M., Quach, H. Q., Punia, S., Enninga, E. A. L., Fedyshyn, Y., Girsch, J. H., . . . Chakraborty, R. (2024). Vertical Transmission of SARS-CoV-2-Specific Antibodies and Cytokine Profiles in Pregnancy. JOURNAL OF INFECTIOUS DISEASES, 229(2), 473-484. doi:10.1093/infdis/jiad399

Fain, C. E., Zheng, J., Jin, F., Ayasoufi, K., Wu, Y., Lilley, M. T., . . . Johnson, A. J. (2024). Discrete class I molecules on brain endothelium differentially regulate neuropathology in experimental cerebral malaria. BRAIN, 147(2), 566-589. doi:10.1093/brain/awad319

Wu, Y., Hu, S. S., Zhang, R., Goplen, N. P., Gao, X., Narasimhan, H., . . . Sun, J. (2023). Single cell RNA sequencing unravels mechanisms underlying senescence-like phenotypes of alveolar macrophages. ISCIENCE, 26(7). doi:10.1016/j.isci.2023.107197

Zhu, B., Wei, X., Narasimhan, H., Qian, W., Zhang, R., Cheon, I. S., . . . Sun, J. (2023). Inhibition of the mitochondrial pyruvate carrier simultaneously mitigates hyperinflammation and hyperglycemia in COVID-19. SCIENCE IMMUNOLOGY, 8(82). doi:10.1126/sciimmunol.adf0348

Cheon, I. S., Son, Y. M., & Sun, J. (2023). Tissue-resident memory T cells and lung immunopathology. IMMUNOLOGICAL REVIEWS, 316(1), 63-83. doi:10.1111/imr.13201

Cable, J., Sun, J., Cheon, I. S., Vaughan, A. E., Castro, I. A., Stein, S. R., . . . Eddens, T. (2023). Respiratory viruses: New frontiers-a Keystone Symposia report. ANNALS OF THE NEW YORK ACADEMY OF SCIENCES, 1522(1), 60-73. doi:10.1111/nyas.14958

Wei, X., Narasimhan, H., Zhu, B., & Sun, J. (2023). Host Recovery from Respiratory Viral Infection. ANNUAL REVIEW OF IMMUNOLOGY, 41, 277-300. doi:10.1146/annurev-immunol-101921-040450

Arish, M., & Sun, J. (2023). Monocyte and macrophage function in respiratory viral infections. ANIMAL DISEASES, 3(1). doi:10.1186/s44149-023-00095-7

Bingham, G. C., Muehling, L. M., Li, C., Huang, Y., Ma, S. -F., Abebayehu, D., . . . Bonham, C. A. (2024). High-dimensional comparison of monocytes and T cells in post-COVID and idiopathic pulmonary fibrosis. FRONTIERS IN IMMUNOLOGY, 14. doi:10.3389/fimmu.2023.1308594

2022:
Tang, J., & Sun, J. (2023). Lung tissue-resident memory T cells: the gatekeeper to respiratory viral (re)-infection.. Current opinion in immunology, 80, 102278. doi:10.1016/j.coi.2022.102278

Tang, J., Zeng, C., Cox, T. M., Li, C., Son, Y. M., Cheon, I. S., . . . Sun, J. (2022). Respiratory mucosal immunity against SARS-CoV-2 after mRNA vaccination. SCIENCE IMMUNOLOGY, 7(76). doi:10.1126/sciimmunol.add4853

Huang, H., Fang, Y., Jiang, M., Zhang, Y., Biermann, J., Melms, J. C., . . . Que, J. (2022). Contribution of Trp63CreERT2-labeled cells to alveolar regeneration is independent of tuft cells. ELIFE, 11. doi:10.7554/eLife.78217

Hajnik, R. L., Plante, J. A., Liang, Y., Alameh, M. -G., Tang, J., Bonam, S. R., . . . Hu, H. (2022). Dual spike and nucleocapsid mRNA vaccination confer protection against SARS-CoV-2 Omicron and Delta variants in preclinical models. SCIENCE TRANSLATIONAL MEDICINE, 14(662). doi:10.1126/scitranslmed.abq1945

