@Emrah__Simsek

Assistant Professor of (bio)Physics at Univ of Florida. Studying life and death of microbes; biophysics, qBio, systems biology

 Gainesville, FL
Joined May 2012
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  • Following172
  • Followers63
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1/8: In our new paper with @lingchongyou doi.org/10.1038/s41467-025-6…, we show that antibiotics don’t just kill bacteria—they can paralyze Pseudomonas aeruginosa at sublethal doses, halting its spatial expansion.

Spatial proximity dictates bacterial competition and expansion in microbial communities

Nature Communications - Here, the authors show that immotile bacteria degrade antibiotics to alter their environment and facilitate nearby motile competitors to expand. As expansion proceeds, the...

nature.com
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Emrah Şimşek retweeted
Lingchong You@lingchongyouOct 8
1/ Even bacterial communities can get caught in a bad romance they just can't get over. A brief encounter with antibiotics can leave a lasting ecological memory of resistance plasmids persisting for weeks after the drug is gone. @DukeBiodesign @DukeUBME nature.com/articles/s41467-0…

Ecological memory of prolonged plasmid persistence after transient antibiotic exposure

Nature Communications - Zhou, Weiss and colleagues show that a brief antibiotic pulse can prolong plasmid persistence by removing plasmid-free competitors, creating an ecological memory that may...

nature.com
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Our recent collaborative paper is now published in the latest issue of Cell Reports @CellReports accompanied by a cover image highlighting how Bacillus gathers iron in the biofilm for promoting plant growth cell.com/issue/S2211-1247(25…
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7/8: The study started when I tried altering Pseudomonas branching patterns by mixing it with Klebsiella. Expansion stopped well before the dish boundary, and I wanted to know why. My local CFU checks revealed Klebsiella was rare or absent in the final community.
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8/8: @lingchongyou and I realized that, even though Klebsiella disappeared, it was indispensable for Pseudomonas to expand, serving as a hidden initiator. More in the paper for enthusiasts. Now, I continue this line of investigation in my own lab.
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I am very excited to announce that a fully funded PhD position is available in my group. Topic: Synergistic coevolution in mono-specific and multi-species microbial consortia Please RT or forward to interested candidates. Deadline: 11.01.26 More info: shorturl.at/f1TuF
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Replying to @spp2389
@spp2389 A PhD position is available in my lab to work on: Emergence and self-organisation of bacterial metabolism in consortia of cross-feeding bacteria. Please RT Deadline: 12.11.25 More infos 👇 shorturl.at/rAKAT
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A PhD position within the @spp2389 is available in my lab to work on: Emergence and self-organisation of bacterial metabolism in consortia of cross-feeding bacteria. Please RT Deadline: 12.11.25 More infos 👇 shorturl.at/rAKAT
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Emrah Şimşek retweeted
Shekhar lab@sshekhr29 Aug 2025
📢📢Hiring 2 Research Assistants & 2 Postdocs at @EmoryUniversity in Atlanta to study cytoskeletal biophysics/biochemistry. Please RT. RAs: great for recent bachelor's/master's in Physics/Bio/Chem/Biochem. Email CV and interests to [email protected]. shekharlab.org
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I am searching for a senior postdoc (3 +3 years) in the field of theoretical/ computational biology. The position provides the opportunity to interact with experimentalists and develop own research projects. Please RT Deadline: 11/09/2025 Details 👇: shorturl.at/iiiOv
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The position of a senior postdoc (3 +3 years) in the field of theoretical biology is available in my group. The post provides the opportunity to closely interact with experimentalists and develop own research projects. Please RT. Details 👇: shorturl.at/iiiOv
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biorxiv.org/content/10.1101/…

Higher-order epistasis drives evolutionary unpredictability toward novel antibiotic resistance

The rapid evolution of extended-spectrum β-lactamases (ESBLs) represents a global health threat, undermining the efficacy of β-lactams, the most extensively used antibiotic class. To elucidate the...

biorxiv.org
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Emrah Şimşek retweeted
Yasa Baig@BaigYasa7 Jul 2025
Was extremely fun to work on this paper with @jerrywliu and finally fulfilling our 7 year plan from year one of undergrad to write a paper together! One of many I hope!
Jerry Liu
@jerrywliu7 Jul 2025
1/10 ML can solve PDEs – but precision🔬is still a challenge. Towards high-precision methods for scientific problems, we introduce BWLer 🎳, a new architecture for physics-informed learning achieving (near-)machine-precision (up to 10⁻¹² RMSE) on benchmark PDEs. 🧵How it works:
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Emrah Şimşek retweeted
Romero lab@romerolab18 May 2025
Excited to share @NathanielBlalo2 and @srivsesh preprint teaching protein language models to generate beyond what evolution has explored. They introduce Reinforcement Learning with eXperimental Feedback (RLXF) to steer generation toward enhanced and non-natural functions.
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Ophelia@oventurelli28 May 2025
Excited to share our latest work on unraveling the role of a key metabolic pathway in human gut microbiome assembly and health-relevant metabolites—powered by machine learning! Led by the talented Yiyi Liu sciencedirect.com/science/ar…
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