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D. Nissley · SciRah

Researcher profile · Semantic Scholar

D. Nissley

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D. Nissley — researcher profile on SciRah

h-index: 29
Works: 132
Citations: 4,589

Most-cited papers

Undermining glutaminolysis bolsters chemotherapy while NRF2 promotes chemoresistance in KRAS-driven pancreatic cancers
Suman Mukhopadhyay, D. Goswami, P. Adiseshaiah, W. Burgan +5 more
2020Cancer Research226 citations Open access
Semantic Scholar
ssGSEA score-based Ras dependency indexes derived from gene expression data reveal potential Ras addiction mechanisms with possible clinical implications
M. Yi, D. Nissley, F. McCormick, R. Stephens
2020Scientific Reports186 citations Open access
Semantic Scholar
KRAS interaction with RAF1 RAS-binding domain and cysteine-rich domain provides insights into RAS-mediated RAF activation
Timothy H. Tran, A. Chan, L. C. Young, Lakshman K. Bindu +10 more
2020Nature Communications141 citations Open access
Semantic Scholar
Machine learning–driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins
H. Ingólfsson, Chris Neale, T. Carpenter, R. Shrestha +38 more
2020Proceedings of the National Academy of Sciences of the United States of America84 citations Open access
Semantic Scholar
Structures of N-terminally processed KRAS provide insight into the role of N-acetylation
S. Dharmaiah, Timothy H. Tran, S. Messing, Constance Agamasu +9 more
2019Scientific Reports65 citations Open access
Semantic Scholar
Structural Insights into the SPRED1-Neurofibromin-KRAS Complex and Disruption of SPRED1-Neurofibromin Interaction by Oncogenic EGFR
Wu-Peng Yan, Evan Markegard, S. Dharmaiah, A. Urisman +6 more
2020Cell Reports58 citations Open access
Semantic Scholar
The small molecule BI-2852 induces a nonfunctional dimer of KRAS
Timothy H. Tran, P. Alexander, S. Dharmaiah, Constance Agamasu +6 more
2020Proceedings of the National Academy of Sciences of the United States of America57 citations Open access
Semantic Scholar
Discovery of BBO-8520, a First-In-Class Direct and Covalent Dual Inhibitor of GTP-Bound (ON) and GDP-Bound (OFF) KRASG12C
A. Maciag, J. Stice, Bin Wang, Alok K. Sharma +31 more
2024Cancer Discovery50 citations Open access
Semantic Scholar
Uncovering a membrane-distal conformation of KRAS available to recruit RAF to the plasma membrane
Que N. Van, C. López, M. Tonelli, Troy Taylor +25 more
2020Proceedings of the National Academy of Sciences of the United States of America49 citations Open access
Semantic Scholar
Machine Learning-Driven Multiscale Modeling: Bridging the Scales with a Next-Generation Simulation Infrastructure
H. Ingólfsson, H. Bhatia, Fikret Aydin, T. Oppelstrup +27 more
2023Journal of Chemical Theory and Computation44 citations Open access
Semantic Scholar
KRAS Prenylation Is Required for Bivalent Binding with Calmodulin in a Nucleotide-Independent Manner
Constance Agamasu, R. Ghirlando, Troy Taylor, S. Messing +6 more
2019Biophysical Journal43 citations Open access
Semantic Scholar
Biochemical and structural analyses reveal that the tumor suppressor neurofibromin (NF1) forms a high-affinity dimer
M. Sherekar, Sae-Won Han, R. Ghirlando, S. Messing +13 more
2019Journal of Biological Chemistry42 citations Open access
Semantic Scholar
Structure of the SHOC2–MRAS–PP1C complex provides insights into RAF activation and Noonan syndrome
D. Bonsor, P. Alexander, Kelly R. Snead, N. Hartig +9 more
2022bioRxiv41 citations Open access
Semantic Scholar
Comparative analysis of KRAS4a and KRAS4b splice variants reveals distinctive structural and functional properties
M. Whitley, Timothy H. Tran, Megan Rigby, Ming Yi +13 more
2024Science Advances38 citations Open access
Semantic Scholar
BBO-10203 inhibits tumor growth without inducing hyperglycemia by blocking RAS-PI3Kα interaction.
D. Simanshu, R. Xu, J. Stice, D. Czyzyk +37 more
2025Science33 citations
Semantic Scholar
Destabilizing NF1 variants act in a dominant negative manner through neurofibromin dimerization
L. C. Young, Ruby Goldstein de Salazar, Sae-Won Han, Ziwen Huang +12 more
2023Proceedings of the National Academy of Sciences of the United States of America29 citations Open access