Arish, M., Qian, W., Narasimhan, H., & Sun, J. (2023). COVID-19 immunopathology: From acute diseases to chronic sequelae. JOURNAL OF MEDICAL VIROLOGY, 95(1). doi:10.1002/jmv.28122

Narasimhan, H., Wu, Y., Goplen, N. P., & Sun, J. (2022). Immune determinants of chronic sequelae after respiratory viral infection. SCIENCE IMMUNOLOGY, 7(73). doi:10.1126/sciimmunol.abm7996

Fu, Y., Pajulas, A., Wang, J., Zhou, B., Cannon, A., Cheung, C. C. L., . . . Kaplan, M. H. (2022). Mouse pulmonary interstitial macrophages mediate the pro-tumorigenic effects of IL-9. NATURE COMMUNICATIONS, 13(1). doi:10.1038/s41467-022-31596-7

Ulrich, B. J., Kharwadkar, R., Chu, M., Pajulas, A., Muralidharan, C., Koh, B., . . . Kaplan, M. H. (2022). Allergic airway recall responses require IL-9 from resident memory CD4+ T cells. SCIENCE IMMUNOLOGY, 7(69). doi:10.1126/sciimmunol.abg9296

Fu, Y., Wang, J., Zhou, B., Pajulas, A., Gao, H., Ramdas, B., . . . Kaplan, M. H. (2022). An IL-9-pulmonary macrophage axis defines the allergic lung inflammatory environment. SCIENCE IMMUNOLOGY, 7(68). doi:10.1126/sciimmunol.abi9768

Gao, X., Zhu, B., Wu, Y., Li, C., Zhou, X., Tang, J., & Sun, J. (2022). TFAM-Dependent Mitochondrial Metabolism Is Required for Alveolar Macrophage Maintenance and Homeostasis. JOURNAL OF IMMUNOLOGY, 208(6), 1456-1466. doi:10.4049/jimmunol.2100741

Wu, X., Kasmani, M. Y., Zheng, S., Khatun, A., Chen, Y., Winkler, W., . . . Cui, W. (2022). BATF promotes group 2 innate lymphoid cell-mediated lung tissue protection during acute respiratory virus infection. SCIENCE IMMUNOLOGY, 7(67). doi:10.1126/sciimmunol.abc9934

Jianguo Tao, MD. PhD.

2023:

Yuan, R., Wang, M. Y., Bi, C., Zhao, X., & Tao, J. (2023). MCL1 as a therapeutic vulnerability in Burkitt lymphoma. LEUKEMIA, 37(4), 934-937. doi:10.1038/s41375-023-01827-x

Bon Trinh, PhD.

2024:
Qiu K, Vu D, Wang L, Bookstaver A, Dinh TN, Goldfarb AN, Tenen DG, Trinh BQ. Chromatin structure and 3D architecture define differential functions of PU.1 cis regulatory elements in human blood cell lineages. BioRxiv, 2024, under revision

Korczmar E*, Bookstaver A*, Ober E, Goldfarb A, Tenen DG, Trinh BQ. Regulating expression of the lineage gene PU.1 in normal development and diseases: the role of cis-regulatory elements. Front Biosci, 2024, PMID: 38939973

Ebralidze AK, Umarino S, Bassal MA, Zhang H, Budnik, B, Monteleone E, Kappei D, Liu YV, Tenen DE, Coffey R, Sheen MR, Zhang Y, Wanet A, Trinh BQ, Poli V, Angarica VE, Magallanes RT, Benoukraf T, Crane-Robinson C, Di Ruscio A, Tenen DG. Formation and recycling of an active epigenetic mark mediated by cell cycle-specific RNAs. BioRxiv, undereview

Umarino S, Ebralidze AK, Monteleone E, Zhang Y, Trinh BQ, Di Ruscio A, Tenen DG. S-phase induced RNAs initiate formation of DNA replication origin. BioRxiv, under review

2023:
Coffey R, Tenen DG, Trinh BQ. RUNX1 as an RNA-binding transcription factor in blood cell development and diseases. Gene Expression Omnibus. Accession: GSE244530. 2023

2022:
Zhao X, Bartholdy B, Yamamoto Y, Evans EK, Alberich-Jordà M, Staber P, Benoukraf T, Zhang P, Zhang J, Trinh BQ, Crispino JD, Hoang T, Bassal MA, Tenen DG. PU.1 - c-Jun interaction is crucial for PU.1 function in myeloid development. Communications Biology. 2022, PMID: 36104445.

