Mohammed AlQuraishi

发表

Differentiable biology: using deep learning for biophysics-based and data-driven modeling of molecular mechanisms

P. Sorger, Mohammed AlQuraishi, Mohammed Alquraishi, 2021, Nature Methods.

AlphaFold at CASP13

Mohammed AlQuraishi, Mohammed AlQuraishi, Mohammed Alquraishi, 2019, Bioinform..

Direct inference of protein–DNA interactions using compressed sensing methods

Mohammed AlQuraishi, Harley H. McAdams, H. McAdams, 2011, Proceedings of the National Academy of Sciences.

Single-sequence protein structure prediction using language models from deep learning

G. Church, P. Sorger, Mohammed AlQuraishi, 2021, bioRxiv.

Machine learning in protein structure prediction.

Mohammed AlQuraishi, Mohammed Alquraishi, 2021, Current opinion in chemical biology.

Value of Adding Bioelectrical Impedance Analysis to Anthropometric Indices in the Diagnosis of Metabolic Syndrome in 10–16 Years Old Schoolgirls

Mohammed AlQuraishi, M. Abulmeaty, M. El-sharkawy, 2022, Healthcare.

Three enhancements to the inference of statistical protein‐DNA potentials

H. McAdams, Mohammed AlQuraishi, Mohammed Alquraishi, 2013, Proteins.

A multiscale statistical mechanical framework integrates biophysical and genomic data to assemble cancer networks

Gavin MacBeath, Peter K. Sorger, Mohammed AlQuraishi, 2014, Nature Genetics.

Zyflamend induces apoptosis in pancreatic cancer cells via modulation of the JNK pathway

Mohammed AlQuraishi, J. Whelan, D. Donohoe, 2020, Cell Communication and Signaling.

Structural bioinformatics AlphaFold at CASP 13

Mohammed AlQuraishi, Mohammed Alquraishi, 2019 .

Structural Bioinformatics

Mohammed AlQuraishi, 2019, F1000Research Channels.

End-to-end differentiable learning of protein structure

Mohammed AlQuraishi, Mohammed Alquraishi, 2018, bioRxiv.

Protein-structure prediction revolutionized

Mohammed AlQuraishi, 2021, Nature.

Podocyte specific deletion of PKM2 ameliorates LPS-induced podocyte injury through beta-catenin

Mohammed AlQuraishi, Yi Zhao, L. Nodit, 2022, Cell communication and signaling : CCS.

Zyflamend, a unique herbal blend, induces cell death and inhibits adipogenesis through the coordinated regulation of PKA and JNK

Mohammed AlQuraishi, J. Whelan, D. Donohoe, 2020, Adipocyte.

High-throughput deep learning variant effect prediction with Sequence UNET

P. Beltrão, Mohammed AlQuraishi, Alistair S. Dunham, 2022, bioRxiv.

High-throughput deep learning variant effect prediction with Sequence UNET

P. Beltrão, Mohammed AlQuraishi, Alistair S. Dunham, 2022, bioRxiv.

Diagnostic Value of Inflammatory Markers in Elderly Arab Women with Sarcopenia

Mohammed AlQuraishi, N. Al-Daghri, Shaun Sabico, 2022, Diagnostics.

Single-sequence protein structure prediction using a language model and deep learning

George M. Church, P. Sorger, Mohammed AlQuraishi, 2022, Nature Biotechnology.

OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization

Brian D. Weitzner, Marta M. Stepniewska-Dziubinska, Stella Rose Biderman, 2022, bioRxiv.

Computational structure prediction methods enable the systematic identification of oncogenic mutations

A. Ferrando, R. Rabadán, Hossein Khiabanian, 2022, bioRxiv.

OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization

Brian D. Weitzner, Marta M. Stepniewska-Dziubinska, Stella Rose Biderman, 2022, bioRxiv.

Zyflamend induces apoptosis in pancreatic cancer cells via modulation of the JNK pathway

Mohammed AlQuraishi, J. Whelan, Dexter L. Puckett, 2020, Cell Communication and Signaling.

End-to-end differentiable learning of protein structure

Mohammed AlQuraishi, 2018, bioRxiv.

Protein structure prediction by AlphaFold2: are attention and symmetries all you need?

P. Sorger, Mohammed AlQuraishi, N. Bouatta, 2021, Acta crystallographica. Section D, Structural biology.

The Role of PKM2 in Metabolic Reprogramming: Insights into the Regulatory Roles of Non-Coding RNAs

Mohammed AlQuraishi, Winyoo Chowanadisai, Dexter L. Puckett, 2021, International journal of molecular sciences.

