txid562[Organism:exp] - PMC

Shaima Muhammednazaar, Jiaqi Yao, Matthew R. Necelis, Yein C. Park, Zhongtian Shen, Michael D. Bridges, Ruiqiong Guo, Nicole Swope, May S. Rhee, Miyeon Kim, Kelly H. Kim, Wayne L. Hubbell, Karen G. Fleming, Linda Columbus, Seung-gu Kang, Heedeok Hong

Version 2. bioRxiv. Preprint. 2023 May 31 [revised 2024 Dec 23]. doi: 10.1101/2023.05.30.542905

PMCID:: PMC10312574

Article

Select item 110423675.

Discovery of RNA-Protein Molecular Clamps Using Proteome-Wide Stability Assays

Stanley I. Goldstein, Alice C. Fan, Zihao Wang, Sai K. Naineni, Regina Cencic, Steve B. Garcia-Gutierrez, Kesha Patel, Sidong Huang, Lauren E. Brown, Andrew Emili, John A. Porco, Jr.

Version 2. bioRxiv. Preprint. 2024 Apr 19 [revised 2024 Dec 21]. doi: 10.1101/2024.04.19.590252

Published in:: J Proteome Res. 2025 Mar 12

PMCID:: PMC11042367

Article PDF–6.3M

Select item 109800806.

Functional associations of evolutionarily recent human genes exhibit sensitivity to the 3D genome landscape and disease

Katherine Fleck, Victor Luria, Nitanta Garag, Amir Karger, Trevor Hunter, Daniel Marten, William Phu, Kee-Myoung Nam, Nenad Sestan, Anne H. O’Donnell-Luria, Jelena Erceg

Version 2. bioRxiv. Preprint. 2024 Mar 17 [revised 2024 Nov 22]. doi: 10.1101/2024.03.17.585403

PMCID:: PMC10980080

Article PDF–6.5M

Select item 108023327.

Non-genetic adaptation by collective migration

Lam Vo, Fotios Avgidis, Henry H. Mattingly, Karah Edmonds, Isabel Burger, Ravi Balasubramanian, Thomas S. Shimizu, Barbara I. Kazmierczak, Thierry Emonet

Version 3. bioRxiv. Preprint. 2024 Jan 3 [revised 2024 Nov 21]. doi: 10.1101/2024.01.02.573956

Published in:: Proc Natl Acad Sci U S A. 2025 Feb 25; 122(8): e2423774122.

PMCID:: PMC10802332

Article

Select item 105411208.

A transcriptionally active lipid vesicle encloses the injected Chimalliviridae genome in early infection

Emily G. Armbruster, Phoolwanti Rani, Jina Lee, Niklas Klusch, Joshua Hutchings, Lizbeth Y. Hoffman, Hannah Buschkaemper, Eray Enustun, Benjamin A. Adler, Koe Inlow, Arica R. VanderWal, Madelynn Y. Hoffman, Daksh Daksh, Ann Aindow, Amar Deep, Zaida K. Rodriguez, Chase J. Morgan, Majid Ghassemian, Thomas G. Laughlin, Emeric Charles, Brady F. Cress, David F. Savage, Jennifer A. Doudna, Kit Pogliano, Kevin D. Corbett, Elizabeth Villa, Joe Pogliano

Version 2. bioRxiv. Preprint. 2023 Sep 21 [revised 2024 Oct 22]. doi: 10.1101/2023.09.20.558163

PMCID:: PMC10541120

Article PDF–27M

Select item 109251399.

Binding Site Maturation Modulated by Molecular Density Underlies Ndc80 Binding to Kinetochore Receptor CENP-T

Ekaterina V. Tarasovetc, Gunter B. Sissoko, Aleksandr Maiorov, Anna S. Mukhina, Fazoil I. Ataullakhanov, Iain M. Cheeseman, Ekaterina L. Grishchuk

Version 2. bioRxiv. Preprint. 2024 Feb 26 [revised 2024 Oct 14]. doi: 10.1101/2024.02.25.581584

Published in:: Proc Natl Acad Sci U S A. 2024 Dec 24; 121(52): e2401344121.

PMCID:: PMC10925139

Article PDF–1.4M

Select item 1063486710.

RpoS activates formation of Salmonella Typhi biofilms and drives persistence in the gall bladder

Stuti K. Desai, Yiyang Zhou, Rahul Dilawari, Andrew L. Routh, Vsevolod Popov, Linda J. Kenney

Version 3. bioRxiv. Preprint. 2023 Oct 26 [revised 2024 Oct 7]. doi: 10.1101/2023.10.26.564249

PMCID:: PMC10634867

Article PDF–2.0M

Select item 1040211011.

Functional analysis of cyclic diguanylate-modulating proteins in Vibrio fischeri

Ruth Y. Isenberg, Chandler S. Holschbach, Jing Gao, Mark J. Mandel

Version 4. bioRxiv. Preprint. 2023 Jul 24 [revised 2024 Sep 24]. doi: 10.1101/2023.07.24.550417

Published in:: mSystems. 2024 Nov; 9(11): e00956-24.

PMCID:: PMC10402110

Article PDF–2.4M

Select item 1076921012.

High-throughput discovery of inhibitory protein fragments with AlphaFold

Andrew Savinov, Sebastian Swanson, Amy E. Keating, Gene-Wei Li

Version 2. bioRxiv. Preprint. 2023 Dec 20 [revised 2024 Sep 19]. doi: 10.1101/2023.12.19.572389

Published in:: Proc Natl Acad Sci U S A. 2025 Feb 11; 122(6): e2322412122.

