Published and Contributed Works

Stephen S. Marshall, Michiel J.M. Niesen, Axel Müller, Katrin Tiemann, Shyam M. Saladi, Rachel P. Galimidi, Bin Zhang, William M. Clemons Jr., Thomas F. Miller III. 2016. A Link between Integral Membrane Protein Expression and Simulated Integration Efficiency. Cell Reports 16:2169–2177. doi:10.1016/j.celrep.2016.07.042
I wrote software for a single analysis. This work is not included in this thesis document.

Brandon J. Henderson, Stephen Grant, Betty W. Chu, Rezvan Shahoei, Stephanie M. Huard, Shyam M. Saladi, Emad Tajkhorshid, Dennis A. Dougherty, Henry A. Lester. 2018. Menthol Stereoisomers Exhibit Different Effects on \(\alpha_4\beta_2\) nAChR Upregulation and Dopamine Neuron Spontaneous Firing. eNeuro 5:ENEURO.0465–18.2018. doi:10.1523/ENEURO.0465-18.2018
I wrote code and carried out a single analysis. This work is not included in this thesis document.

Shyam M. Saladi, Nauman Javed, Axel Müller, William M. Clemons Jr. 2018. A statistical model for improved membrane protein expression using sequence-derived features. Journal of Biological Chemistry 293:4913–4927. doi:10.1074/jbc.RA117.001052
I designed the work, performed the experiments, developed the analytical methods, primarily wrote all software, and collaboratively wrote the manuscript.

Shyam M. Saladi. 2019. JetFighter: Towards figure accuracy and accessibility. eLife Labs https://elifesciences.org/labs/c2292989
I designed the work, developed the analytical methods, wrote all software, and wrote the manuscript.

Devang Mehta, Yaw Bediako, Charlotte M. de Winde, Hedyeh Ebrahimi, Florencia Fernández-Chiappe, Vinodh Ilangovan, Carolina Paz Quezada, Julia L. Riley, Shyam M. Saladi, Andy Tay A, Tracy Weissgerber. 2020. Ways to increase equity, diversity and inclusion. eLife 9:e60438. doi:10.7554/eLife.60438
I contributed collaboratively to this work and helped write the manuscript. This work is not included in this thesis document.

Tracy Weissgerber, Yaw Bediako Y, Charlotte M. de Winde, Hedyeh Ebrahimi, Florencia Fernández-Chiappe, Vinodh Ilangovan, Devang Mehta, Charlotte M. Paz Quezada, Julia L. Riley, Shyam M. Saladi, Sarvenaz Sarabipour, Andy Tay. 2020. Mitigating the impact of conference and travel cancellations on researchers’ futures. eLife 9:e57032. doi:10.7554/eLife.57032
I contributed collaboratively to this work and helped write the manuscript. This work is not included in this thesis document.

Shyam M. Saladi, Ailiena O. Maggiolo, Kate Radford, William M. Clemons Jr. 2020. Structural biologists, let’s mind our colors. bioRxiv Biochemistry (preprint). doi:10.1101/2020.09.22.308593
I designed the work, developed the analytical methods, wrote all software, and primarily wrote the manuscript.

Michelle Y. Fry*, Shyam M. Saladi*, Alexandre Cunha, William M. Clemons Jr. 2021b. Sequence-based features that are determinant for tail-anchored membrane protein sorting in eukaryotes. Traffic 22:306–318. doi:10.1111/tra.12809
I helped design the work, developed the analytical methods, primarily wrote the software, and collaboratively wrote the manuscript.

Michelle Y. Fry*, Shyam M. Saladi*, William M. Clemons Jr. 2021a. The STI1-domain is a flexible alpha-helical fold with a hydrophobic groove. Protein Science 30:882–898. doi:10.1002/pro.4049
I helped design the work, developed the analytical methods, primarily wrote the software, and collaboratively wrote the manuscript.