Pyruvate kinase M2: A simple molecule with complex functions.

Amal S. Humidat, Mohammed AlQuraishi, J. Whelan, 2019, Free radical biology & medicine.

Unified rational protein engineering with sequence-only deep representation learning

George M. Church, Surojit Biswas, Mohammed AlQuraishi, 2019, bioRxiv.

ProteinNet: a standardized data set for machine learning of protein structure

Mohammed AlQuraishi, 2019, BMC Bioinformatics.

BIOPHYSICAL PREDICTION OF PROTEIN-PEPTIDE INTERACTIONS AND SIGNALING NETWORKS USING MACHINE LEARNING

Peter K. Sorger, Mohammed AlQuraishi, Joseph M. Cunningham, 2019, Nature Methods.

Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2

J. A. Patino-Galindo, P. Sorger, R. Rabadán, 2021, Genome medicine.

Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2

Peter K. Sorger, Ratul Chowdhury, Raul Rabadan, 2020, Genome Medicine.

Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2

J. A. Patino-Galindo, P. Sorger, Y. Guan, 2020, Genome Medicine.

Structural biology at the scale of proteomes

Mohammed AlQuraishi, N. Bouatta, Mohammed Alquraishi, 2023, Nature Structural & Molecular Biology.

Generating Novel, Designable, and Diverse Protein Structures by Equivariantly Diffusing Oriented Residue Clouds

Mohammed AlQuraishi, Yeqing Lin, 2023, ArXiv.

Reproducibility will only come with data liberation

P. Sorger, Mohammed AlQuraishi, Mohammed Alquraishi, 2016, Science Translational Medicine.

ProteinNet: a standardized data set for machine learning of protein structure

Mohammed AlQuraishi, Mohammed AlQuraishi, Mohammed Alquraishi, 2019, BMC Bioinformatics.

Unified rational protein engineering with sequence-based deep representation learning

E. C. Alley, G. Church, Mohammed AlQuraishi, 2019, Nature Methods.

pNeRF: Parallelized Conversion from Internal to Cartesian Coordinates

Mohammed AlQuraishi, Mohammed AlQuraishi, 2018, bioRxiv.

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

Shengdong Tang, Xide Xia, Mohammed AlQuraishi, 2015, BMC Bioinformatics.

Generating Novel, Designable, and Diverse Protein Structures by Equivariantly Diffusing Oriented Residue Clouds

Mohammed AlQuraishi, Yeqing Lin, Mohammed Alquraishi, 2023, ICML.

Protein Structure Prediction Using a Maximum Likelihood Formulation of a Recurrent Geometric Network

Mallory R. Tollefson, M. Schnieders, Mohammed AlQuraishi, 2021, bioRxiv.

Structural Bioinformatics

Mohammed AlQuraishi, Vijai Singh, D. Patel, 2019, Essentials of Bioinformatics, Volume I.

Parallelized Natural Extension Reference Frame: Parallelized Conversion from Internal to Cartesian Coordinates

Mohammed AlQuraishi, Mohammed AlQuraishi, 2019, J. Comput. Chem..

OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization

Brian D. Weitzner, Marta M. Stepniewska-Dziubinska, Stella Rose Biderman, 2023, bioRxiv.

OpenProteinSet: Training data for structural biology at scale

Daniel Berenberg, Ian Fisk, Mohammed AlQuraishi, 2023, NeurIPS.

Bioinformatics Analysis of has-miR-181a in some Covid-19 Vaccinated People in Al-Najaf Province

Mohammed AlQuraishi, Mohammad Alzeyadi, 2023, Egyptian Academic Journal of Biological Sciences C Physiology and Molecular Biology.

Accurate Protein Structure Prediction by Embeddings and Deep Learning Representations pdf

Anand Kannan, Iddo Drori, Chen Keasar, 2019, ArXiv.

A Hybrid Structure-Based Machine Learning Approach for Predicting Kinase Inhibition by Small Molecules

Peter S. Kutchukian, P. Sorger, Mohammed AlQuraishi, 2023, J. Chem. Inf. Model..

A multiscale statistical mechanical framework integrates biophysical and genomic data to assemble cancer networks

P. Sorger, G. MacBeath, Mohammed AlQuraishi, 2014, Nature Genetics.