Chongzhi Zang, PhD.

2024:
Tian, M., Wang, Z., Su, Z., Shibata, E., Shibata, Y., Dutta, A., & Zang, C. (2024). Integrative analysis of DNA replication origins and ORC-/MCM-binding sites in human cells reveals a lack of overlap. ELIFE, 12. doi:10.7554/eLife.89548

Young, H. M. R., Hou, P. -C., Bartosik, A. R., Atkin, N. D., Wang, L., Wang, Z., . . . Wang, Y. -H. (2024). DNA fragility at topologically associated domain boundaries is promoted by alternative DNA secondary structure and topoisomerase II activity. NUCLEIC ACIDS RESEARCH, 52(7), 3837-3855. doi:10.1093/nar/gkae164

Zhao, X., Hu, W., Park, S. R., Zhu, S., Hu, S. S., Zang, C., . . . Xue, H. -H. (2024). The transcriptional cofactor Tle3 reciprocally controls effector and central memory CD8+T cell fates (vol 25, pg 294, 2024). NATURE IMMUNOLOGY, 25(4), 717. doi:10.1038/s41590-024-01780-6

Cho, H. J., Wang, Z., Cong, Y., Bekiranov, S., Zhang, A., & Zang, C. (2024). DARDN: A Deep-Learning Approach for CTCF Binding Sequence Classification and Oncogenic Regulatory Feature Discovery. GENES, 15(2). doi:10.3390/genes15020144

Zhao, X., Hu, W., Park, S. R., Zhu, S., Hu, S. S., Zang, C., . . . Xue, H. -H. (2024). The transcriptional cofactor Tle3 reciprocally controls effector and central memory CD8+ T cell fates. NATURE IMMUNOLOGY, 25(2). doi:10.1038/s41590-023-01720-w

2023:
Tian, M., Wang, Z., Su, Z., Shibata, E., Shibata, Y., Dutta, A., & Zang, C. (2023). Integrative analysis of DNA replication origins and ORC/MCM binding sites in human cells reveals a lack of overlap.. bioRxiv. doi:10.1101/2023.07.25.550556

Jie, S., Narasimhan, H., Cheon, I. S., Qian, W., Hu, S., Parimon, T., . . . Chen, P. (2023). Proximal immune-epithelial progenitor interactions drive chronic tissue sequelae post COVID-19. doi:10.21203/rs.3.rs-3587418/v1

Mosquera, J. V., Auguste, G., Wong, D., Turner, A. W., Hodonsky, C. J., Alvarez-Yela, A. C., . . . Miller, C. L. (2023). Integrative single-cell meta-analysis reveals disease-relevant vascular cell states and markers in human atherosclerosis. CELL REPORTS, 42(11). doi:10.1016/j.celrep.2023.113380

Cheng, Y., Hu, M., Yang, B., Jensen, T. B., Yang, T., Yu, R., . . . Wang, S. (2023). Perturb-tracing enables high-content screening of multiscale 3D genome regulators.. bioRxiv. doi:10.1101/2023.01.31.525983

Dinda, M., Fine, R. D., Saha, S., Wang, Z., Zang, C., Li, M., & Smith, J. S. (2023). Fob1-dependent condensin recruitment and loop extrusion on yeast chromosome III. PLOS GENETICS, 19(4). doi:10.1371/journal.pgen.1010705

Cho, H. J., Shu, M., Bekiranov, S., Zang, C., & Zhang, A. (2023). Interpretable meta-learning of multi-omics data for survival analysis and pathway enrichment. BIOINFORMATICS, 39(4). doi:10.1093/bioinformatics/btad113

2022:
Hu, S. S., Liu, L., Li, Q., Ma, W., Guertin, M. J., Meyer, C. A., . . . Zang, C. (2022). Intrinsic bias estimation for improved analysis of bulk and single-cell chromatin accessibility profiles using SELMA. NATURE COMMUNICATIONS, 13(1). doi:10.1038/s41467-022-33194-z

Jiang, Y., Harigaya, Y., Zhang, Z., Zhang, H., Zang, C., & Zhang, N. R. (2022). Nonparametric single-cell multiomic characterization of trio relationships between transcription factors, target genes, and cis-regulatory regions. CELL SYSTEMS, 13(9), 737-+. doi:10.1016/j.cels.2022.08.004