Andrew I. Jewett, David Stelter, Jason Lambert, Shyam M. Saladi, Otello M. Roscioni, Matteo Ricci, Ludovic Autin, Martina Maritan, Saeed M. Bashusqeh, Tom Keyes, Remus T. Dame, Joan-Emma Shea, Grant J. Jensen, David S. Goodsell. 2021. Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics. Journal of Molecular Biology 433:166841. doi:10.1016/j.jmb.2021.166841
I helped helped design one aspect of the software. This manuscript is not included in this thesis document.

Ku-Feng Lin, Michelle Y. Fry*, Shyam M. Saladi*, William M. Clemons Jr. 2021. Molecular basis of tail-anchored integral membrane protein recognition by the co-chaperone Sgt2. Journal of Biological Chemistry 296:100441. doi:10.1016/j.jbc.2021.100441
I helped develop the analytical methods, wrote the software, and collaboratively wrote the manuscript.

Tracy Weissgerber, Nico Riedel, Halil Kilicoglu, Cyril Labbé, Peter Eckmann, Gerben Ter Riet, Jennifer Byrne, Guillaume Cabanac, Amanda Capes-Davis, Bertrand Favier, Shyam M. Saladi, Peter Grabitz, Alexandra Bannach-Brown, Robert Schulz, Sarah McCann, Rene Bernard, Anita Bandrowski. 2021. Automated screening of COVID-19 preprints: Can we help authors to improve transparency and reproducibility? Nature Medicine 27:6–7. doi:10.1038/s41591-020-01203-7
I provided the original proof-of-concept and contributed software to this work. This work is not included in this thesis document.

Michelle Y. Fry, Vladimíra Najdrová, Ailiena O. Maggiolo, Shyam M. Saladi, Pavel Doležal, William M. Clemons Jr. 2022. Structurally derived universal mechanism for the catalytic cycle of the tail-anchored targeting factor Get3. Nature Structural & Molecular Biology 29:820–830. doi:10.1038/s41594-022-00798-4
I contributed software analyses to this work. This work is not included in this thesis document.

Brianne A. Kent, Constance Holman, Emmanuella Amoako, Alberto Antonietti, James M. Azam, Hanne Ballhausen, Yaw Bediako, Anat M. Belasen, Clarissa F. Carneiro, Yen-Chung Chen, Ewoud B. Compeer, Chelsea A.C. Connor, Sophia Crüwell, Humberto Debat, Emma Dorris, Hedyeh Ebrahimi, Jeffrey C. Erlich, Florencia Fernández-Chiappe, Felix Fischer, Małgorzata Anna Gazda, Toivo Glatz, Peter Grabitz, Verena Heise, David G. Kent, Hung Lo, Gary McDowell, Devang Mehta, Wolf-Julian Neumann, Kleber Neves, Mark Patterson, Naomi C. Penfold, Sophie K. Piper, Iratxe Puebla, Peter K. Quashie, Carolina Paz Quezada, Julia L. Riley, Jessica L. Rohmann, Shyam M. Saladi, Benjamin Schwessinger, Bob Siegerink, Paulina Stehlik, Alexandra Tzilivaki, Kate D.L. Umbers, Aalok Varma, Kaivalya Walavalkar, Charlotte M. de Winde, Cecelia Zaza, Tracey L. Weissgerber. 2022. Recommendations for empowering early career researchers to improve research culture and practice. PLoS Biology 20:e3001680. doi:10.1371/journal.pbio.3001680
I contributed collaboratively to this work. This work is not included in this thesis document.

Alexandra N. Barlow*, Manu M.S.*, Shyam M. Saladi, Paul T. Tarr, Yashpal Yadav, Aye M. M. Thinn, Yun Zhu, Arthur D. Laganowsky, William M. Clemons Jr, Sureshkumar Ramasamy. 2023. Structures of Get3d reveal a distinct architecture associated with the emergence of photosynthesis. Journal of Biological Chemistry 299:104752. doi:10.1016/j.jbc.2023.104752
I designed the computational approach, wrote and performed the software analysis, and wrote the respective section of the manuscript. Only a subset of this work is included in this thesis document.

* indicates equal contribution