Publications

From the Hendrix group:

Bell J, Larson M, Kutzler M, Bionaz M, Löhr CV, Hendrix D. (2019)

miRWoods: Enhanced precursor detection and stacked random forests for the sensitive detection of microRNAs.

PLoS Comput Biol. Oct 9;15(10):e1007309. doi: 10.1371/journal.pcbi.1007309. eCollection 2019 Oct.
From the Johnson group:

Golbek TW, Padmanarayana M, Roeters SJ, Weidner T, Johnson CP, Baio JE. (2019)

Otoferlin C2F Domain-Induced Changes in Membrane Structure Observed by Sum Frequency Generation.

Biophys J. Sep 17. pii: S0006-3495(19)30784-2. doi: 10.1016/j.bpj.2019.09.010. [Epub ahead of print]
From the Johnson group:

Manchanda A, Chatterjee P, Bonventre JA, Haggard DE, Kindt KS, Tanguay RL, Johnson CP. (2019)

Otoferlin Depletion Results in Abnormal Synaptic Ribbons and Altered Intracellular Calcium Levels in Zebrafish.

Sci Rep. Oct 3;9(1):14273. doi: 10.1038/s41598-019-50710-2.
From the Mehl group:

Bednar RM, Golbek TW, Kean KM, Brown WJ, Jana S, Baio JE, Karplus PA, Mehl RA. (2019)

Immobilization of Proteins with Controlled Load and Orientation.

ACS Appl Mater Interfaces. Sep 26. doi: 10.1021/acsami.9b12746.
From the Hendrix group:

Huang L, Zhang H, Deng D, Zhao K, Liu K, Hendrix DA, Mathews DH. (2019)

LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search.

Bioinformatics. Jul 15;35(14):i295-i304. doi: 10.1093/bioinformatics/btz375.
From the Gombart group:

Kulkarni NN, Takahashi T, Sanford JA, Tong Y, Gombart AF, Hinds B, Cheng JY, Gallo RL. (2019)

Innate immune dysfunction in rosacea promotes photosensitivity and vascular adhesion molecule expression.

J Invest Dermatol. Aug 28. pii: S0022-202X(19)33154-9. doi: 10.1016/j.jid.2019.08.436. [Epub ahead of print]
From the Hendrix group:

Ritter N, Ali T, Kopitchinski N, Schuster P, Beisaw A, Hendrix DA, Schulz MH, Müller-McNicoll M, Dimmeler S, Grote P. (2019)

The lncRNA Locus Handsdown Regulates Cardiac Gene Programs and Is Essential for Early Mouse Development.

Dev Cell. Aug 12. pii: S1534-5807(19)30585-4. doi: 10.1016/j.devcel.2019.07.013. [Epub ahead of print]
From the Beckman group:

Kovacs M, Trias E, Varela V, Ibarburu S, Beckman JS, Moura IC, Hermine O, King PH, Si Y, Kwon Y, Barbeito L. (2019)

CD34 Identifies a Subset of Proliferating Microglial Cells Associated with Degenerating Motor Neurons in ALS.

Int J Mol Sci. Aug 9;20(16). pii: E3880. doi: 10.3390/ijms20163880
From the Gombart group:

Chen S, Ge L, Wang H, Cheng Y, Gorantla S, Poluektova LY, Gombart AF, Xie J. (2019)

Eluted 25-hydroxyvitamin D3 from Radially aligned Nanofiber Scaffolds Enhances Cathelicidin Production While Reducing Inflammatory Response in Human Immune System-Engrafted Mice.

Acta Biomater. Aug 3. pii: S1742-7061(19)30552-5. doi: 10.1016/j.actbio.2019.08.005. [Epub ahead of print]
From the Merrill group:

Shearn CT, Fennimore B, Orlicky DJ, Gao YR, Saba LM, Battista KD, Aivazidis S, Assiri M, Harris PS, Michel C, Merrill GF, Schmidt EE, Colgan SP, Petersen DR. (2019)

Cholestatic liver disease results increased production of reactive aldehydes and an atypical periportal hepatic antioxidant response.