Smith, R. J., Zhang, H., Hu, S. S., Yung, T., Francis, R., Lee, L., . . . Kim, T. -H. (2022). Single-cell chromatin profiling of the primitive gut tube reveals regulatory dynamics underlying lineage fate decisions. NATURE COMMUNICATIONS, 13(1). doi:10.1038/s41467-022-30624-w

Turner, A. W., Hu, S. S., Mosquera, J. V., Ma, W. F., Hodonsky, C. J., Wong, D., . . . Miller, C. L. (2022). Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk. NATURE GENETICS, 54(6), 804-+. doi:10.1038/s41588-022-01069-0

Shan, Q., Hu, S. S., Zhu, S., Chen, X., Badovinac, V. P., Peng, W., . . . Xue, H. -H. (2022). Tcf1 preprograms the mobilization of glycolysis in central memory CD8+ T cells during recall responses. NATURE IMMUNOLOGY, 23(3), 386-+. doi:10.1038/s41590-022-01131-3

Lamberti, W. F., & Zang, C. (2022). Extracting physical characteristics of higher-order chromatin structures from 3D image data. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 20, 3387-3398. doi:10.1016/j.csbj.2022.06.018

Tian Zhang, PhD.

2023:
Aydin, S., Pham, D. T., Zhang, T., Keele, G. R., Skelly, D. A., Paulo, J. A., . . . Munger, S. C. (2023). Genetic dissection of the pluripotent proteome through multi-omics data integration. CELL GENOMICS, 3(4). doi:10.1016/j.xgen.2023.100283

Zhang, T., Keele, G. R., Gyuricza, I. G., Vincent, M., Brunton, C., Bell, T. A., . . . Churchill, G. A. (2023). Multi-omics analysis identifies drivers of protein phosphorylation. GENOME BIOLOGY, 24(1). doi:10.1186/s13059-023-02892-2

Yu, Q., Liu, X., Keller, M. P., Navarrete-Perea, J., Zhang, T., Fu, S., . . . Gygi, S. P. (2023). Sample multiplexing-based targeted pathway proteomics with real-time analytics reveals the impact of genetic variation on protein expression. NATURE COMMUNICATIONS, 14(1). doi:10.1038/s41467-023-36269-7

2022:
Xiao, H., Bozi, L. H. M., Sun, Y., Riley, C. L., Philip, V. M., Chen, M., . . . Chouchani, E. T. (2022). Architecture of the outbred brown fat proteome defines regulators of metabolic physiology. CELL, 185(24), 4654-+. doi:10.1016/j.cell.2022.10.003

Zhang, T. (2022). TMT29 plex: Higher order multiplexing with inherent interference correction. PROTEOMICS, 22(19-20). doi:10.1002/pmic.202200260

Si, L., Bai, H., Oh, C. Y., Jiang, A., Hong, F., Zhang, T., . . . Ingber, D. E. (2022). Self-assembling short immunostimulatory duplex RNAs with broad-spectrum antiviral activity. MOLECULAR THERAPY NUCLEIC ACIDS, 29, 923-940. doi:10.1016/j.omtn.2022.08.031

Verdaguer, M. P., Zhang, T., Surve, S., Paulo, J. A., Wallace, C., Watkins, S. C., . . . Sorkin, A. (2022). Time-resolved proximity labeling of protein networks associated with ligand-activated EGFR. CELL REPORTS, 39(11). doi:10.1016/j.celrep.2022.110950

Suski, J. M., Ratnayeke, N., Braun, M., Zhang, T., Strmiska, V., Michowski, W., . . . Sicinski, P. (2022). CDC7-independent G1/S transition revealed by targeted protein degradation. NATURE, 605(7909), 357-+. doi:10.1038/s41586-022-04698-x

Zhang, T., Fassl, A., Vaites, L. P., Fu, S., Sicinski, P., Paulo, J. A., & Gygi, S. P. (2022). Interrogating Kinase-Substrate Relationships with Proximity Labeling and Phosphorylation Enrichment. JOURNAL OF PROTEOME RESEARCH, 21(2), 494-506. doi:10.1021/acs.jproteome.1c00865