Publications

From the Hendrix group:

Hill ST, Kuintzle R, Teegarden A, Merrill E 3rd, Danaee P, Hendrix DA. (2018)

A deep recurrent neural network discovers complex biological rules to decipher RNA protein-coding potential.

Nucleic Acids Res. Jul 9. doi: 10.1093/nar/gky567. [Epub ahead of print]
From the Hendrix group:

Danaee P, Rouches M, Wiley M, Deng D, Huang L, Hendrix D. (2018)

bpRNA: large-scale automated annotation and analysis of RNA secondary structure.

Nucleic Acids Res. Jun 20;46(11):5381-5394. doi: 10.1093/nar/gky285.
From the Freitag group:

Thieme KG, Gerke J, Sasse C, Valerius O, Thieme S, Karimi R, Heinrich AK, Finkernagel F, Smith K, Bode HB, Freitag M, Ram AFJ, Braus GH. (2018)

Velvet domain protein VosA represses the zinc cluster transcription factor SclB regulatory network for Aspergillus nidulans asexual development, oxidative stress response and secondary metabolism.

PLoS Genet. Jul 25;14(7):e1007511. doi: 10.1371/journal.pgen.1007511. [Epub ahead of print]
From the Freitag group:

Bormann J, Heinze C, Blum C, Mentges M, Brockmann A, Alder A, Landt SK, Josephson B, Indenbirken D, Spohn M, Plitzko B, Loesgen S, Freitag M, Schäfer W. (2018)

Expression of a structural protein of the mycovirus FgV-ch9 negatively affects the transcript level of a novel symptom alleviation factor and causes virus-infection like symptoms in Fusarium graminearum.

J Virol. Jun 13. pii: JVI.00326-18. doi: 10.1128/JVI.00326-18. [Epub ahead of print]
From the Qiu group:

Wang P, Tseng KF, Gao Y, Cianfrocco M, Guo L, Qiu W. (2018)

The Central Stalk Determines the Motility of Mitotic Kinesin-14 Homodimers.

Curr Biol. Jul 23;28(14):2302-2308.e3. doi: 10.1016/j.cub.2018.05.026. Epub 2018 Jul 12.
From the Qiu & Mehl group:

Popchock AR, Jana S, Mehl RA, Qiu W. (2018)

Engineering Heterodimeric Kinesins through Genetic Incorporation of Noncanonical Amino Acids.

ACS Chem Biol. Jun 12. doi: 10.1021/acschembio.8b00399. [Epub ahead of print]
From the Mehl group:

Carlsson AC, Scholfield MR, Rowe RK, Ford MC, Alexander AT, Mehl RA, Ho PS. (2018)

Increasing Enzyme Stability and Activity through Hydrogen Bond-Enhanced Halogen Bonds.

Biochemistry. Jul 17;57(28):4135-4147. doi: 10.1021/acs.biochem.8b00603. Epub 2018 Jul 3.
From the Mehl group:

Porter JJ, Mehl RA. (2018)

Genetic Code Expansion: A Powerful Tool for Understanding the Physiological Consequences of Oxidative Stress Protein Modifications.

Oxid Med Cell Longev. Apr 23;2018:7607463. doi: 10.1155/2018/7607463. eCollection 2018. Review.
From the Gombart group:

Jiang J, Zhang Y, Indra AK, Ganguli-Indra G, Le MN, Wang H, Hollins RR, Reilly DA, Carlson MA, Gallo RL, Gombart AF, Xie J. (2018)

1α,25-dihydroxyvitamin D3-eluting nanofibrous dressings induce endogenous antimicrobial peptide expression.

Nanomedicine (Lond). Jun;13(12):1417-1432. doi: 10.2217/nnm-2018-0011. Epub 2018 Jul 4.
From the Beckman group:

van der Vliet A, Dick TP, Aust SD, Koppenol WH, Ursini F, Kettle AJ, Beckman JS, O'Donnell V, Darley-Usmar V, Lancaster J Jr, Hogg N, Davies KJA, Forman HJ, Janssen-Heininger YMW. (2018)

Rust never sleeps: The continuing story of the Iron Bolt.

Free Radic Biol Med. Jun 18;124:353-357. doi: 10.1016/j.freeradbiomed.2018.06.017. [Epub ahead of print] Review.
From the Greenwood group:

Pearce MC, Gamble JT, Kopparapu PR, O'Donnell EF, Mueller MJ, Jang HS, Greenwood JA, Satterthwait AC, Tanguay RL, Zhang XK, Kolluri SK. (2018)

Induction of apoptosis and suppression of tumor growth by Nur77-derived Bcl-2 converting peptide in chemoresistant lung cancer cells.

Oncotarget. May 25;9(40):26072-26085. doi: 10.18632/oncotarget.25437. eCollection 2018 May 25.
From the Merrill group:

Petersen DR, Saba LM, Sayin VI, Papagiannakopoulos T, Schmidt EE, Merrill GF, Orlicky DJ, Shearn CT. (2018)

Elevated Nrf-2 responses are insufficient to mitigate protein carbonylation in hepatospecific PTEN deletion mice.

PLoS One. May 25;13(5):e0198139. doi: 10.1371/journal.pone.0198139. eCollection 2018.

Biochemistry and Biophysics

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A deep recurrent neural network discovers complex biological rules to decipher RNA protein-coding potential.

bpRNA: large-scale automated annotation and analysis of RNA secondary structure.

Velvet domain protein VosA represses the zinc cluster transcription factor SclB regulatory network for Aspergillus nidulans asexual development, oxidative stress response and secondary metabolism.

Expression of a structural protein of the mycovirus FgV-ch9 negatively affects the transcript level of a novel symptom alleviation factor and causes virus-infection like symptoms in Fusarium graminearum.

The Central Stalk Determines the Motility of Mitotic Kinesin-14 Homodimers.

Engineering Heterodimeric Kinesins through Genetic Incorporation of Noncanonical Amino Acids.

Increasing Enzyme Stability and Activity through Hydrogen Bond-Enhanced Halogen Bonds.

Genetic Code Expansion: A Powerful Tool for Understanding the Physiological Consequences of Oxidative Stress Protein Modifications.

1α,25-dihydroxyvitamin D3-eluting nanofibrous dressings induce endogenous antimicrobial peptide expression.

Rust never sleeps: The continuing story of the Iron Bolt.

Induction of apoptosis and suppression of tumor growth by Nur77-derived Bcl-2 converting peptide in chemoresistant lung cancer cells.

Elevated Nrf-2 responses are insufficient to mitigate protein carbonylation in hepatospecific PTEN deletion mice.

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