Publications

2022

Ghobadi A, Landmann J, Carter A, Cooper ML, Selli ME, Chang J, Baker M, Miller CA, Ferraro F, Chen DY, Smith AM, LaValle TA, Duncavage EJ, Chou J, Tam V, Benoun JM, Nater J, Scholler N, Milletti F, Vezan R, Bot A, Rossi JM, Singh N. Discovery of a novel genomic alteration that renders leukemic cells resistant to CD19-targeted immunotherapies. Blood Adv. 2022 Jul 20:bloodadvances.2022007705. doi: 10.1182/bloodadvances.2022007705. Epub ahead of print. PMID: 35858291.

Hryc CF, Baker ML. Beyond the Backbone: The Next Generation of Pathwalking Utilities for Model Building in CryoEM Density Maps. Biomolecules. 2022 Jun 2;12(6):773. doi: 10.3390/biom12060773. PMID: 35740898; PMCID: PMC9220806.

Hryc CF, Baker ML. AlphaFold2 and CryoEM: Revisiting CryoEM modeling in near-atomic resolution density maps. iScience. 2022 May 30;25(7):104496. doi:10.1016/j.isci.2022.104496. PMID: 35733789; PMCID: PMC9207676.

Liu X, Khara P, Baker ML, Christie PJ, Hu B. Structure of a type IV secretion system core complex encoded by multi-drug resistance F plasmids. Nat Commun. 2022 Jan 19;13(1):379. doi: 10.1038/s41467-022-28058-5. Erratum in: Nat Commun. 2022 May 16;13(1):2837. PMID: 35046412; PMCID: PMC8770708.

Fairbrother, H. E. , Carpenter, P. B. , Cunha, S. R. , Khamees, D. . Innovations in Active Education Techniques: Team Based Learning, Flipping the Classroom, and Think-Pair-Share. In: Ramavhoya, A. P. I. , Mutshatshi, T. E. , Mothiba, T. M. , editors. Health and Educational Success – Recent Perspectives [Working Title] [Internet]. London: IntechOpen; 2022 [cited 2022 Oct 03].

Xu P, Chen C, Zhang Y, Dzieciatkowska M, Brown BC, Zhang W, Xie T, Abdulmalik O, Song A, Tong C, Qi H, Roach R, Kellems RE, D’Alessandro A, Xia Y.Cell Metab. 2022 Feb 1;34(2):299-316.e6. doi: 10.1016/j.cmet.2021.12.019. PMID: 35108516.

Song A, Wen AQ, Wen YE, Dzieciatkowska M, Kellems RE, Juneja HS, D’Alessandro A, Xia Y. FASEB J. 2022 May;36(5):e22246. doi: 10.1096/fj.202101500RR. PMID: 35405035.

2021

Chen M, Shi X, Yu Z, Fan G, Serysheva II, Baker ML, Luisi BF, Ludtke SJ, Wang Z. In situ structure of the AcrAB-TolC efflux pump at subnanometer resolution. Structure. 2022 Jan 6;30(1):107-113.e3. doi: 10.1016/j.str.2021.08.008. Epub 2021 Sep 9. PMID: 34506732; PMCID: PMC8741639.

Baker MR, Fan G, Seryshev AB, Agosto MA, Baker ML, Serysheva II. Cryo-EM structure of type 1 IP₃R channel in a lipid bilayer. Commun Biol. 2021 May 25;4(1):625. doi: 10.1038/s42003-021-02156-4. PMID: 34035440; PMCID: PMC8149723.

Baker ML, Dirksen RT, Hamilton SL. How mutations in RYR1 that cause malignant hyperthermia increase RYR1 sensitivity to activators. Cell Calcium. 2021 Apr 19;97:102412. doi: 10.1016/j.ceca.2021.102412. Epub ahead of print. PMID:33905995.

