Publications

152 entries « 1 of 4 »

2024

Finsberg, Henrik; Charwat, Verena; Healy, Kevin E.; Wall, Samuel T.

Automatic motion estimation with applications to hiPSC-CMs Journal Article

In: BIOMEDICAL PHYSICS & ENGINEERING EXPRESS, vol. 10, no. 6, 2024, ISSN: 2057-1976.

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Chen, Kai; Han, Hesong; Zhao, Sheng; Xu, Bryant; Yin, Boyan; Lawanprasert, Atip; Trinidad, Marena; Burgstone, Benjamin W.; Murthy, Niren; Doudna, Jennifer A.

Lung and liver editing by lipid nanoparticle delivery of a stable CRISPR-Cas9 ribonucleoprotein Journal Article

In: NATURE BIOTECHNOLOGY, 2024, ISSN: 1087-0156.

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Baker, Jordan J.; Shi, Jie; Wang, Shangying; Mujica, Elena M.; Bianco, Simone; Capponi, Sara; Dueber, John E.

ML-enhanced peroxisome capacity enables compartmentalization of multienzyme pathway Journal Article

In: NATURE CHEMICAL BIOLOGY, 2024, ISSN: 1552-4450.

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Valiei, Amin; Dickson, Andrew; Aminian-Dehkordi, Javad; Mofrad, Mohammad R. K.

Metabolic interactions shape emergent biofilm structures in a conceptual model of gut mucosal bacterial communities Journal Article

In: NPJ BIOFILMS AND MICROBIOMES, vol. 10, no. 1, 2024.

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Peretz, Cheryl A. C.; Kennedy, Vanessa E.; Walia, Anushka; Delley, Cyrille L.; Koh, Andrew; Tran, Elaine; Clark, Iain C.; Hayford, Corey E.; D'Amato, Chris; Xue, Yi; Fontanez, Kristina M.; May-Zhang, Aaron A.; Smithers, Trinity; Agam, Yigal; Wang, Qian; Dai, Hai-ping; Roy, Ritu; Logan, Aaron C.; Perl, Alexander E.; Abate, Adam; Olshen, Adam; Smith, Catherine C.

Multiomic single cell sequencing identifies stemlike nature of mixed phenotype acute leukemia Journal Article

In: NATURE COMMUNICATIONS, vol. 15, no. 1, 2024.

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Qi, Yalin; Han, Hesong; Liu, Albert; Zhao, Sheng; Lawanprasert, Atip; Nielsen, Josefine Eilso; Choudhary, Hema; Liang, Dengpan; Barron, Annelise E.; Murthy, Niren

Ethylene oxide graft copolymers reduce the immunogenicity of lipid nanoparticles Journal Article

In: RSC ADVANCES, vol. 14, no. 41, pp. 30071-30076, 2024.

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Heindel, Joseph P.; Sami, Selim; Head-Gordon, Teresa

Completely Multipolar Model as a General Framework for Many-Body Interactions as Illustrated for Water Journal Article

In: JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 20, no. 19, pp. 8594-8608, 2024, ISSN: 1549-9618.

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Cha, Junghwa; Ding, Erika A.; Carvalho, Emily M.; Fowler, Annabelle; Aghi, Manish K.; Kumar, Sanjay

Collagen VI deposition primes the glioblastoma microenvironment for invasion through mechanostimulation of β-catenin signaling Journal Article

In: PNAS NEXUS, vol. 3, no. 9, 2024.

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Zhang, Yizhe; Naguro, Isao; Ryuno, Hiroki; Herr, Amy E.

ContactBlot: Microfluidic Control and Measurement of the Cell-Cell Contact State to Assess Contact-Inhibited ERK Signaling Journal Article

In: ANALYTICAL CHEMISTRY, vol. 96, no. 38, pp. 15330-15337, 2024, ISSN: 0003-2700.

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Elie, Julie E.; Muroy, Sandra E.; Genzel, Daria; Na, Tong; Beyer, Lisa A.; Swiderski, Donald L.; Raphael, Yehoash; Yartsev, Michael M.

Role of auditory feedback for vocal production learning in the fruit bat Journal Article

In: CURRENT BIOLOGY, vol. 34, no. 17, 2024, ISSN: 0960-9822.

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Snyder, Madeleine C.; Qi, Kevin K.; Yartsev, Michael M.

