PUBLICATIONS | TADESSE LAB

Our Publications

We present surface-enhanced Raman spectroscopy (SERS) combined with machine learning (ML) as a powerful tool for providing interpretable insights into the transcriptome, proteome, and metabolome at the single-cell level. Recent advances in nanophotonics enhance Raman scattering for rapid, strong label-free spectroscopy, while ML approaches enable precise spectral analysis.

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From Genotype to Phenotype: Raman Spectroscopy and Machine Learning for Label-Free Single-Cell Analysis

Yirui Zhang, Kai Chang, Babatunde Ogunlade, Liam Herndon, Loza F Tadesse, Amanda R Kirane, Jennifer A Dionne

ACS Nano, 2024

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We present a rapid, culture-free, and antibiotic incubation-free drug susceptibility test for tuberculosis (TB) using Raman spectroscopy and machine learning. Recent developments in these techniques allow us to achieve over 98% accuracy in classifying resistant versus susceptible Mycobacterium tuberculosis (Mtb) strains on dried samples, and approximately 79% accuracy on patient sputum samples.

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Rapid, antibiotic incubation-free determination of tuberculosis drug resistance using machine learning and Raman spectroscopy

Babatunde Ogunlade, Loza F Tadesse, Hongquan Li, Nhat Vu, Niaz Banaei, Amy K Barczak, Amr AE Saleh, Manu Prakash, Jennifer A Dionne

Proceedings of the National Academy of Sciences 121, 2024

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We present the establishment of an open-access web-based repository for microbiological Raman spectroscopy data called 'MicrobioRaman'. Inspired by successful research databases like GenBank, this repository minimizes the risk of data loss and offers a long-term reference for analysis with enhanced accessibility and transparency.

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MicrobioRaman: an open-access web repository for microbiological Raman spectroscopy data

Kang Soo Lee, Zachary Landry, Awais Athar, Uria Alcolombri, Pratchaya Pramoj Na Ayutthaya, David Berry, Philippe de Bettignies, Ji-Xin Cheng, Gabor Csucs, Li Cui, Volker Deckert, Thomas Dieing, Jennifer Dionne, Ondrej Doskocil, Glen D’Souza, Cristina García-Timermans, Notburga Gierlinger, Keisuke Goda, Roland Hatzenpichler, Richard J Henshaw, Wei E Huang, Ievgeniia Iermak, Natalia P Ivleva, Janina Kneipp, Patrick Kubryk, Kirsten Küsel, Tae Kwon Lee, Sung Sik Lee, Bo Ma, Clara Martínez-Pérez, Pavel Matousek, Rainer U Meckenstock, Wei Min, Peter Mojzeš, Oliver Müller, Naresh Kumar, Per Halkjær Nielsen, Ioan Notingher, Márton Palatinszky, Fátima C Pereira, Giuseppe Pezzotti, Zdenek Pilat, Filip Plesinger, Jürgen Popp, Alexander J Probst, Alessandra Riva, Amr AE Saleh, Ota Samek, Haley M Sapers, Olga T Schubert, Astrid KM Stubbusch, Loza F Tadesse, Gordon T Taylor, Michael Wagner, Jing Wang, Huabing Yin, Yang Yue, Renato Zenobi, Jacopo Zini, Ugis Sarkans, Roman Stocker

Nature Microbiology, 2024

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We present a novel approach using Sharpness-Aware Minimization (SAM) to address current limitations in Raman spectroscopy for antibiotic resistance testing. By enhancing model generalization and optimizing hyperparameters across diverse datasets, SAM achieves significant accuracy improvements—up to 10.7% on individual splits and an average increase of 2.5% across all splits—compared to traditional methods like Adam.

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Sharpness-Aware Minimization (SAM) Improves Classification Accuracy of Bacterial Raman Spectral Data Enabling Portable Diagnostics

Kaitlin Zareno, Jarett Dewbury, Siamak Sorooshyari, Hossein Mobahi, Loza F Tadesse

ICLR 5th Workshop on practical ML for limited/low resource settings, 2024

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We present antibody-coated Dynabeads as strong Raman reporter labels whose effect can be considered a Raman parallel of immunofluorescent probes. Recent developments in techniques for separating target-bound Dynabeads from unbound Dynabeads makes such an implementation feasible with high specificity.

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More than magnetic isolation: Dynabeads as strong Raman reporters toward simultaneous capture and identification of targets

Lee J, McDonald M, Mhlanga N, Kang JW, Karnik R, Tadesse LF

Pre-print, 2023

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We introduce an innovative approach combining acoustic bioprinting with Surface-enhanced Raman spectroscopy (SERS) and machine learning (ML) for precise pathogen detection in complex samples like blood, urine, and wastewater. Using an acoustic bioprinter, we digitize samples into millions of droplets, each containing a few cells, enhanced with gold nanorods (GNRs) for up to 1500× SERS signal improvement.

