Carnegie Mellon University


LaPeruta, A.J., Hedayati, S., Micic,J., Fitzgerald,F., Kim, D., Oualline,G., and Woolford,J.L.  Yeast ribosome biogenesis factors Puf6 and Nog2 and ribosomal proteins uL2 and eL43 act in concert to facilitate the release of nascent large ribosomal subunits from the nucleolus. Nucleic Acids Research (2023)

Bryce S, Stolzer M, Crosby D, Yang R, Durand D, Lee TH. Human atlastin-3 is a constitutive ER membrane fusion catalyst. J Cell Biol (2023) 222 (7). doi: e202211021.

A. Klimas, B. Gallagher, P. Wijesekara, S. Fekir, E. F. DiBernardo, Z. Cheng, D. Stolz, F. Cambi, S. Watkins, S. L. Brody, A. Horani, A. L. Barth, C. Moore, X. Ren, Y. Zhao*. Magnify is a universal molecular anchoring strategy for expansion microscopy. Nature Biotechnology published 02 Jan. 2023.

Koh ZH, Bishop WE, Kawashima T, Jeon BB, Srinivasan R, Kuhlman SJ, Ahrens MB, Chase SM, Yu BM Dimensionality reduction of calcium-imaged neuronal population activity. Nature Computational Science 2022 Dec 29. doi: 10.1038/s43588-022-00390-2.

F. Han, S. Gu, A. Klimas, N. Zhao, Y. Zhao* (co-corresponding), S-C, Chen*. Three-dimensional nanofabrication via ultrafast laser patterning and kinetically regulated material assembly. Science, 2022, 378, 6626. doi: 10.1126/science.abm8420.

Jeon BB, Fuchs, T, Chase SM, Kuhlman SJ. Visual experience has opposing influences on the quality of stimulus representation in adult primary visual cortex. eLife 2022 Nov 2;11:e80361. doi: 10.7554/eLife.80361. PMID: 36321876.

Szent-Gyorgyi C, Perkins LA, Schmidt BF, Liu Z, Bruchez MP, van de Weerd R. Bottom-Up Design: A Modular Golden Gate Assembly Platform of Yeast Plasmids for Simultaneous Secretion and Surface Display of Distinct FAP Fusion Proteins. ACS Synth Biol. 2022 Oct 19. doi: 10.1021/acssynbio.2c00283. Online ahead of print.

LaPeruta AJ, Micic J, Woolford JL Jr. Additional principles that govern the release of pre-ribosomes from the nucleolus into the nucleoplasm in yeast. Nucleic Acids Res. 2022 Jun 23:gkac430. doi: 10.1093/nar/gkac430. Epub ahead of print. PMID: 35736211

Cui X, Xue Y, McCormack C, Garces A, Rachman TW, Yi Y, Stolzer M, Durand D. Simulating domain architecture evolution. Bioinformatics. 2022 Jun 24;38(Suppl 1):i134-i142. doi: 10.1093/bioinformatics/btac242. PMID: 35758772; PMCID: PMC9236583.

Jeon BB, Fuchs T, Chase SM, Kuhlman SJ. Existing function in primary visual cortex is not perturbed by new skill acquisition of a non-matched sensory task. Nature Communication. 2022 Jun 25;13(1):3638. doi: 10.1038/s41467-022-31440-y.

L. Shi, A. Klimas, B. Gallagher, Z. Cheng, F. Fu, P. Wijesekara, Y. Miao, X. Ren, Y Zhao* (co-corresponding author), W Min*. Super-resolution vibrational imaging using expansion stimulated Raman scattering microscopy. Advanced Science, 2022, 2200315. doi: 10.1002/advs.202200315.

A. Abdelfattah, S. Ahuja, T. Akkin, S.R. Allu, D.A. Boas, J. Brake, E.M. Buckley, ..., Y. Zhao. Neurophotonic tools for microscopic measurements and manipulation: status report. Neurophotonics, 2022, 9 (S1), 013001 [Review]. doi: 10.1117/1.NPh.9.S1.013001.

