The power and limits of predicting exon-exon interactions using protein 3D structures
Liebold J, Moral-Morales AD, Manalastas-Cantos K, Tsoy O, Kurtz S, Baumbach J, and Newaz K
bioRxiv,
2025
Transcription factor prediction using protein 3D secondary structures
Liebold J*, Neuhaus F*, Geiser J, Kurtz S, Baumbach J, and Newaz K
Bioinformatics,
2025
Prognostic importance of splicing-triggered aberrations of protein complex interfaces in cancer
Newaz K, Schaefers C, Weisel K, Baumbach J, and Frishman D
NAR Genomics and Bioinformatics,
2024
Towards future directions in data-integrative supervised prediction of human aging-related genes
Li Q, Newaz K, and Milenković T
Bioinformatics Advances,
2022
Multi‐layer sequential network analysis improves protein 3D structural classification
Newaz K, Piland J, Clark PL, Emrich SJ, Li J, and Milenković T
Proteins: Structure, Function, and Bioinformatics,
2022
Improved supervised prediction of aging-related genes via weighted dynamic network analysis
Li Q*, Newaz K*, and Milenković T
BMC Bioinformatics,
2021
Network analysis of synonymous codon usage
Newaz K, Wright G, Piland J, Li J, Clark PL, Emrich SJ, and Milenković T
Bioinformatics,
2020
Inference of a dynamic aging-related biological subnetwork via network propagation
Newaz K and Milenković T
IEEE/ACM transactions on computational biology and bioinformatics,
2020
Network-based protein structural classification
Newaz K, Ghalehnovi M*, Rahnama A*, Antsaklis PJ, and Milenković T
Royal Society Open Science,
2020
Graphlets in network science and computational biology
Newaz K and Milenković T
Analyzing network data in biology and medicine: an interdisciplinary textbook for biological, medical and computational scientists,
2019
Weighted graphlets and deep neural networks for protein structure classification
Guo H, Newaz K, Emrich SJ, Milenković T, and Li J
arXiv,
2019
GRAFENE: Graphlet-based alignment-free network approach integrates 3D structural and sequence (residue order) data to improve protein structural comparison
Faisal FE*, Newaz K*, Chaney JL, Li J, Emrich SJ, Clark PL, and Milenković T
Scientific Reports,
2017
Identification of major signaling pathways in prion disease progression using network analysis
Newaz K, Sriram K, and Bera D
PLOS ONE,
2015