Neural representation of human experimenters in the bat hippocampus Journal Article

In: NATURE NEUROSCIENCE, vol. 27, no. 9, 2024, ISSN: 1097-6256.

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Shan, Xinzhu; Zhao, Zhiqiang; Lai, Pingping; Liu, Yuxiu; Li, Buyao; Ke, Yubin; Jiang, Hanqiu; Zhou, Yilong; Li, Wenzhe; Wang, Qian; Qin, Pengxia; Xue, Yizhe; Zhang, Zihan; Wei, Chenlong; Ma, Bin; Liu, Wei; Luo, Cong; Lu, Xueguang; Lin, Jiaqi; Shu, Li; Jie, Yin; Xian, Xunde; Delcassian, Derfogail; Ge, Yifan; Miao, Lei

RNA nanotherapeutics with fibrosis overexpression and retention for MASH treatment Journal Article

In: NATURE COMMUNICATIONS, vol. 15, no. 1, 2024.

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Lam, Bonnie; Velasquez, Mark; Ogiyama, Tomoko; Godines, Kevin; Szu, Fan-Yun; Velasquez-Mao, A. J.; Alghuraibawi, Wissam; Wang, Jingshen; Messersmith, Phillip B.; Vandsburger, Moriel H.

Imaging of adeno-associated viral capsids for purposes of gene editing using CEST NMR/MRI Journal Article

In: MAGNETIC RESONANCE IN MEDICINE, vol. 92, no. 2, pp. 792-806, 2024, ISSN: 0740-3194.

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Mandal, Sneha; Pillai, Vijayamohanan K.; Ponraj, Mano Ranjana; Thushara, K. M.; Bhagavathsingh, Jebasingh; Grage, Stephan L.; Peng, Xihong; Kang, Jeon Woong; Liepmann, Dorian; Kannan, Arunachala Nadar Mada; Thavasi, Velmurugan; Renugopalakrishnan, Venkatesan

van der Waals gap modulation of graphene oxide through mono-Boc ethylenediamine anchoring for superior Li-ion batteries Journal Article

In: ENERGY ADVANCES, vol. 3, no. 8, pp. 1977-1991, 2024.

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Snyder, Madeleine C.; Yartsev, Michael M.

Hippocampal neurons encode identities and positions of human experimenters Journal Article

In: NATURE NEUROSCIENCE, vol. 27, no. 8, pp. 1632, 2024, ISSN: 1097-6256.

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Coulibaly, Jean T.; Silue, Kigbafori D.; de Leon Derby, Maria Diaz; Fletcher, Daniel A.; Fisher, Karla N.; Andrews, Jason R.; Bogoch, Isaac I.

Rapid and Comprehensive Screening for Urogenital and Gastrointestinal Schistosomiasis with Handheld Digital Microscopy Combined with Circulating Cathodic Antigen Testing Journal Article

In: AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE, vol. 111, no. 2, pp. 387-390, 2024, ISSN: 0002-9637.

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Chae, Inseok; Shivkumar, Arjun; Doyle, Fiona M.; Lee, Seung-Wuk

Virus-Based Separation of Rare Earth Elements Journal Article

In: NANO LETTERS, vol. 24, no. 32, pp. 9946-9952, 2024, ISSN: 1530-6984.

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Pal, Subhajit; Shin, Jisoo; Defrates, Kelsey; Arslan, Mustafa; Dale, Katelyn; Chen, Hannah; Ramirez, Dominic; Messersmith, Phillip B.

Recyclable surgical, consumer, and industrial adhesives of poly(α-lipoic acid) Journal Article

In: SCIENCE, vol. 385, no. 6711, pp. 877-883, 2024, ISSN: 0036-8075.

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Zhao, Sheng; Gao, Kewa; Han, Hesong; Stenzel, Michael; Yin, Boyan; Song, Hengyue; Lawanprasert, Atip; Nielsen, Josefine Eilso; Sharma, Rohit; Arogundade, Opeyemi H.; Pimcharoen, Sopida; Chen, Yu-Ju; Paul, Abhik; Tuma, Jan; Collins, Michael G.; Wyle, Yofiel; Cranick, Matileen Grace; Burgstone, Benjamin W.; Perez, Barbara S.; Barron, Annelise E.; Smith, Andrew M.; Lee, Hye Young; Wang, Aijun; Murthy, Niren

Acid-degradable lipid nanoparticles enhance the delivery of mRNA Journal Article

In: NATURE NANOTECHNOLOGY, 2024, ISSN: 1748-3387.

