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ORCIDYuri Khudyakov
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2020 – today
- 2024
[c29]Yaroslav Zharov
, Yury Khudyakov, Evgeniia Fedotova, Evgeny Grigorenko, Egor Bogomolov:
Tool-augmented LLMs as a Universal Interface for IDEs. IDE@ICSE 2024: 40-42- [i1]Yaroslav Zharov, Yury Khudyakov, Evgeniia Fedotova, Evgeny Grigorenko, Egor Bogomolov:
Tool-Augmented LLMs as a Universal Interface for IDEs. CoRR abs/2402.11635 (2024) - 2023
- [j18]David S. Campo, Alexander Mosa, Yury Khudyakov:
A Novel Information-Theory-Based Genetic Distance That Approximates Phenotypic Differences. J. Comput. Biol. 30(4): 420-431 (2023) - 2022
- [j17]Walker Gussler, David S. Campo, Zoya Dimitrova, Pavel Skums, Yury Khudyakov:
Primary case inference in viral outbreaks through analysis of intra-host variant population. BMC Bioinform. 23(1): 62 (2022) - [c28]Pavel Skums, Fatemeh Mohebbi, Vyacheslav Tsyvina, Pelin Icer, Sumathi Ramachandran, Yury Khudyakov:
SOPHIE: Viral Outbreak Investigation and Transmission History Reconstruction in a Joint Phylogenetic and Network Theory Framework. RECOMB 2022: 369-370 - 2020
- [j16]David S. Campo, Yury Khudyakov:
Convex hulls in hamming space enable efficient search for similarity and clustering of genomic sequences. BMC Bioinform. 21-S(18): 482 (2020)
2010 – 2019
- 2019
- [c27]Yury Khudyakov, Ion I. Mandoiu, Pavel Skums, Alexander Zelikovsky:
Workshop on Computational Advances in Molecular Epidemiology. BCB 2019: 561 - 2018
- [j15]Pavel Skums, Alex Zelikovsky, Rahul Singh, Walker Gussler, Zoya Dimitrova, Sergey Knyazev, Igor Mandric, Sumathi Ramachandran, David S. Campo, Deeptanshu Jha, Leonid Bunimovich, Elizabeth Costenbader, Connie Sexton, Siobhán O'Connor, Guo-liang Xia, Yury Khudyakov:
QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data. Bioinform. 34(1): 163-170 (2018) - [j14]Seth Sims, Atkinson G. Longmire, David S. Campo, Sumathi Ramachandran, Magdalena Medrzycki, Lilia Ganova-Raeva, Yulin Lin, Amanda Sue, Hong Thai, Alexander Zelikovsky, Yury Khudyakov:
Automated quality control for a molecular surveillance system. BMC Bioinform. 19-S(11): 358:1-358:15 (2018) - [j13]Viachaslau Tsyvina, David S. Campo, Seth Sims, Alex Zelikovsky, Yury Khudyakov, Pavel Skums:
Fast estimation of genetic relatedness between members of heterogeneous populations of closely related genomic variants. BMC Bioinform. 19-S(11): 360:1-360:10 (2018) - [c26]Yury Khudyakov, Ion I. Mandoiu, Pavel Skums, Alexander Zelikovsky:
ACM-BCB 2018 Computational Advances in Molecular Epidemiology (CAME) Chairs' Welcome. BCB 2018: 574 - 2017
- [c25]Yury Khudyakov, Ion I. Mandoiu, Pavel Skums, Alexander Zelikovsky:
CAME 2017: 6th Workshop on Computational Advances in Molecular Epidemiology. BCB 2017: 775 - [c24]Sunitha Basodi, Pelin Burcak Icer, Pavel Skums, Yury Khudyakov, Alexander Zelikovsky, Yi Pan:
Classification of HCV infections through sequence image normalization. ICCABS 2017: 1 - [c23]Pelin Icer Baykal, Alexander Artyomenko, Sumathi Ramachandran, Yury Khudyakov, Alex Zelikovsky, Pavel Skums:
Assessment of HCV infection stage as recent or chronic using multi-parameter analysis and machine learning. ICCABS 2017: 1 - [c22]Viachaslau Tsyvina, David S. Campo, Seth Sims, Alex Zelikovsky, Yury Khudyakov, Pavel Skums:
Efficient filtering algorithm for detection of genetic similarity between large genomic datasets. ICCABS 2017: 1 - [c21]Alexander Artyomenko, Pelin B. Icer, Pavel Skums, Sumathi Ramachandran, Yury Khudyakov, Alex Zelikovsky:
Agent-Based in Silico Evolution of HCV Quasispecies. ISBRA 2017: 420-424 - [c20]Deeptanshu Jha, Pavel Skums, Alex Zelikovsky, Yury Khudyakov, Rahul Singh:
Modeling the Spread of HIV and HCV Infections Based on Identification and Characterization of High-Risk Communities Using Social Media. ISBRA 2017: 425-430 - 2016