Semantic Scholar
AI Meets Exascale Computing: Advancing Cancer Research With Large-Scale High Performance Computing
Tanmoy Bhattacharya, T. Brettin, J. Doroshow, Yvonne A. Evrard +12 more
2019Frontiers in Oncology29 citations Open access
Semantic Scholar
Structural insights into isoform-specific RAS-PI3Kα interactions and the role of RAS in PI3Kα activation
D. Czyzyk, Wu-Peng Yan, S. Messing, William Gillette +8 more
2025Nature Communications28 citations Open access
Semantic Scholar
The confluence of machine learning and multiscale simulations.
H. Bhatia, Fikret Aydin, T. Carpenter, F. Lightstone +4 more
2023Current Opinion in Structural Biology24 citations Open access
Semantic Scholar
Exploring CRD mobility during RAS/RAF engagement at the membrane.
Kien Nguyen, C. López, Chris Neale, Que N. Van +26 more
2022Biophysical Journal23 citations Open access
Semantic Scholar
Insights into the Cross Talk between Effector and Allosteric Lobes of KRAS from Methyl Conformational Dynamics
Fa-an Chao, S. Dharmaiah, Troy Taylor, S. Messing +7 more
2022Journal of the American Chemical Society22 citations Open access
Semantic Scholar
Classical RAS proteins are not essential for paradoxical ERK activation induced by RAF inhibitors
L. P. Lai, Nicole Fer, W. Burgan, Vanessa E. Wall +5 more
2022Proceedings of the National Academy of Sciences of the United States of America21 citations Open access
Semantic Scholar
Structural dynamics of RAF1-HSP90-CDC37 and HSP90 complexes reveal asymmetric client interactions and key structural elements
Lorenzo I. Finci, Mayukh Chakrabarti, Gulcin Gulten, Joseph Finney +8 more
2024Communications Biology20 citations Open access
Semantic Scholar
Membrane interactions of the globular domain and the hypervariable region of KRAS4b define its unique diffusion behavior
D. Goswami, De Chen, Yue Yang, Prabhakar R. Gudla +14 more
2020eLife20 citations Open access
Semantic Scholar
Membrane lipids drive formation of KRAS4b-RAF1 RBDCRD nanoclusters on the membrane
R. Shrestha, T. Carpenter, Que N. Van, Constance Agamasu +16 more
2024Communications Biology19 citations Open access
Semantic Scholar
Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework.
C. López, Xiaohua Zhang, Fikret Aydin, R. Shrestha +22 more
2022Journal of Chemical Theory and Computation18 citations Open access
Semantic Scholar
Structural Basis for LZTR1 Recognition of RAS GTPases for Degradation
S. Dharmaiah, D. Bonsor, Stephanie P. Mo, Alvaro Fernandez-Cabrera +8 more
2025Science16 citations
Semantic Scholar
Revealing the mechanism of action of a first-in-class covalent inhibitor of KRASG12C (ON) and other functional properties of oncogenic KRAS by 31P NMR
Alok K. Sharma, Jun Pei, Yue Yang, M. Dyba +12 more
2024Journal of Biological Chemistry16 citations Open access
Semantic Scholar
Biophysical and structural analysis of KRAS switch-II pocket inhibitors reveals allele-specific binding constraints
Patrick A Alexander, Albert H. Chan, Dana Rabara, Monalisa Swain +12 more
2025Journal of Biological Chemistry15 citations Open access
Semantic Scholar
Recapitulation of cell-like KRAS4b membrane dynamics on complex biomimetic membranes
R. Shrestha, De Chen, Peter H. Frank, D. Nissley +1 more
2021iScience13 citations Open access
Semantic Scholar
Cell surface protein enrichment for biomarker and drug target discovery using mass spectrometry-based proteomics
Xiao-Ying Ye, J. Kaczmarczyk, B. Luke, R. Saul +3 more
202010 citations
Semantic Scholar
Comprehensive structure-function analysis reveals gain- and loss-of-function mechanisms impacting oncogenic KRAS activity
Jason J. Kwon, Julien Dilly, Shengwu Liu, Eejung Kim +25 more
2024bioRxiv9 citations Open access
Semantic Scholar
Reduced dynamic complexity allows structure elucidation of an excited state of KRASG13D
Fa-an Chao, A. Chan, S. Dharmaiah, C. Schwieters +8 more
2023Communications Biology9 citations Open access
Semantic Scholar
RAS internal tandem duplication disrupts GTPase-activating protein (GAP) binding to activate oncogenic signaling
A. Nelson, T. Turbyville, S. Dharmaiah, Megan Rigby +12 more
2020Journal of Biological Chemistry9 citations Open access
Semantic Scholar
Blocking C-terminal processing of KRAS4b via a direct covalent attack on the CaaX-box cysteine
