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For: Faisal FE, Newaz K, Chaney JL, Li J, Emrich SJ, Clark PL, Milenković T. GRAFENE: Graphlet-based alignment-free network approach integrates 3D structural and sequence (residue order) data to improve protein structural comparison. Sci Rep 2017;7:14890. [PMID: 29097661 DOI: 10.1038/s41598-017-14411-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 10/11/2017] [Indexed: 12/26/2022]  Open
Number Cited by Other Article(s)
1
Newaz K, Schaefers C, Weisel K, Baumbach J, Frishman D. Prognostic importance of splicing-triggered aberrations of protein complex interfaces in cancer. NAR Genom Bioinform 2024;6:lqae133. [PMID: 39328266 PMCID: PMC11426328 DOI: 10.1093/nargab/lqae133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2024] [Revised: 08/30/2024] [Accepted: 09/13/2024] [Indexed: 09/28/2024]  Open
2
Zitnik M, Li MM, Wells A, Glass K, Morselli Gysi D, Krishnan A, Murali TM, Radivojac P, Roy S, Baudot A, Bozdag S, Chen DZ, Cowen L, Devkota K, Gitter A, Gosline SJC, Gu P, Guzzi PH, Huang H, Jiang M, Kesimoglu ZN, Koyuturk M, Ma J, Pico AR, Pržulj N, Przytycka TM, Raphael BJ, Ritz A, Sharan R, Shen Y, Singh M, Slonim DK, Tong H, Yang XH, Yoon BJ, Yu H, Milenković T. Current and future directions in network biology. BIOINFORMATICS ADVANCES 2024;4:vbae099. [PMID: 39143982 PMCID: PMC11321866 DOI: 10.1093/bioadv/vbae099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 05/31/2024] [Accepted: 07/08/2024] [Indexed: 08/16/2024]
3
Hamamsy T, Morton JT, Blackwell R, Berenberg D, Carriero N, Gligorijevic V, Strauss CEM, Leman JK, Cho K, Bonneau R. Protein remote homology detection and structural alignment using deep learning. Nat Biotechnol 2024;42:975-985. [PMID: 37679542 PMCID: PMC11180608 DOI: 10.1038/s41587-023-01917-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 07/26/2023] [Indexed: 09/09/2023]
4
Huang J, Li J, Chen Q, Wang X, Chen G, Tang J. Freeprotmap: waiting-free prediction method for protein distance map. BMC Bioinformatics 2024;25:176. [PMID: 38704533 PMCID: PMC11069170 DOI: 10.1186/s12859-024-05771-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/09/2024] [Indexed: 05/06/2024]  Open
5
Lecca P, Lecca M. Graph embedding and geometric deep learning relevance to network biology and structural chemistry. Front Artif Intell 2023;6:1256352. [PMID: 38035201 PMCID: PMC10687447 DOI: 10.3389/frai.2023.1256352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/16/2023] [Indexed: 12/02/2023]  Open
6
Piccardi C. Metrics for network comparison using egonet feature distributions. Sci Rep 2023;13:14657. [PMID: 37669967 PMCID: PMC10480166 DOI: 10.1038/s41598-023-40938-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 08/18/2023] [Indexed: 09/07/2023]  Open
7
Koehler Leman J, Szczerbiak P, Renfrew PD, Gligorijevic V, Berenberg D, Vatanen T, Taylor BC, Chandler C, Janssen S, Pataki A, Carriero N, Fisk I, Xavier RJ, Knight R, Bonneau R, Kosciolek T. Sequence-structure-function relationships in the microbial protein universe. Nat Commun 2023;14:2351. [PMID: 37100781 PMCID: PMC10133388 DOI: 10.1038/s41467-023-37896-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 04/05/2023] [Indexed: 04/28/2023]  Open
8
Newaz K, Piland J, Clark PL, Emrich SJ, Li J, Milenković T. Multi-layer sequential network analysis improves protein 3D structural classification. Proteins 2022;90:1721-1731. [PMID: 35441395 PMCID: PMC9356989 DOI: 10.1002/prot.26349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 03/04/2022] [Accepted: 03/30/2022] [Indexed: 11/08/2022]