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Montes, Andre R.; Barroso, Anahi; Wang, Wei; O'Connell, Grace D.; Tepole, Adrian B.; Mofrad, Mohammad R. K.

Integrin mechanosensing relies on a pivot-clip mechanism to reinforce cell adhesion Journal Article

In: BIOPHYSICAL JOURNAL, vol. 123, no. 16, pp. 2443-2454, 2024, ISSN: 0006-3495.

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Chae, Inseok; Chung, Woo-Jae; Jin, Hyo-Eon; Yang, Robert J.; Kim, Han; Lim, Butaek; Lee, Hee Jung; Kim, Sun-Young; Lee, Seung-Wuk

Evolutionary Design of Self-Templated Supramolecular Fibrils Using M13 Bacteriophage for Tissue Engineering Journal Article

In: NANO LETTERS, vol. 24, no. 33, pp. 10388-10395, 2024, ISSN: 1530-6984.

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Dickson, Andrew; Mofrad, Mohammad R. K.

Fine-tuning protein embeddings for functional similarity evaluation Journal Article

In: BIOINFORMATICS, vol. 40, no. 8, 2024, ISSN: 1367-4803.

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Qiao, Eric; Baek, Jieung; Fulmore, Camille; Song, Myoung; Kim, Taek-Soo; Kumar, Sanjay; Schaffer, David V.

Spectrin mediates 3D-specific matrix stress-relaxation response in neural stem cell lineage commitment Journal Article

In: SCIENCE ADVANCES, vol. 10, no. 31, 2024, ISSN: 2375-2548.

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Gharizadeh, Ali; Abbasi, Karim; Ghareyazi, Amin; Mofrad, Mohammad R. K.; Rabiee, Hamid R.

HGTDR: Advancing drug repurposing with heterogeneous graph transformers Journal Article

In: BIOINFORMATICS, vol. 40, no. 7, 2024, ISSN: 1367-4803.

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Reinhardt, Clorice R.; Manetsch, Melissa T.; Li, Wan-Lu; Roman-Leshkov, Yuriy; Head-Gordon, Teresa; Kulik, Heather J.

Computational Screening of Putative Catalyst Transition Metal Complexes as Guests in a Ga4L6 <SUP>12-</SUP> Nanocage Journal Article

In: INORGANIC CHEMISTRY, vol. 63, no. 31, pp. 14609-14622, 2024, ISSN: 0020-1669.

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Lang, Stuart; Fletcher, Daniel A.; Petit, Alain-Pierre; Luise, Nicola; Fyfe, Paul; Zuccotto, Fabio; Porter, David; Hope, Anthony; Bellany, Fiona; Kerr, Catrina; Mackenzie, Claire J.; Wyatt, Paul G.; Gray, David W.

Application of an NMR/Crystallography Fragment Screening Platform for the Assessment and Rapid Discovery of New HIV-CA Binding Fragments Journal Article

In: CHEMMEDCHEM, vol. 19, no. 13, 2024, ISSN: 1860-7179.

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Zhang, Oufan; Naik, Shubhankar A.; Liu, Zi Hao; Forman-Kay, Julie; Head-Gordon, Teresa

A curated rotamer library for common post-translational modifications of proteins Journal Article

In: BIOINFORMATICS, vol. 40, no. 7, 2024, ISSN: 1367-4803.

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Qiao, Eric; Fulmore, Camille A.; Schaffer, David V.; Kumar, Sanjay

Substrate stress relaxation regulates neural stem cell fate commitment Journal Article

In: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 121, no. 28, 2024, ISSN: 0027-8424.

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Liu, Yang; Herr, Amy E.

DropBlot: single-cell western blotting of chemically fixed cancer cells Journal Article

In: NATURE COMMUNICATIONS, vol. 15, no. 1, 2024.

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Kim, Han; Lee, Seung-Wuk

Molecular Mechanisms and Enhancement of Piezoelectricity in the M13 Virus Journal Article

In: ADVANCED FUNCTIONAL MATERIALS, 2024, ISSN: 1616-301X.

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Durrant, Matthew G.; Perry, Nicholas T.; Pai, James J.; Jangid, Aditya R.; Athukoralage, Januka S.; Hiraizumi, Masahiro; McSpedon, John P.; Pawluk, April; Nishimasu, Hiroshi; Konermann, Silvana; Hsu, Patrick D.