A. Maciag, Yue Yang, Alok K. Sharma, David M. Turner +30 more
2025Proceedings of the National Academy of Sciences of the United States of America8 citations Open access
Semantic Scholar
Generating Protein Structures for Pathway Discovery Using Deep Learning
Konstantia Georgouli, Robert Stephany, Jeremy O. B. Tempkin, Cláudio P. Santiago +11 more
2024Journal of Chemical Theory and Computation8 citations Open access
Semantic Scholar
An In Vitro BRAF Activation Assay Elucidates Molecular Mechanisms Driving Disassembly of the Autoinhibited BRAF State
Daniel A. Ritt, David E. Durrant, Matthew R. Drew, S. Sandin +22 more
2025bioRxiv7 citations
Semantic Scholar
Abstract RF02-02: BBO-10203, a first-in-class, orally bioavailable, selective covalent small molecule that inhibits RAS-driven PI3Kalpha activity without affecting glucose metabolism
P. Beltran, Simanshu Dhirendra, R. Xu, Ming Chen +20 more
2024Cancer Research7 citations
Semantic Scholar
Abstract ND07: BBO-8520, a first-in-class, direct inhibitor of KRASG12C (ON), locks GTP-bound KRASG12C in the state 1 conformation resulting in rapid and complete blockade of effector binding
A. Maciag, J. Stice, Bin Wang, Alok K. Sharma +29 more
2024Cancer Research7 citations
Semantic Scholar
A Top-Down Proteomic Assay to Evaluate KRAS4B-Compound Engagement
Robert A. D’Ippolito, Dana Rabara, Maria Abreu Blanco, Emily O. Alberico +14 more
2024Analytical Chemistry7 citations Open access
Semantic Scholar
Discovery of BBO-11818, a Potent and Selective Noncovalent Inhibitor of (ON) and (OFF) KRAS with Activity against Multiple Oncogenic Mutants
Carlos Stahlhut, A. Maciag, Kyle A Sullivan, Kanchan Singh +32 more
2026Cancer Discovery5 citations Open access
Semantic Scholar
Structure of SHOC2-KRAS-PP1C complex reveals RAS isoform-specific determinants and insights into targeting complex assembly by RAS inhibitors
D. Bonsor, Lorenzo I. Finci, Jacob R. Potter, Lucy C. Young +8 more
2026Nature Communications5 citations Open access
Semantic Scholar
Machine Learning-driven Multiscale MD Workflows: The Mini-MuMMI Experience
Loïc Pottier, Konstantia Georgouli, T. Carpenter, Fikret Aydin +7 more
2025arXiv.org5 citations
Semantic Scholar
Abstract 4378: BBO-11818, an orally bioavailable, highly potent and non-covalent pan-KRAS inhibitor demonstrates robust anti-tumor activity in KRAS-mutant preclinical models
Carlos E. Stahlhut Espinosa, Kanchan Singh, Zuhui Zhang, Kyle A Sullivan +27 more
2025Cancer Research5 citations
Semantic Scholar
Dynamics and lipid membrane coupling of the RAS-RAF complex revealed via multiscale simulations
T. Carpenter, Fikret Aydin, Chris Neale, Que N. Van +36 more
2025Biophysical Journal5 citations Open access
Semantic Scholar
Enhanced Exploration of Protein Conformational Space through Integration of Ultra-Coarse-Grained Models to Multiscale Workflows
Fikret Aydin, Konstantia Georgouli, Loïc Pottier, T. Oppelstrup +7 more
2025Journal of Physical Chemistry B4 citations Open access
Semantic Scholar
Natural Product Graveoline Modulates Kirsten Rat Sarcoma Viral Oncogene Homologue (KRAS) Membrane Association: Insights from Advanced Spectroscopic Studies.
Gabriel Cornilescu, L. Bindu, Louise M. Sternicki, Fa-an Chao +14 more
2024ACS Pharmacology & Translational Science4 citations Open access
Semantic Scholar
Abstract PS7-04: BBO-10203, a first-in-class, orally bioavailable, selective blocker of the PI3Kα:RAS interaction inhibits tumor growth alone and in combination with standard of care therapies in breast cancer models without inducing hyperglycemia
K. Sinkevicius, J. Stice, E. Riegler, Si-Yu Feng +19 more
2025Clinical Cancer Research3 citations
Semantic Scholar
Author Correction: Membrane lipids drive formation of KRAS4b-RAF1 RBDCRD nanoclusters on the membrane
R. Shrestha, T. Carpenter, Que N. Van, Constance Agamasu +16 more
2024Communications Biology3 citations Open access
Semantic Scholar
KRAS4a and KRAS4b show distinct lipid-dependent regulation of RAS-RAF membrane dynamics
Konstantia Georgouli, Jeremy O. B. Tempkin, Liam G. Stanton, T. Oppelstrup +30 more
2026Journal of Biological Chemistry2 citations Open access
Semantic Scholar

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