Lawson CL, Kryshtafovych A, Adams PD, Afonine PV, Baker ML, Barad BA, Bond P, Burnley T, Cao R, Cheng J, Chojnowski G, Cowtan K, Dill KA, DiMaio F, Farrell DP, Fraser JS, Herzik MA Jr, Hoh SW, Hou J, Hung LW, Igaev M, Joseph AP, Kihara D, Kumar D, Mittal S, Monastyrskyy B, Olek M, Palmer CM, Patwardhan A, Perez A, Pfab J, Pintilie GD, Richardson JS, Rosenthal PB, Sarkar D, Schäfer LU, Schmid MF, Schröder GF, Shekhar M, Si D, Singharoy A, Terashi G, Terwilliger TC, Vaiana A, Wang L, Wang Z, Wankowicz SA, Williams CJ, Winn M, Wu T, Yu X, Zhang K, Berman HM, Chiu W. Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge. Nat Methods. 2021 Feb;18(2):156-164. doi:10.1038/s41592-020-01051-w. Epub 2021 Feb 4. PMID: 33542514; PMCID: PMC7864804.

Fousek K, Watanabe J, Joseph SK, George A, An X, Byrd TT, Morris JS, Luong A, Martínez-Paniagua MA, Sanber K, Navai SA, Gad AZ, Salsman VS, Mathew PR, Kim HN, Wagner DL, Brunetti L, Jang A, Baker ML, Varadarajan N, Hegde M, Kim YM, Heisterkamp N, Abdel-Azim H, Ahmed N. CAR T-cells that target acute B-lineage leukemia irrespective of CD19 expression. Leukemia. 2021 Jan;35(1):75-89. doi:10.1038/s41375-020-0792-2. Epub 2020 Mar 24. PMID: 32205861; PMCID: PMC7519582.

Dowhan, W., Bogdanov, M.: Eugene P. Kennedy’s Legacy: Defining bacterial phospholipid pathways and function. Front. Mol. Biosci. 8, 666203 (2021). PMCID 8027125.

Pyrshev K, Yesylevskyy S, Bogdanov, M, TTAPE-Me dye is not selective for cardiolipin and responds to anionic phospholipids nonspecifically, Biophys. J. 120, 3776-86 (2021) PMCID 8456184.

Qiang Q, Manalo JM, Sun H, Zhang Y, Song A, Wen AQ, Wen YE, Chen C, Liu H, Cui Y, Nemkov T, Reisz JA, Edwards Iii G, Perreira FA, Kellems RE, Soto C, D’Alessandro A, Xia Y. PLoS Biol. 2021 Jun 17;19(6):e3001239. doi: 10.1371/journal.pbio.3001239. eCollection 2021 Jun. PMID: 34138843.

2020

Wang HJ, Lee CS, Yee RSZ, Groom L, Friedman I, Babcock L, Georgiou DK, Hong J, Hanna AD, Recio J, Choi JM, Chang T, Agha NH, Romero J, Sarkar P, Voermans N, Gaber MW, Jung SY, Baker ML, Pautler RG, Dirksen RT, Riazi S, Hamilton SL. Adaptive thermogenesis enhances the life-threatening response to heat in mice with an Ryr1 mutation. Nat Commun. 2020 Oct 9;11(1):5099. doi:10.1038/s41467-020-18865-z. PMID: 33037202; PMCID: PMC7547078.