Crosby D, Mikolaj MR, Nyenhuis SB, Bryce S, Hinshaw JE, Lee TH. Reconstitution of human atlastin fusion activity reveals autoinhibition by the C terminus. J Cell Biol. 2022 Feb 7;221(2):e202107070. doi: 10.1083/jcb.202107070. Epub 2021 Nov 24. PMID: 34817557

Spix TA, Nanivadekar S, Toong N, Kaplow IM, Isett BR, Goksen Y, Pfenning AR, Gittis AH. Population-specific neuromodulation prolongs therapeutic benefits of deep brain stimulation. Science. 2021 Oct 8;374(6564):201-206. doi: 10.1126/science.abi7852. Epub 2021 Oct 7. PMID: 34618556

Biedka S, Schmidt BF, Frey NM, Boothman SM, Minden JS, Lucas A. Reversible Click Chemistry Tag for Universal Proteome Sample Preparation for Top-Down and Bottom-Up Analysis. J Proteome Res. 2021 Oct 1;20(10):4787-4800. doi: 10.1021/acs.jproteome.1c00443. Epub 2021 Sep 15. PMID: 34524823

Karimi K, Agalakov S, Telmer CA, Beatman TR, Pells TJ, Arshinoff BI, Ku CJ, Foley S, Hinman VF, Ettensohn CA, Vize PD. Classifying domain-specific text documents containing ambiguous keywords. Database (Oxford). 2021 Sep 29;2021:baab062. doi: 10.1093/database/baab062. PMID: 34585729

Kuang Z, Wang Y, Li Y, Ye C, Ruhn KA, Behrendt CL, Olson EN, Hooper LV. The intestinal microbiota programs diurnal rhythms in host metabolism through histone deacetylase 3. Science. 2019 Sep 27;365(6460):1428-1434. doi: 10.1126/science.aaw3134. PMID: 31604271

Khor JM, Guerrero-Santoro J, Douglas W, Ettensohn CA. Global patterns of enhancer activity during sea urchin embryogenesis assessed by eRNA profiling. Genome Res. 2021 Jul 30:gr.275684.121. doi: 10.1101/gr.275684.121. Epub ahead of print. PMID: 34330790

Rodgers CC, Nogueira R, Pil BC, Greeman EA, Park JM, Hong YK, Fusi S, Bruno RM. Sensorimotor strategies and neuronal representations for shape discrimination. Neuron. 2021 Jul 21;109(14):2308-2325.e10. doi: 10.1016/j.neuron.2021.05.019. Epub 2021 Jun 15. PMID: 34133944

Yerneni SS, Werner S, Azambuja JH, Ludwig N, Eutsey R, Aggarwal SD, Lucas PC, Bailey N, Whiteside TL, Campbell PG, Hiller NL. Pneumococcal Extracellular Vesicles Modulate Host Immunity. mBio. 2021 Jul 13:e0165721. doi: 10.1128/mBio.01657-21. Epub ahead of print. PMID: 34253061

Gallagher BR, Zhao Y. Expansion microscopy: A powerful nanoscale imaging tool for neuroscientists. Neurobiol Dis. 2021 Jul;154:105362. doi: 10.1016/j.nbd.2021.105362. Epub 2021 Apr 2. PMID: 33813047

Keith SA, Bishop C, Fallacaro S, McCartney BM. Arc1 and the microbiota together modulate growth and metabolic traits in Drosophila. Development. 2021 Jul 9:dev.195222. doi: 10.1242/dev.195222. PMID: 34240138

Aggarwal SD, Lloyd AJ, Yerneni SS, Narciso AR, Shepherd J, Roper DI, Dowson CG, Filipe SR, Hiller NL. A molecular link between cell wall biosynthesis, translation fidelity, and stringent response in Streptococcus pneumoniae. Proc Natl Acad Sci U S A. 2021 Apr 6;118(14):e2018089118. doi: 10.1073/pnas.2018089118. PMID: 33785594