9
Gu S, Jiang M, Guzzi PH, Milenković T. Modeling multi-scale data via a network of networks. Bioinformatics 2022;38:2544-2553. [PMID: 35238343 PMCID: PMC9048659 DOI: 10.1093/bioinformatics/btac133] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 02/01/2022] [Accepted: 02/28/2022] [Indexed: 11/12/2022]  Open
10
Prabantu VM, Gadiyaram V, Vishveshwara S, Srinivasan N. Understanding structural variability in proteins using protein structural networks. Curr Res Struct Biol 2022;4:134-145. [PMID: 35586857 PMCID: PMC9108755 DOI: 10.1016/j.crstbi.2022.04.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/01/2022] [Accepted: 04/09/2022] [Indexed: 11/13/2022]  Open
11
Brysbaert G, Lensink MF. Centrality Measures in Residue Interaction Networks to Highlight Amino Acids in Protein–Protein Binding. FRONTIERS IN BIOINFORMATICS 2021;1:684970. [PMID: 36303777 PMCID: PMC9581030 DOI: 10.3389/fbinf.2021.684970] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/17/2021] [Indexed: 12/21/2022]  Open
12
Newaz K, Wright G, Piland J, Li J, Clark PL, Emrich SJ, Milenković T. Network analysis of synonymous codon usage. Bioinformatics 2020;36:4876-4884. [PMID: 32609328 DOI: 10.1093/bioinformatics/btaa603] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 05/05/2020] [Accepted: 06/22/2020] [Indexed: 12/25/2022]  Open
13
Hasan MA, Lonardi S. DeeplyEssential: a deep neural network for predicting essential genes in microbes. BMC Bioinformatics 2020;21:367. [PMID: 32998698 PMCID: PMC7525945 DOI: 10.1186/s12859-020-03688-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
14
Malod-Dognin N, Pancaldi V, Valencia A, Pržulj N. Chromatin network markers of leukemia. Bioinformatics 2020;36:i455-i463. [PMID: 32657405 PMCID: PMC7355288 DOI: 10.1093/bioinformatics/btaa445] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]  Open
15
Newaz K, Ghalehnovi M, Rahnama A, Antsaklis PJ, Milenković T. Network-based protein structural classification. ROYAL SOCIETY OPEN SCIENCE 2020;7:191461. [PMID: 32742675 PMCID: PMC7353965 DOI: 10.1098/rsos.191461] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
16
Quantitative description and classification of protein structures by a novel robust amino acid network: interaction selective network (ISN). Sci Rep 2019. [PMCID: PMC6853966 DOI: 10.1038/s41598-019-52766-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
17
Tantardini M, Ieva F, Tajoli L, Piccardi C. Comparing methods for comparing networks. Sci Rep 2019;9:17557. [PMID: 31772246 PMCID: PMC6879644 DOI: 10.1038/s41598-019-53708-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 10/25/2019] [Indexed: 11/17/2022]  Open
18
Malod-Dognin N, Pržulj N. Functional geometry of protein interactomes. Bioinformatics 2019;35:3727-3734. [PMID: 30821317 DOI: 10.1093/bioinformatics/btz146] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 01/15/2019] [Accepted: 02/25/2019] [Indexed: 12/14/2022]  Open
19
Zhao Y, Xue X, Xie X. An alignment-free measure based on physicochemical properties of amino acids for protein sequence comparison. Comput Biol Chem 2019;80:10-15. [PMID: 30851619 DOI: 10.1016/j.compbiolchem.2019.01.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 12/30/2018] [Accepted: 01/17/2019] [Indexed: 01/21/2023]
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