Bridge RNAs direct programmable recombination of target and donor DNA Journal Article

In: NATURE, vol. 630, no. 8018, 2024, ISSN: 0028-0836.

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Talebi, Salmonn; Gai, Siyu; Sossin, Aaron; Zhu, Vivian; Tong, Elizabeth; Mofrad, Mohammad R. K.

Deep Learning for Perfusion Cerebral Blood Flow (CBF) and Volume (CBV) Predictions and Diagnostics Journal Article

In: ANNALS OF BIOMEDICAL ENGINEERING, vol. 52, no. 6, pp. 1568-1575, 2024, ISSN: 0090-6964.

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Baek, Jieung; Kumar, Sanjay; Schaffer, David V.

Dynamic light-responsive RhoA activity regulates mechanosensitive stem cell fate decision in 3D matrices Journal Article

In: BIOMATERIALS ADVANCES, vol. 160, 2024.

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Amofa, Kwasi Yeboa; Patterson, Katherine Michelle; Ortiz, Jessica; Kumar, Sanjay

Dissecting TGF-β-induced glioblastoma invasion with engineered hyaluronic acid hydrogels Journal Article

In: APL BIOENGINEERING, vol. 8, no. 2, 2024, ISSN: 2473-2877.

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Hiraizumi, Masahiro; Perry, Nicholas T.; Durrant, Matthew G.; Soma, Teppei; Nagahata, Naoto; Okazaki, Sae; Athukoralage, Januka S.; Isayama, Yukari; Pai, James J.; Pawluk, April; Konermann, Silvana; Yamashita, Keitaro; Hsu, Patrick D.; Nishimasu, Hiroshi

Structural mechanism of bridge RNA-guided recombination Journal Article

In: NATURE, vol. 630, no. 8018, 2024, ISSN: 0028-0836.

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Sami, Selim; LaCour, R. Allen; Heindel, Joseph P.; Head-Gordon, Teresa

Simple and Accurate One-Body Energy and Dipole Moment Surfaces for Water and Beyond Journal Article

In: JOURNAL OF PHYSICAL CHEMISTRY LETTERS, vol. 15, no. 26, pp. 6712-6721, 2024, ISSN: 1948-7185.

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Li, Jie; Zhang, Oufan; Sun, Kunyang; Wang, Yingze; Guan, Xingyi; Bagni, Dorian; Haghighatlari, Mojtaba; Kearns, Fiona L.; Parks, Conor; Amaro, Rommie E.; Head-Gordon, Teresa

Mining for Potent Inhibitors through Artificial Intelligence and Physics: A Unified Methodology for Ligand Based and Structure Based Drug Design Journal Article

In: JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2024, ISSN: 1549-9596.

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Refaei, Roeya; Lee, Kyueui; Lee, Goun Amy; Demian, Paul; Mansouri, Fouad El; Messersmith, Phillip B.; Lamrani, Mouad; Khaddor, Mohamed; Allali, Nabil

Functionalized Surface Coatings for Rigid Contact Lenses Journal Article

In: JOURNAL OF FUNCTIONAL BIOMATERIALS, vol. 15, no. 6, 2024.

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Lomeli, Gabriela; Herr, Amy E.

Reducing Cathodic Drift during Isoelectric Focusing Using Microscale Immobilized pH Gradient Gels Journal Article

In: ANALYTICAL CHEMISTRY, vol. 96, no. 21, pp. 8648-8656, 2024, ISSN: 0003-2700.

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Shen, Konlin; Flood, Jake J.; Zhang, Zhihuizi; Ha, Alvin; Shy, Brian R.; Dueber, John E.; Douglas, Shawn M.

Engineering an Escherichia coli strain for production of long single-stranded DNA Journal Article

In: NUCLEIC ACIDS RESEARCH, vol. 52, no. 7, pp. 4098-4107, 2024, ISSN: 0305-1048.

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Defrates, Kelsey G.; Tong, Elaine; Cheng, Jing; Heber-Katz, Ellen; Messersmith, Phillip B.

A Pro-Regenerative Supramolecular Prodrug Protects Against and Repairs Colon Damage in Experimental Colitis Journal Article

In: ADVANCED SCIENCE, vol. 11, no. 13, 2024.

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Heindel, Joseph P.; LaCour, R. Allen; Head-Gordon, Teresa

The role of charge in microdroplet redox chemistry Journal Article

In: NATURE COMMUNICATIONS, vol. 15, no. 1, 2024.