Missinato MA, Zuppo DA, Watkins SC, Bruchez MP, Tsang M. Zebrafish heart regenerates after chemoptogenetic cardiomyocyte depletion. Dev Dyn. 2021 Jan 26. doi: 10.1002/dvdy.305. Epub ahead of print. PMID: 33501711

Khor JM, Ettensohn CA. Transcription Factors of the Alx Family: Evolutionarily Conserved Regulators of Deuterostome Skeletogenesis. Front Genet. 2020 Nov 23;11:569314. doi: 10.3389/fgene.2020.569314. PMID: 33329706

Zhang H. The glassiness of hardening protein droplets. Science. 2020 Dec 11;370(6522):1271-1272. doi: 10.1126/science.abe9745. PMID: 33303604

Liang P, Kolodieznyi D, Creeger Y, Ballou B, Bruchez MP. Subcellular Singlet Oxygen and Cell Death: Location Matters. Front Chem. 2020 Nov 17;8:592941. doi: 10.3389/fchem.2020.592941. PMID: 33282833

Cary GA, McCauley BS, Zueva O, Pattinato J, Longabaugh W, Hinman VF. Systematic comparison of sea urchin and sea star developmental gene regulatory networks explains how novelty is incorporated in early development. Nat Commun. 2020 Dec 4;11(1):6235. doi: 10.1038/s41467-020-20023-4. PMID: 33277483

Bernhard SM, Lee J, Zhu M, Hsu A, Erskine A, Hires SA, Barth AL. An automated homecage system for multiwhisker detection and discrimination learning in mice. PLoS One. 2020 Dec 2;15(12):e0232916. doi: 10.1371/journal.pone.0232916. PMID: 33264281

Kowalewski NN, Kauttonen J, Stan PL, Jeon BB, Fuchs T, Chase SM, Lee TS, Kuhlman SJ. Development of Natural Scene Representation in Primary Visual Cortex Requires Early Postnatal Experience. Curr Biol. 2021 Jan 25;31(2):369-380.e5. doi: 10.1016/j.cub.2020.10.046. Epub 2020 Nov 20. PMID: 33220181

Lawler AJ, Brown AR, Bouchard RS, Toong N, Kim Y, Velraj N, Fox G, Kleyman M, Kang B, Gittis AH, Pfenning AR. Cell Type-Specific Oxidative Stress Genomic Signatures in the Globus Pallidus of Dopamine-Depleted Mice. J Neurosci. 2020 Dec 9;40(50):9772-9783. doi: 10.1523/JNEUROSCI.1634-20.2020. Epub 2020 Nov 13. PMID: 33188066

Singewald K, Bogetti X, Sinha K, Rule GS, Saxena S. Double Histidine Based EPR Measurements at Physiological Temperatures Permit Site-Specific Elucidation of Hidden Dynamics in Enzymes. Angew Chem Int Ed Engl. 2020 Dec 14;59(51):23040-23044. doi: 10.1002/anie.202009982. Epub 2020 Oct 13. PMID: 32910837

Phillips RS, Rosner I, Gittis AH, Rubin JE. The effects of chloride dynamics on substantia nigra pars reticulata responses to pallidal and striatal inputs. Elife. 2020 Sep 7;9:e55592. doi: 10.7554/eLife.55592. PMID: 32894224

Klimas A, Zhao Y. Expansion Microscopy: Toward Nanoscale Imaging of a Diverse Range of Biomolecules. ACS Nano. 2020 Jul 28;14(7):7689-7695. doi: 10.1021/acsnano.0c04374. Epub 2020 Jul 6. PMID: 32628828

Micic J, Li Y, Wu S, Wilson D, Tutuncuoglu B, Gao N, Woolford JL Jr. Coupling of 5S RNP rotation with maturation of functional centers during large ribosomal subunit assembly. Nat Commun. 2020 Jul 27;11(1):3751. doi: 10.1038/s41467-020-17534-5. PMID: 32719344

Jacqueline C, Lee A, Frey N, Minden JS, Finn OJ. Inflammation-induced, abnormal expression of self-molecules on epithelial cells: targets for tumor immunoprevention. Cancer Immunol Res. 2020;canimm.0870.2019. doi:10.1158/2326-6066.CIR-19-0870. PMID: 32467324

