| 1 |
Cancer: More than a geneticist’s Pandora’s box |
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| Kritika Saxena, Ayalur Raghu Subbalakshmi, Prakash Kulkarni, Mohit Kumar Jolly |
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| Journal of Biosciences. 2022; 47(2) |
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| 2 |
A hybrid modeling environment to describe aggregates of cells heterogeneous for genotype and behavior with possible phenotypic transitions |
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| Giulia Chiari, Marcello Edoardo Delitala, David Morselli, Marco Scianna |
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| International Journal of Non-Linear Mechanics. 2022; : 104063 |
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| 3 |
Intrinsically Disordered Proteins: Critical Components of the Wetware |
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| Prakash Kulkarni, Supriyo Bhattacharya, Srisairam Achuthan, Amita Behal, Mohit Kumar Jolly, Sourabh Kotnala, Atish Mohanty, Govindan Rangarajan, Ravi Salgia, Vladimir Uversky |
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| Chemical Reviews. 2022; |
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| 4 |
Intrinsically disordered proteins: Ensembles at the limits of Anfinsen's dogma |
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| Prakash Kulkarni, Vitor B. P. Leite, Susmita Roy, Supriyo Bhattacharyya, Atish Mohanty, Srisairam Achuthan, Divyoj Singh, Rajeswari Appadurai, Govindan Rangarajan, Keith Weninger, John Orban, Anand Srivastava, Mohit Kumar Jolly, Jose N. Onuchic, Vladimir N. Uversky, Ravi Salgia |
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| Biophysics Reviews. 2022; 3(1): 011306 |
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| 5 |
A phenotype-structured model to reproduce the avascular growth of a tumor and its interaction with the surrounding environment |
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| Giada Fiandaca, Sara Bernardi, Marco Scianna, Marcello Edoardo Delitala |
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| Journal of Theoretical Biology. 2021; : 110980 |
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| 6 |
The somatic molecular evolution of cancer: Mutation, selection, and epistasis |
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| Krishna Dasari,Jason A. Somarelli,Sudhir Kumar,Jeffrey P. Townsend |
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| Progress in Biophysics and Molecular Biology. 2021; |
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| 7 |
Group Behavior and Emergence of Cancer Drug Resistance |
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| Supriyo Bhattacharya,Atish Mohanty,Srisairam Achuthan,Sourabh Kotnala,Mohit Kumar Jolly,Prakash Kulkarni,Ravi Salgia |
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| Trends in Cancer. 2021; |
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| 8 |
Protein conformational dynamics and phenotypic switching |
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| Prakash Kulkarni, Srisairam Achuthan, Supriyo Bhattacharya, Mohit Kumar Jolly, Sourabh Kotnala, Vitor B. P. Leite, Atish Mohanty, John Orban, Susmita Roy, Govindan Rangarajan, Ravi Salgia |
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| Biophysical Reviews. 2021; |
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| 9 |
Protein folding, misfolding, and un/non-folding: overview of the SP16 Session at the 20th IUPAB congress, 45th Annual Meeting of SBBf, and 50th Annual Meeting of SBBq |
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| Vladimir N. Uversky |
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| Biophysical Reviews. 2021; |
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| 10 |
Operating principles of circular toggle polygons |
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| Souvadra Hati,Atchuta Srinivas Duddu,Mohit Kumar Jolly |
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| Physical Biology. 2021; 18(4): 046003 |
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| 11 |
ESRP1 regulates alternative splicing of CARM1 to sensitize small cell lung cancer cells to chemotherapy by inhibiting TGF-ß/Smad signaling |
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| Meng Zheng,Yuchun Niu,Junguo Bu,Shumei Liang,Zhilin Zhang,Jianhua Liu,Linlang Guo,Zhihua Zhang,Qiongyao Wang |
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| Aging. 2021; 13(3): 3554 |
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| 12 |
miR-144-3p inhibited the growth, metastasis and epithelial-mesenchymal transition of colorectal adenocarcinoma by targeting ZEB1/2 |
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| Taiyuan Li,Cheng Tang,Zhixiang Huang,Lingling Yang,Hua Dai,Bo Tang,Benping Xiao,Jianfeng Li,Xiong Lei |
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| Aging. 2021; 13(13): 17349 |
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| 13 |
Dynamic Phenotypic Switching and Group Behavior Help Non-Small Cell Lung Cancer Cells Evade Chemotherapy |
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| Arin Nam, Atish Mohanty, Supriyo Bhattacharya, Sourabh Kotnala, Srisairam Achuthan, Kishore Hari, Saumya Srivastava, Linlin Guo, Anusha Nathan, Rishov Chatterjee, Maneesh Jain, Mohd W. Nasser, Surinder Kumar Batra, Govindan Rangarajan, Erminia Massarelli, Herbert Levine, Mohit Kumar Jolly, Prakash Kulkarni, Ravi Salgia |