- [j12]Xiaojun Xu, Hong Thai, Kathryn M. Kitrinos, Guo-liang Xia, Anuj Gaggar, Matthew Paulson, Lilia Ganova-Raeva, Yury Khudyakov, James Lara:
Modeling the functional state of the reverse transcriptase of hepatitis B virus and its application to probing drug-protein interaction. BMC Bioinform. 17(S-8): 280 (2016) - 2015
- [j11]Pavel Skums, Alexander Artyomenko, Olga Glebova, Sumathi Ramachandran, Ion I. Mandoiu, David S. Campo, Zoya Dimitrova, Alex Zelikovsky, Yuri Khudyakov:
Computational framework for next-generation sequencing of heterogeneous viral populations using combinatorial pooling. Bioinform. 31(5): 682-690 (2015) - [c19]James Lara, Yury Khudyakov, Livia Rossi, Gilberto Vaughan:
Highlights: Predicting the cross-immunoreactivity of hepatitis C virus hyper-variable region 1 peptides using polynomial neural networks. ICCABS 2015: 1 - [c18]Inna Rytsareva, Seth Sims, Sriram P. Chockalingam, Srinivas Aluru, David S. Campo, Cansu Tetik, Sharma V. Thankachan, Yury Khudyakov, Yueli Zheng, Chirag Jain, Amanda Sue:
Efficient detection of viral transmission with threshold-based methods. ICCABS 2015: 1-6 - [c17]Pavel Skums, Olga Glebova, David S. Campo, Nana Li, Zoya Dimitrova, Seth Sims, Leonid Bunimovich, Alex Zelikovsky, Yury Khudyakov:
Algorithms for prediction of viral transmission using analysis of intra-host viral populations. ICCABS 2015: 1 - 2014
- [j10]James Lara, F. Xavier López-Labrador, Fernando González-Candelas, Marina Berenguer, Yuri Khudyakov:
Computational models of liver fibrosis progression for hepatitis C virus chronic infection. BMC Bioinform. 15(S-8): S5 (2014) - [c16]David S. Campo, Zoya Dimitrova, Guo-liang Xia, Pavel Skums, Lilia Ganova-Raeva, Yuri Khudyakov:
New computational methods for assessing the genetic relatedness of close viral variants. ICCABS 2014: 1 - [c15]Pavel Skums, Alexander Artyomenko, Olga Glebova, Alex Zelikovsky, David S. Campo, Zoya Dimitrova, Yuri Khudyakov:
Detection of genetic relatedness between viral samples using EM-based clustering of next-generation sequencing data. ICCABS 2014: 1 - 2013
- [j9]Pavel Skums, Nicholas Mancuso, Alexander Artyomenko, Bassam Tork, Ion I. Mandoiu, Yuri Khudyakov, Alex Zelikovsky:
Reconstruction of viral population structure from next-generation sequencing data using multicommodity flows. BMC Bioinform. 14(S-9): S2 (2013) - [c14]David S. Campo, Zoya Dimitrova, Pavel Skums, Yuri Khudyakov:
Mutational robustness of hepatitis C virus intra-host variants. ICCABS 2013: 1 - [c13]James Lara, Yuri Khudyakov, F. Xavier López-Labrador, Fernando González-Candelas, Marina Berenguer:
Hepatitis C virus genetic association to rate of liver fibrosis progression. ICCABS 2013: 1 - [c12]Pavel Skums, David S. Campo, Zoya Dimitrova, Leonid Bunimovich, Yuri Khudyakov:
Computational analysis and modelling of intra-host adaptation of hepatitis C virus: The role of immune cross-reactivity of HCV quasispecies. ICCABS 2013: 1 - [c11]Pavel Skums, Olga Glebova, Alex Zelikovsky, Ion I. Mandoiu, Yuri Khudyakov:
Optimizing pooling strategies for the massive next-generation sequencing of viral samples. ICCABS 2013: 1 - [c10]Pavel Skums, Olga Glebova, Alex Zelikovsky, Zoya Dimitrova, David Stiven Campo Rendon, Lilia Ganova-Raeva, Yuri Khudyakov:
Alignment of DNA Mass-Spectral Profiles Using Network Flows. ISBRA 2013: 149-160 - 2012
- [j8]Pavel Skums, Zoya Dimitrova, David S. Campo, Gilberto Vaughan, Livia Rossi, Joseph C. Forbi, Jonny Yokosawa, Alex Zelikovsky, Yuri Khudyakov:
Efficient error correction for next-generation sequencing of viral amplicons. BMC Bioinform. 13(S-10): S6 (2012) - [j7]Irina V. Astrakhantseva, David S. Campo, Aufra Araujo, Chong-Gee Teo, Yuri Khudyakov, Saleem Kamili:
Differences in variability of hypervariable region 1 of hepatitis C virus (HCV) between acute and chronic stages of HCV infection. Silico Biol. 11(5-6): 163-173 (2012) - [j6]David S. Campo, Zoya Dimitrova, James Lara, Mike Purdy, Hong Thai, Sumathi Ramachandran, Lilia Ganova-Raeva, X. Zhai, Joseph C. Forbi, Chong-Gee Teo, Yuri Khudyakov:
Coordinated evolution of the Hepatitis B Virus Polymerase. Silico Biol. 11(5-6): 175-182 (2012) - [j5]Zoya Dimitrova, David S. Campo, Sumathi Ramachandran, Gilberto Vaughan, Lilia Ganova-Raeva, Yulin Lin, Joseph C. Forbi, Guo-liang Xia, Pavel Skums, Brian L. Pearlman, Yuri Khudyakov:
Evaluation of viral heterogeneity using next-generation sequencing, end-point limiting-dilution and mass spectrometry. Silico Biol. 11(5-6): 183-192 (2012) - [j4]James Lara, Yuri Khudyakov:
Association of antigenic properties to structure of the hepatitis C virus NS3 protein. Silico Biol. 11(5-6): 203-212 (2012) - [j3]James Lara, John E. Tavis, Maureen J. Donlin, William M. Lee, He-Jun Yuan, Brian L. Pearlman, Gilberto Vaughan, Joseph C. Forbi, Guo-liang Xia, Yuri Khudyakov:
Coordinated evolution among hepatitis C virus genomic sites is coupled to host factors and resistance to interferon. Silico Biol. 11(5-6): 213-224 (2012) - [j2]Pavel Skums, David S. Campo, Zoya Dimitrova, Gilberto Vaughan, Daryl T. Lau, Yuri Khudyakov:
Numerical detection, measuring and analysis of differential interferon resistance for individual HCV intra-host variants and its influence on the therapy response. Silico Biol. 11(5-6): 263-269 (2012) - 2011
- [c9]David S. Campo, Zoya Dimitrova, James Lara, Mike Purdy, Hong Thai, Sumathi Ramachandran, Lilia Ganova-Raeva, X. Zhai, Joseph C. Forbi, Chong-Gee Teo, Yuri Khudyakov:
Network of coordinated substitutions in the Hepatitis B virus polymerase. BIBM Workshops 2011: 64-71 - [c8]Irina V. Astrakhantseva, David S. Campo, Aufra Araujo, Chong-Gee Teo, Yuri Khudyakov, Saleem Kamili:
Variation in physicochemical properties of the hypervariable region 1 during acute and chronic stages of hepatitis C virus infection. BIBM Workshops 2011: 72-78 - [c7]Zoya Dimitrova, David S. Campo, Sumathi Ramachandran, Gilberto Vaughan, Lilia Ganova-Raeva, Yulin Lin, Joseph C. Forbi, Guo-liang Xia, Pavel Skums, Brian L. Pearlman, Yuri Khudyakov:
Assessments of intra- and inter-host diversity of hepatitis C virus using Next Generation Sequencing and Mass spectrometry. BIBM Workshops 2011: 79-86 - [c6]James Lara, John E. Tavis, Maureen J. Donlin, William M. Lee, He-Jun Yuan, Brian L. Pearlman, Gilberto Vaughan, Joseph C. Forbi, Guo-liang Xia, Yuri Khudyakov:
Host-specific HCV evolution and response to the combined interferon and ribavirin therapy. BIBM Workshops 2011: 102-109 - [c5]James Lara, Yuri Khudyakov:
Modeling antigenic property of the hepatitis C virus NS3 protein. BIBM Workshops 2011: 110-117 - [c4]Pavel Skums, David S. Campo, Zoya Dimitrova, Gilberto Vaughan, Daryl T. Lau, Yuri Khudyakov:
Modelling differential interferon resistance of HCV quasispecies. BIBM Workshops 2011: 144-148
2000 – 2009
- 2008
- [j1]James Lara, Robert M. Wohlhueter, Zoya Dimitrova, Yuri Khudyakov:
Artificial neural network for prediction of antigenic activity for a major conformational epitope in the hepatitis C virus NS3 protein. Bioinform. 24(17): 1858-1864 (2008) - [c3]David S. Campo, Zoya Dimitrova, Yuri Khudyakov:
Physicochemical Correlation between Amino Acid Sites in Short Sequences under Selective Pressure. ISBRA 2008: 146-158 - [c2]Kelly Westbrooks, Irina Astrovskaya, David S. Campo, Yuri Khudyakov, Piotr Berman, Alexander Zelikovsky:
HCV Quasispecies Assembly Using Network Flows. ISBRA 2008: 159-170 - [c1]James Lara, Zoya Dimitrova, Yuri Khudyakov:
Invited Keynote Talk: Integrative Viral Molecular Epidemiology: Hepatitis C Virus Modeling. ISBRA 2008: 355-366
Coauthor Index
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last updated on 2024-10-23 21:26 CEST by the dblp team
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