Free Radic Biol Med. Aug 1;143:101-114. doi: 10.1016/j.freeradbiomed.2019.07.036. [Epub ahead of print]
From the Franco group:

Robinson MM, Sather BK, Burney ER, Ehrlicher SE, Stierwalt HD, Franco MC, Newsom SA. (2019)

Robust intrinsic differences in mitochondrial respiration and H2O2 emission between L6 and C2C12 cells.

Am J Physiol Cell Physiol. Aug 1. 317(2):C339-C347. doi: 10.1152/ajpcell.00343.2018. Epub May 15.
From the Hendrix group:

Sall K, Dekkers BJW, Nonogaki M, Katsuragawa Y, Koyari R, Hendrix D, Willems LAJ, Bentsink L, Nonogaki H. (2019)

DELAY OF GERMINATION1-LIKE4 acts as an inducer of seed reserve accumulation.

Plant J. Jul 29. doi: 10.1111/tpj.14485. [Epub ahead of print]
From the Barbar & Hendrix group:

Jespersen N, Estelle A, Waugh N, Davey NE, Blikstad C, Ammon YC, Akhmanova A, Ivarsson Y, Hendrix DA, Barbar E. (2019)

Systematic identification of recognition motifs for the hub protein LC8.

Life Sci Alliance. Jul 2;2(4). pii: e201900366. doi: 10.26508/lsa.201900366. Print 2019 Aug.
From the Franco group:

Pestoni JC, Klingeman Plati S, Valdivia Camacho OD, Fuse MA, Onatunde M, Sparrow NA, Karajannis MA, Fernández-Valle C, Franco MC. (2019)

Peroxynitrite supports a metabolic reprogramming in merlin-deficient Schwann cells and promotes cell survival.

J Biol Chem. Jul 26;294(30):11354-11368. doi: 10.1074/jbc.RA118.007152. Epub 2019 Jun 6.
From the Mehl group:

Van Fossen EM, Bednar RM, Mehl RA. (2019)

Engineering Spatial Orthogonality into Protein Translation.

Biochemistry. Jul 25. doi: 10.1021/acs.biochem.9b00569. [Epub ahead of print]

Biochemistry and Biophysics

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miRWoods: Enhanced precursor detection and stacked random forests for the sensitive detection of microRNAs.

Otoferlin C2F Domain-Induced Changes in Membrane Structure Observed by Sum Frequency Generation.

Otoferlin Depletion Results in Abnormal Synaptic Ribbons and Altered Intracellular Calcium Levels in Zebrafish.

Immobilization of Proteins with Controlled Load and Orientation.

LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search.

Innate immune dysfunction in rosacea promotes photosensitivity and vascular adhesion molecule expression.

The lncRNA Locus Handsdown Regulates Cardiac Gene Programs and Is Essential for Early Mouse Development.

CD34 Identifies a Subset of Proliferating Microglial Cells Associated with Degenerating Motor Neurons in ALS.

Eluted 25-hydroxyvitamin D3 from Radially aligned Nanofiber Scaffolds Enhances Cathelicidin Production While Reducing Inflammatory Response in Human Immune System-Engrafted Mice.

Cholestatic liver disease results increased production of reactive aldehydes and an atypical periportal hepatic antioxidant response.

Robust intrinsic differences in mitochondrial respiration and H2O2 emission between L6 and C2C12 cells.

DELAY OF GERMINATION1-LIKE4 acts as an inducer of seed reserve accumulation.

Systematic identification of recognition motifs for the hub protein LC8.

Peroxynitrite supports a metabolic reprogramming in merlin-deficient Schwann cells and promotes cell survival.

Engineering Spatial Orthogonality into Protein Translation.

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