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| Biomolecules. 2021; 12(1): 8 |
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| 14 |
Coupled Feedback Loops Involving PAGE4, EMT and Notch Signaling Can Give Rise to Non-Genetic Heterogeneity in Prostate Cancer Cells |
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| Divyoj Singh,Federico Bocci,Prakash Kulkarni,Mohit Kumar Jolly |
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| Entropy. 2021; 23(3): 288 |
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| 15 |
Multi-Stability and Consequent Phenotypic Plasticity in AMPK-Akt Double Negative Feedback Loop in Cancer Cells |
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| Adithya Chedere,Kishore Hari,Saurav Kumar,Annapoorni Rangarajan,Mohit Kumar Jolly |
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| Journal of Clinical Medicine. 2021; 10(3): 472 |
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| 16 |
A Theoretical Approach to Coupling the Epithelial-Mesenchymal Transition (EMT) to Extracellular Matrix (ECM) Stiffness via LOXL2 |
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| Youyuan Deng,Priyanka Chakraborty,Mohit Kumar Jolly,Herbert Levine |
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| Cancers. 2021; 13(7): 1609 |
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| 17 |
Emergent Properties of the HNF4a-PPAR? Network May Drive Consequent Phenotypic Plasticity in NAFLD |
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| Sarthak Sahoo,Divyoj Singh,Priyanka Chakraborty,Mohit Kumar Jolly |
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| Journal of Clinical Medicine. 2020; 9(3): 870 |
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| 18 |
NFATc Acts as a Non-Canonical Phenotypic Stability Factor for a Hybrid Epithelial/Mesenchymal Phenotype |
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| Ayalur Raghu Subbalakshmi,Deepali Kundnani,Kuheli Biswas,Anandamohan Ghosh,Samir M. Hanash,Satyendra C. Tripathi,Mohit Kumar Jolly |
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| Frontiers in Oncology. 2020; 10 |
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| 19 |
Intrinsically Disordered Proteins: Insights from Poincaré, Waddington, and Lamarck |
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| Prakash Kulkarni |
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| Biomolecules. 2020; 10(11): 1490 |
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| 20 |
Senescence-Associated Pro-inflammatory Cytokines and Tumor Cell Plasticity |
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| Jean Paul Vernot |
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| Frontiers in Molecular Biosciences. 2020; 7 |
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| 21 |
SEGN: Inferring real-time gene networks mediating phenotypic plasticity |
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| Libo Jiang,Christopher H. Griffin,Rongling Wu |
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| Computational and Structural Biotechnology Journal. 2020; 18: 2510 |
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| 22 |
DAXX inhibits cancer stemness and epithelial–mesenchymal transition in gastric cancer |
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| Chaofan Wu,Hui Ding,Shuochen Wang,Yangxin Li,Song-Bai Liu,Xiaoxiao Wang,Jiqing Zheng,Ting Xue,Hesham M. Amin,Yao-Hua Song,Jin Zhou |
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| British Journal of Cancer. 2020; |
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| 23 |
NRF2 activates a partial epithelial-mesenchymal transition and is maximally present in a hybrid epithelial/mesenchymal phenotype |
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| Federico Bocci,Satyendra C Tripathi,Samuel A Vilchez Mercedes,Jason T George,Julian P Casabar,Pak Kin Wong,Samir M Hanash,Herbert Levine,José N Onuchic,Mohit Kumar Jolly |
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| Integrative Biology. 2019; |
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| 24 |
Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level |
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| Xingcheng Lin,Prakash Kulkarni,Federico Bocci,Nicholas Schafer,Susmita Roy,Min-Yeh Tsai,Yanan He,Yihong Chen,Krithika Rajagopalan,Steven Mooney,Yu Zeng,Keith Weninger,Alex Grishaev,José Onuchic,Herbert Levine,Peter Wolynes,Ravi Salgia,Govindan Rangarajan,Vladimir Uversky,John Orban,Mohit Jolly |
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| Biomolecules. 2019; 9(2): 77 |
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| 25 |
Interrogation of Phenotypic Plasticity between Epithelial and Mesenchymal States in Breast Cancer |
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| Stefano Bhatia,Stefano Monkman,Stefano Blick,Stefano Pinto,Stefano Waltham,Stefano Nagaraj,Stefano Thompson |
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| Journal of Clinical Medicine. 2019; 8(6): 893 |
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| 26 |
Dynamics of Phenotypic Heterogeneity during EMT and Stemness in Cancer Progression |
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| Herbert Jolly,Herbert Celià-Terrassa |
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| Journal of Clinical Medicine. 2019; 8(10): 1542 |
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| 27 |
Phenotypic Plasticity, Bet-Hedging, and Androgen Independence in Prostate Cancer: Role of Non-Genetic Heterogeneity |