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Combining acoustic bioprinting with AI-assisted Raman spectroscopy for high-throughput identification of bacteria in blood

Fareeha Safir, Nhat Vu, Loza F Tadesse, Kamyar Firouzi, Niaz Banaei, Stefanie S Jeffrey, Amr AE Saleh, Butrus (Pierre) T Khuri-Yakub, Jennifer A Dionne

Nano Letters 23, 2023

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We present advancements in Surface-enhanced Raman spectroscopy (SERS) aimed at improving infectious disease diagnosis, particularly in pandemic scenarios. Addressing challenges such as spectral signal consistency, interpretability complexity, and workflow efficiency, we highlight recent innovations: (1) enhanced label-free SERS substrates and data processing algorithms to improve signal reliability and interpretability for comprehensive pathogen screening assays ...

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Toward rapid infectious disease diagnosis with advances in surface-enhanced Raman spectroscopy

Loza F Tadesse, Fareeha Safir, Chi-Sing Ho, Ximena Hasbach, Butrus Pierre Khuri-Yakub, Stefanie S Jeffrey, Amr AE Saleh, Jennifer Dionne

The Journal of Chemical Physics 152, 2020

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We present a study on bacterial liquid-SERS, focusing on plasmonic and electrostatic interactions between gold nanorods and bacteria to achieve uniformly enhanced SERS signals. By synthesizing nanorods with various plasmon resonances and studying Gram-negative (Escherichia coli, Serratia marcescens) and Gram-positive (Staphylococcus aureus, Staphylococcus epidermidis) bacteria in water, we demonstrate significant SERS enhancement.

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Plasmonic and Electrostatic Interactions Enable Uniformly Enhanced Liquid Bacterial Surface-Enhanced Raman Scattering (SERS)

Loza F Tadesse, Chi-Sing Ho, Dong-Hua Chen, Hamed Arami, Niaz Banaei, Sanjiv S Gambhir, Stefanie S Jeffrey, Amr AE Saleh, Jennifer Dionne

Nano letters 20, 2020

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We explore the profound impact of chirality across various scales, emphasizing its critical role in molecular properties and biological functions. Molecular chirality, evident in mirror-image molecules or enantiomers, influences diverse fields from neurodegenerative disorders to pharmaceutical efficacy. Despite its importance, sensing and separating chiral compounds remain challenging, particularly in trace quantities found in biological samples or pharmaceuticals.

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Nanophotonic platforms for chiral sensing and separation

Michelle L Solomon, Amr AE Saleh, Lisa V Poulikakos, John M Abendroth, Loza F Tadesse, Jennifer A Dionne

Accounts of chemical research 53, 2020

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We explore the potential of transition metal oxide (TMO) cathodes in Li-oxygen batteries, aiming to overcome limitations in rechargeability due to cathode passivation by nonconductive discharge products. Despite challenges, TMOs have shown promise by enabling lower charging potentials compared to carbon-only cathodes, potentially enhancing oxygen evolution efficiency.

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Effect of Transition Metal Oxide Cathodes on the Oxygen Evolution Reaction in Li–O2 Batteries

Dahyun Oh, Kumar Virwani, Loza Tadesse, Mark Jurich, Nagaphani Aetukuri, Leslie E Thompson, Ho-Cheol Kim, Donald S Bethune

The Journal of Physical Chemistry C 121, 2017

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We explore the optical properties of conjugated energetic molecules (CEMs), emphasizing their potential for direct optical initiation due to high nitrogen content and enhanced safety characteristics. Using time-dependent density functional theory, we investigated the one-photon absorption (OPA) and two-photon absorption (TPA) of both monomers and dimers derived from experimentally determined crystal structures of CEMs.

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Cooperative enhancement of the nonlinear optical response in conjugated energetic materials: A TD-DFT study

Andrew E Sifain, Loza F Tadesse, Josiah A Bjorgaard, David E Chavez, Oleg V Prezhdo, R Jason Scharff, Sergei Tretiak

The Journal of Chemical Physics 146, 2017

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We explore the use of bacteria as natural and sustainable pore templates for creating porous structures, overcoming synthetic difficulties, process complexities, and high costs associated with synthetic porogens. Cultured bacteria, being readily available and cost-effective, require no chemical synthesis and offer variability in size and shape.

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Biotemplating pores with size and shape diversity for Li-oxygen Battery Cathodes

Dahyun Oh, Cagla Ozgit-Akgun, Esin Akca, Leslie E Thompson, Loza F Tadesse, Ho-Cheol Kim, Gökhan Demirci, Robert D Miller, Hareem Maune

Scientific reports 7, 2017

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Our Patents

Polymer-coated beads serving as Raman reporter for simultaneous target binding and identification

Filed, Appl. No. : 63/501,380

Label-free, real-time, whole-cell response monitoring with liquid Raman spectroscopy

Filed, Appl. No.: PCT/US2021/048668.2021

Biotemplating pores with size and shape diversity for Li-oxygen Battery Cathodes

Porous sheets US20180050913A1, 2018