Donovan LK, Delaidelli A, Joseph SK, Bielamowicz K, Fousek K, Holgado BL, Manno A, Srikanthan D, Gad AZ, Van Ommeren R, Przelicki D, Richman C, Ramaswamy V, Daniels C, Pallota JG, Douglas T, Joynt ACM, Haapasalo J, Nor C, Vladoiu MC, Kuzan-Fischer CM, Garzia L, Mack SC, Varadharajan S, Baker ML, Hendrikse L, Ly M, Kharas K, Balin P, Wu X, Qin L, Huang N, Stucklin AG, Morrissy AS, Cavalli FMG, Luu B, Suarez R, De Antonellis P, Michealraj A, Rastan A, Hegde M, Komosa M, Sirbu O, Kumar SA, Abdullaev Z, Faria CC, Yip S, Hukin J, Tabori U, Hawkins C, Aldape K, Daugaard M, Maris JM, Sorensen PH, Ahmed N, Taylor MD. Locoregional delivery of CAR T cells to the cerebrospinal fluid for treatment of metastatic medulloblastoma and ependymoma. Nat Med. 2020 May;26(5):720-731. doi:10.1038/s41591-020-0827-2. Epub 2020 Apr 27. Erratum in: Nat Med. 2021 Jun;27(6):1117-1120. PMID: 32341580; PMCID: PMC8815773.

Mileykovskaya, E, Yoo, S-H.,Dowhan, W, Chen, Z:Nobiletin: Targeting the Circadian Network to Promote Bioenergetics and Healthy Aging. Biochemistry (Moscow) 85: 1554-59 (2020).

Bogdanov M, Pyrshev K, Yesylevskyy S, Ryabichko S, Boiko V, Ivanchenko P, Kiyamova R, Guan Z, Ramseyer C, Dowhan W, Phospholipid distribution in the cytoplasmic membrane of Gram-negative bacteria is highly asymmetric, dynamic and cell shape dependent. Sci. Adv. 6, eaaz6333 (2020). PMCID 7269648.

Ryabichko S, de Melo Ferreira V, Vitrac H, Kiyamova R, Dowhan W, Bogdanov M, Cardiolipin is required in vivo for the stability of bacterial translocon and optimal membrane protein translocation and insertion. Sci. Reports. 10, 6296 (2020). PMCID 7156725.

Vitrac H, Mallampalli VKPS, Azinas S, Dowhan W, Structural and functional adaptability of sucrose and lactose permeases from Escherichia coli to the membrane lipid composition. Biochemistry, 59, 1854-1868 (2020) PMCID 7500855.

Nohara K, Kim E, Wirianto M, Mileykovskaya E, Dowhan W, Chen Z, Yoo S-H, Cardiolipin Synthesis in Skeletal Muscle Is Rhythmic and Modifiable by Age and Diet. Oxid. Med. Cell. Long. 2020, 5304768 (2020). PMCID 7313160.

Iriyama T, Wang W, Parchim NF, Sayama S, Kumasawa K, Nagamatsu T, Song A, Xia Y, Kellems RE. FASEB J. 2020 Mar;34(3):4041-4054. doi: 10.1096/fj.201902583R. Epub 2020 Jan 12. PMID: 31930569.

Xie T, Chen C, Peng Z, Brown BC, Reisz JA, Xu P, Zhou Z, Song A, Zhang Y, Bogdanov MV, Kellems RE, D’Alessandro A, Zhang W, Xia Y. Circ Res. 2020 Jul 17;127(3):360-375. doi: 10.1161/CIRCRESAHA.119.316298. Epub 2020 Apr 14. PMID: 32284030.

Sayama S, Song A, Brown BC, Couturier J, Cai X, Xu P, Chen C, Zheng Y, Iriyama T, Sibai B, Longo M, Kellems RE, D’Alessandro A, Xia Y. JCI Insight. 2020 May 21;5(10):e130205. doi: 10.1172/jci.insight.130205. PMID: 32434995.

Manalo JM, Liu H, Ding D, Hicks J, Sun H, Salvi R, Kellems RE, Pereira FA, Xia Y. FASEB J. 2020 Dec;34(12):15771-15787. doi: 10.1096/fj.202000939R. Epub 2020 Nov 1. PMID: 33131093. 

Chen, C.-Y. A., Strouz, K., Huang, K.-L., and Shyu, A.-B.: Tob2 phosphorylation regulates global mRNA turnover to reshape transcriptome and impact cell proliferation. RNA, 26:1143-1159, 2020. PMID: 32404348.