Geramita MA, Yttri EA, Ahmari SE. The two-step task, avoidance, and OCD. J Neurosci Res. 2020;98(6):1007-1019. doi:10.1002/jnr.24594. PMID: 32282095

Bucur O, Fu F, Calderon M, et al. Nanoscale imaging of clinical specimens using conventional and rapid-expansion pathology. Nat Protoc. 2020;15(5):1649-1672. doi:10.1038/s41596-020-0300-1. PMID: 32238952

Xie W, Jiao B, Bai Q, et al. Chemoptogenetic ablation of neuronal mitochondria in vivo with spatiotemporal precision and controllable severity. Elife. 2020;9:e51845. Published 2020 Mar 17. doi:10.7554/eLife.51845. PMID: 32180546

Ettensohn CA. The gene regulatory control of sea urchin gastrulation. Mech Dev. 2020;162:103599. doi:10.1016/j.mod.2020.103599. PMID: 32119908

Canady TD, Berlyoung AS, Martinez JA, et al. Enhanced Hybridization Selectivity Using Structured GammaPNA Probes. Molecules. 2020;25(4):970. Published 2020 Feb 21. doi:10.3390/molecules25040970. PMID: 32098111

Belsey PP, Nicholas MA, Yttri EA. Open-Source Joystick Manipulandum for Decision-Making, Reaching, and Motor Control Studies in Mice. eNeuro. 2020;7(2):ENEURO.0523-19.2020. Published 2020 Apr 3. doi:10.1523/ENEURO.0523-19.2020. PMID: 32094292

Perkins LA, Bruchez MP. Fluorogen activating protein toolset for protein trafficking measurements. Traffic. 2020;21(4):333-348. doi:10.1111/tra.12722. PMID: 32080949

Forrester A, Rathjen SJ, Daniela Garcia-Castillo M, et al. Functional dissection of the retrograde Shiga toxin trafficking inhibitor Retro-2. Nat Chem Biol. 2020;16(3):327-336. doi:10.1038/s41589-020-0474-4. PMID: 32080624

Yalcintas EP, Ackerman DS, Korkmaz E, Telmer CA, Jarvik JW, Campbell PG, Bruchez MP, Ozdoganlar OB. Analysis of In Vitro Cytotoxicity of Carbohydrate-Based Materials Used for Dissolvable Microneedle Arrays. Pharm Res. 2020 Jan 15;37(3):33. doi: 10.1007/s11095-019-2748-7. PMID: 31942659

Chen MD, Fucci IJ, Sinha K, Rule GS. dGMP Binding to Thymidylate Kinase from Plasmodium falciparum Shows Half-Site Binding and Induces Protein Dynamics at the Dimer Interface. Biochemistry. 2020 Jan 14. doi: 10.1021/acs.biochem.9b00898. PMID: 31934749

Ruan X, Johnson GR, Bierschenk I, Nitschke R, Boerries M, Busch H, Murphy RF. Image-derived models of cell organization changes during differentiation and drug treatments. Mol Biol Cell. 2019 Nov 27:mbcE19020080. doi: 10.1091/mbc.E19-02-0080. PMID: 31774723

Klimas A, Gallagher B, Zhao Y. Basics of Expansion Microscopy. Curr Protoc Cytom. 2019 Dec;91(1):e67. doi: 10.1002/cpcy.67. PMID: 31763769

Gildor T, Cary GA, Lalzar M, Hinman VF, Ben-Tabou de-Leon S. Developmental transcriptomes of the sea star, Patiria miniata, illuminate how gene expression changes with evolutionary distance.Sci Rep. 2019 Nov 7;9(1):16201. doi: 10.1038/s41598-019-52577-9. PMID: 31700051

Corbit VL, Gittis AH, Ahmari SE. A Model of Restraint: Nucleus Accumbens Fast-Spiking Interneurons Inhibit Unwanted Actions. Biol Psychiatry. 2019 Dec 1;86(11):804-806. doi: 10.1016/j.biopsych.2019.09.014. PMID: 31668219