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Wirthlin, Morgan E.; Schmid, Tobias A.; Elie, Julie E.; Zhang, Xiaomeng; Kowalczyk, Amanda; Redlich, Ruby; Shvareva, Varvara A.; Rakuljic, Ashley; Ji, Maria B.; Bhat, Ninad S.; Kaplow, Irene M.; Schaffer, Daniel E.; Lawler, Alyssa J.; Wang, Andrew Z.; Phan, BaDoi N.; Annaldasula, Siddharth; Brown, Ashley R.; Lu, Tianyu; Lim, Byung Kook; Azim, Eiman; Clark, Nathan L.; Meyer, Wynn K.; Pond, Sergei L. Kosakovsky; Chikina, Maria; Yartsev, Michael M.; Pfenning, Andreas R.; Consortium, Zoonomia

Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements Journal Article

In: SCIENCE, vol. 383, no. 6690, 2024, ISSN: 0036-8075.

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Lee, Hong-Gyun; Rone, Joseph M.; Li, Zhaorong; Akl, Camilo Faust; Shin, Seung Won; Lee, Joon-Hyuk; Flausino, Lucas E.; Pernin, Florian; Chao, Chun-Cheih; Kleemann, Kilian L.; Srun, Lena; Illouz, Tomer; Giovannoni, Federico; Charabati, Marc; Sanmarco, Liliana M.; Kenison, Jessica E.; Piester, Gavin; Zandee, Stephanie E. J.; Antel, Jack P.; Rothhammer, Veit; Wheeler, Michael A.; Prat, Alexandre; Clark, Iain C.; Quintana, Francisco J.

Disease-associated astrocyte epigenetic memory promotes CNS pathology Journal Article

In: NATURE, vol. 627, no. 8005, pp. 865+, 2024, ISSN: 0028-0836.

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Jaeger, Karoline Horgmo; Charwat, Verena; Wall, Samuel; Healy, Kevin E.; Tveito, Aslak

Do calcium channel blockers applied to cardiomyocytes cause increased channel expression resulting in reduced efficacy? Journal Article

In: NPJ SYSTEMS BIOLOGY AND APPLICATIONS, vol. 10, no. 1, 2024.

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Talebi, Salmonn; Tong, Elizabeth; Li, Anna; Yamin, Ghiam; Zaharchuk, Greg; Mofrad, Mohammad R. K.

Exploring the performance and explainability of fine-tuned BERT models for neuroradiology protocol assignment Journal Article

In: BMC MEDICAL INFORMATICS AND DECISION MAKING, vol. 24, no. 1, 2024.

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Takemiya, Kiyoko; Wang, Shelly; Liu, Yu; Murthy, Niren; Goodman, Mark M.; Taylor, W. Robert

Isothermal titration calorimetry analysis of the binding between the maltodextrin binding protein malE of Staphylococcus aureus with maltodextrins of various lengths Journal Article

In: BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, vol. 695, 2024, ISSN: 0006-291X.

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Garcia, Joseph H.; Akins, Erin A.; Jain, Saket; Wolf, Kayla J.; Zhang, Jason; Choudhary, Nikita; Lad, Meeki; Shukla, Poojan; Rios, Jennifer; Seo, Kyounghee; Gill, Sabraj A.; Carson, William H.; Carette, Luis R.; Zheng, Allison C.; Raleigh, David R.; Kumar, Sanjay; Aghi, Manish K.

Multiomic screening of invasive GBM cells reveals targetable transsulfuration pathway alterations Journal Article

In: JOURNAL OF CLINICAL INVESTIGATION, vol. 134, no. 3, 2024, ISSN: 0021-9738.

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Li, Jie; Liang, Jiashu; Wang, Zhe; Ptaszek, Aleksandra L.; Liu, Xiao; Ganoe, Brad; Head-Gordon, Martin; Head-Gordon, Teresa

Highly Accurate Prediction of NMR Chemical Shifts from Low-Level Quantum Mechanics Calculations Using Machine Learning Journal Article

In: JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 20, no. 5, pp. 2152-2166, 2024, ISSN: 1549-9618.

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Khavani, Mohammad; Mehranfar, Aliyeh; Mofrad, Mohammad R. K.

Antimicrobial peptide interactions with bacterial cell membranes Journal Article

In: JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 2024, ISSN: 0739-1102.

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152 entries « 1 of 4 »