PMCID:: PMC10769210

Article PDF–10M

Select item 1082713213.

Staphylococcus aureus counters organic acid anion-mediated inhibition of peptidoglycan cross-linking through robust alanine racemase activity

Sasmita Panda, Yahani P. Jayasinghe, Dhananjay D. Shinde, Emilio Bueno, Amanda Stastny, Blake P. Bertrand, Sujata S. Chaudhari, Tammy Kielian, Felipe Cava, Donald R. Ronning, Vinai C. Thomas

Version 2. bioRxiv. Preprint. 2024 Jan 16 [revised 2024 Sep 17]. doi: 10.1101/2024.01.15.575639

PMCID:: PMC10827132

Article PDF–2.3M

Select item 1024580514.

3D Variability Analysis Reveals a Hidden Conformational Change Controlling Ammonia Transport in Human Asparagine Synthetase

Adriana Coricello, Alanya. J. Nardone, Antonio Lupia, Carmen Gratteri, Matthijn Vos, Vincent Chaptal, Stefano Alcaro, Wen Zhu, Yuichiro Takagi, Nigel G. J. Richards

Version 3. bioRxiv. Preprint. 2023 May 16 [revised 2024 Sep 5]. doi: 10.1101/2023.05.16.541009

Published in:: Nat Commun. 2024; 15: 10538.

PMCID:: PMC10245805

Article PDF–5.4M

Select item 1063494115.

The Evolution of Heteroresistance via Small Colony Variants in Escherichia coli Following Long Term Exposure to Bacteriostatic Antibiotics

Teresa Gil-Gil, Brandon A. Berryhill, Joshua A. Manuel, Andrew P. Smith, Ingrid C. McCall, Fernando Baquero, Bruce R. Levin

Version 3. bioRxiv. Preprint. 2023 Oct 30 [revised 2024 Aug 23]. doi: 10.1101/2023.10.30.564761

Published in:: Nat Commun. 2024; 15: 7936.

PMCID:: PMC10634941

Article PDF–323K

Select item 1054114316.

Engineered transcription-associated Cas9 targeting in eukaryotic cells

Gregory W. Goldberg, Manjunatha Kogenaru, Sarah Keegan, Max A. B. Haase, Larisa Kagermazova, Mauricio A. Arias, Kenenna Onyebeke, Samantha Adams, Daniel K. Beyer, David Fenyö, Marcus B. Noyes, Jef D. Boeke

Version 2. bioRxiv. Preprint. 2023 Sep 18 [revised 2024 Aug 18]. doi: 10.1101/2023.09.18.558319

Published in:: Nat Commun. 2024; 15: 10287.

PMCID:: PMC10541143

Article PDF–1.3M

Select item 1059308217.

PepMLM: Target Sequence-Conditioned Generation of Therapeutic Peptide Binders via Span Masked Language Modeling

Tianlai Chen, Madeleine Dumas, Rio Watson, Sophia Vincoff, Christina Peng, Lin Zhao, Lauren Hong, Sarah Pertsemlidis, Mayumi Shaepers-Cheu, Tian Zi Wang, Divya Srijay, Connor Monticello, Pranay Vure, Rishab Pulugurta, Kseniia Kholina, Shrey Goel, Matthew P. DeLisa, Ray Truant, Hector C. Aguilar, Pranam Chatterjee

Version 3. ArXiv. Preprint. 2023 Oct 5 [revised 2024 Aug 11]: arXiv:2310.03842v3.

PMCID:: PMC10593082

Article PDF–5.1M

Select item 990084618.

Strain tracking with uncertainty quantification

Younhun Kim, Colin J. Worby, Sawal Acharya, Lucas R. van Dijk, Daniel Alfonsetti, Zackary Gromko, Philippe Azimzadeh, Karen Dodson, Georg Gerber, Scott Hultgren, Ashlee M. Earl, Bonnie Berger, Travis E. Gibson

Version 2. bioRxiv. Preprint. 2023 Jan 26 [revised 2024 Jul 23]. doi: 10.1101/2023.01.25.525531

PMCID:: PMC9900846

PDF–1.0M

Select item 1031244919.

Complexes of vertebrate TMC1/2 and CIB2/3 proteins form hair-cell mechanotransduction cation channels

Arnaud P. J. Giese, Wei-Hsiang Weng, Katie S. Kindt, Hui Ho Vanessa Chang, Jonathan S. Montgomery, Evan M. Ratzan, Alisha J. Beirl, Roberto Aponte Rivera, Jeffrey M. Lotthammer, Sanket Walujkar, Mark P. Foster, Omid A. Zobeiri, Jeffrey R. Holt, Saima Riazuddin, Kathleen E. Cullen, Marcos Sotomayor, Zubair M. Ahmed

Version 2. bioRxiv. Preprint. 2023 May 30 [revised 2024 Jul 5]. doi: 10.1101/2023.05.26.542533

Published in:: eLife. 2025; 12: RP89719.

PMCID:: PMC10312449

Article PDF–16M

Select item 1065928420.

Enteric Populations of Escherichia coli are Likely to be Resistant to Phages Due to O Antigen Expression

Brandon A. Berryhill, Kylie B. Burke, Jake Fontaine, Catherine E. Brink, Mason G. Harvill, David A. Goldberg, Konstantinos T. Konstantinidis, Bruce R. Levin, Michael H. Woodworth

Version 2. bioRxiv. Preprint. 2023 Nov 8 [revised 2024 Jul 2]. doi: 10.1101/2023.11.08.566299

PMCID:: PMC10659284

Article PDF–774K

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