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| Mohit Kumar Jolly,Prakash Kulkarni,Keith Weninger,John Orban,Herbert Levine |
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| Frontiers in Oncology. 2018; 8 |
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| 28 |
PAGE4 and Conformational Switching: Insights from Molecular Dynamics Simulations and Implications for Prostate Cancer |
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| Xingcheng Lin,Susmita Roy,Mohit Kumar Jolly,Federico Bocci,Nicholas P. Schafer,Min-Yeh Tsai,Yihong Chen,Yanan He,Alexander Grishaev,Keith Weninger,John Orban,Prakash Kulkarni,Govindan Rangarajan,Herbert Levine,José N. Onuchic |
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| Journal of Molecular Biology. 2018; 430(16): 2422 |
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| 29 |
Intrinsically Disordered Proteins: The Dark Horse of the Dark Proteome |
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| Prakash Kulkarni,Vladimir N. Uversky |
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| PROTEOMICS. 2018; : 1800061 |
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| 30 |
Epithelial/mesenchymal plasticity: how have quantitative mathematical models helped improve our understanding? |
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| Mohit Kumar Jolly,Satyendra C. Tripathi,Jason A. Somarelli,Samir M. Hanash,Herbert Levine |
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| Molecular Oncology. 2017; 11(7): 739 |
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| 31 |
Epithelial-mesenchymal transition, a spectrum of states: Role in lung development, homeostasis, and disease |
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| Mohit Kumar Jolly,Chris Ward,Mathew Suji Eapen,Stephen Myers,Oskar Hallgren,Herbert Levine,Sukhwinder Singh Sohal |
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| Developmental Dynamics. 2017; |
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| 32 |
The GRHL2/ZEB Feedback Loop-A Key Axis in the Regulation of EMT in Breast Cancer |
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| Steven M. Mooney,Vida Talebian,Mohit Kumar Jolly,Dongya Jia,Monica Gromala,Herbert Levine,Brendan J. McConkey |
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| Journal of Cellular Biochemistry. 2017; |
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| 33 |
Phosphorylation-induced conformational dynamics in an intrinsically disordered protein and potential role in phenotypic heterogeneity |
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| Prakash Kulkarni,Mohit Kumar Jolly,Dongya Jia,Steven M. Mooney,Ajay Bhargava,Luciane T. Kagohara,Yihong Chen,Pengyu Hao,Yanan He,Robert W. Veltri,Alexander Grishaev,Keith Weninger,Herbert Levine,John Orban |
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| Proceedings of the National Academy of Sciences. 2017; 114(13): E2644 |
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| 34 |
Adaptive phenotype drives resistance to androgen deprivation therapy in prostate cancer |
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| Nicoletta Ferrari,Ilaria Granata,Matteo Capaia,Marina Piccirillo,Mario Rosario Guarracino,Roberta Venè,Antonella Brizzolara,Andrea Petretto,Elvira Inglese,Martina Morini,Simonetta Astigiano,Adriana Agnese Amaro,Francesco Boccardo,Cecilia Balbi,Paola Barboro |
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| Cell Communication and Signaling. 2017; 15(1) |
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| 35 |
Markers of epithelial-to-mesenchymal transition reflect tumor biology according to patient age and Gleason score in prostate cancer |
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| Dorota Jedroszka,Magdalena Orzechowska,Raneem Hamouz,Karolina Górniak,Andrzej K. Bednarek,Rajeev Samant |
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| PLOS ONE. 2017; 12(12): e0188842 |
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| 36 |
Phenotypic Plasticity and Cell Fate Decisions in Cancer: Insights from Dynamical Systems Theory |
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| Dongya Jia,Mohit Kumar Jolly,Prakash Kulkarni,Herbert Levine |
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| Cancers. 2017; 9(7): 70 |
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| 37 |
Intrinsically disordered proteins and prostate cancer: pouring new wine in an old bottle |
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| Prakash Kulkarni |
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| Asian Journal of Andrology. 2016; 18(5): 659 |
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| 38 |
Somatic Mutations in Prostate Cancer: Closer to Personalized Medicine |
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| M. J. Alvarez-Cubero,L. J. Martinez-Gonzalez,I. Robles-Fernandez,J. Martinez-Herrera,G. Garcia-Rodriguez,M. Pascual-Geler,J. M. Cozar,J. A. Lorente |
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| Molecular Diagnosis & Therapy. 2016; |
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| 39 |
Nickel impact on human health: An intrinsic disorder perspective |
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| Barbara Zambelli,Vladimir N. Uversky,Stefano Ciurli |
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| Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 2016; 1864(12): 1714 |
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