Klimas A, Bucur O, Njeri B, Zhao Y. Nanoscopic Imaging of Human Tissue Sections via Physical and Isotropic Expansion. J Vis Exp. 2019 Sep 25;(151). doi: 10.3791/60195. PMID: 31609342

Barth AL, Ray A. Progressive Circuit Changes during Learning and Disease. Neuron. 2019 Oct 9;104(1):37-46. doi: 10.1016/j.neuron.2019.09.032. Review. PMID: 31600514

Kuljis DA, Park E, Telmer CA, Lee J, Ackerman DS, Bruchez MP, Barth AL. Fluorescence-Based Quantitative Synapse Analysis for Cell Type-Specific Connectomics. eNeuro. 2019 Oct 31;6(5). pii: ENEURO.0193-19.2019. doi: 10.1523/ENEURO.0193-19.2019. Print 2019 Sep/Oct. PMID: 31548370

Lin Y, May GE, Kready H, Nazzaro L, Mao M, Spealman P, Creeger Y, McManus CJ. Impacts of uORF codon identity and position on translation regulation. Nucleic Acids Res. 2019 Aug 8. pii: gkz681. doi: 10.1093/nar/gkz681. PMID: 31392980

Bulgari D, Deitcher DL, Schmidt BF, Carpenter MA, Szent-Gyorgyi C, Bruchez MP, Levitan ES. Activity-evoked and spontaneous opening of synaptic fusion pores. Proc Natl Acad Sci U S A. 2019 Aug 20;116(34):17039-17044. doi: 10.1073/pnas.1905322116. Epub 2019 Aug 5. PMID: 31383765

Yablonska S, Ganesan V, Ferrando LM, Kim J, Pyzel A, Baranova OV, Khattar NK, Larkin TM, Baranov SV, Chen N, Strohlein CE, Stevens DA, Wang X, Chang YF, Schurdak ME, Carlisle DL, Minden JS, Friedlander RM. Mutant huntingtin disrupts mitochondrial proteostasis by interacting with TIM23. Proc Natl Acad Sci U S A. 2019 Aug 13;116(33):16593-16602. doi: 10.1073/pnas.1904101116. Epub 2019 Jul 25. PMID: 31346086

Khor JM, Guerrero-Santoro J, Ettensohn CA. Genome-wide identification of binding sites and gene targets of Alx1, a pivotal regulator of echinoderm skeletogenesis. Development. 2019 Aug 19;146(16). pii: dev180653. doi: 10.1242/dev.180653. PMID: 31331943

Audette NJ, Bernhard SM, Ray A, Stewart LT, Barth AL. Rapid Plasticity of Higher-Order Thalamocortical Inputs during Sensory Learning. Neuron. 2019 Jul 17;103(2):277-291.e4. doi: 10.1016/j.neuron.2019.04.037. Epub 2019 May 28. PMID: 31151774

Mitchell A, Blader I, Bradford P, D'Orazio S, Duprex WP, Ellermeier CD, Fernandez-Sesma A, Imperiale MJ, McMahon K, Pasetti MF, Tringe S. mSphere of Influence: the View from the Microbiologists of the Future. mSphere. 2019 Jun 19;4(3). pii: e00348-19. doi: 10.1128/mSphere.00348-19. PMID: 31217304

Cuomo CA, Fanning S, Gujja S, Zeng Q, Naglik JR, Filler SG, Mitchell AP. Genome Sequence for Candida albicans Clinical Oral Isolate 529L. Microbiol Resour Announc. 2019 Jun 20;8(25). pii: e00554-19. doi: 10.1128/MRA.00554-19. PMID: 31221654

Huang MY, Woolford CA, May G, McManus CJ, Mitchell AP. Circuit diversification in a biofilm regulatory network. PLoS Pathog. 2019 May 22;15(5):e1007787. doi: 10.1371/journal.ppat.1007787. eCollection 2019 May. PMID: 31116789