Publications

You can also find my articles on my Google Scholar profile.

2022

• FUN-PROSE: A Deep Learning Approach to Predict Condition-Specific Gene Expression in Fungi.
  Nambiar, A., Dubinkina, V., Liu, S., & Maslov, S.
  bioRxiv

• A transcriptomic atlas of low pH stress response in multiple Issatchenkia orientalis strains.
  Bhogale, S., Dubinkina, V.*, Hsieh, PH., Dibaeinia P., Nambiar, A., Yoshikuni, Y., Sinha, S., & Maslov, S.
  *in preparation

• Bottlenecks, Modularity, and the Neural Control of Behavior.
  Nande, A., Dubinkina, V.*, Zhang, G., Ravasio, R.*, & Berman, G.
  Frontiers in Behavioral Neuroscience, 16, 1662-5153

• Effect of subacute exposure to PFOS and GenX on gut microbiota-host metabolome homeostasis in male mice.
  Rashid, F.*, Dubinkina, V.*, Maslov, S., & Irudayaraj, J.
  *under review

2021

• A cross-study analysis of drug response prediction in cancer cell lines.
  Xia, F., Allen, J., Balaprakash, P., Brettin, T., Garcia-Cardona, C., Clyde, A., Cohn, J., Doroshow, J., Duan, X., Dubinkina, V., … & Stevens, R.
  Briefings in Bioinformatics, 23(1), bbab356.

• Complementary resource preferences spontaneously emerge in diauxic microbial communities.
  Wang, Z., Goyal, A., Dubinkina, V., George, A. B., Wang, T., Fridman, Y., & Maslov, S.
  Nat Commun 12, 6661.

• Ecology-guided prediction of cross-feeding interactions in the human gut microbiome.
  Goyal, A., Wang, T., Dubinkina, V., Maslov, S. (2021)
  Nat Commun 12, 1335.

2019

• Evidence for a multi-level trophic organization of the human gut microbiome.
  Wang, T., Goyal, A., Dubinkina, V., Maslov, S.
  PLOS Computational Biology, 15(12): e1007524.

• Multistability and regime shifts in microbial communities explained by competition for essential nutrients.
  Dubinkina, V.,</strong> Fridman, Y., Pandey, P. P.*, & Maslov, S.
  eLife, 8.

2018

• Multiple stable states in microbial communities explained by the stable marriage problem.
  Goyal, A.*, Dubinkina, V.*, & Maslov, S.
  The ISME journal, 12(12), 2823.

2017

• Links of gut microbiota composition with alcohol dependence syndrome and alcoholic liver disease.
  Dubinkina, V. B.,</strong>, Tyakht, A. V., Odintsova, V. Y., Yarygin, K. S., Kovarsky, B. A., Pavlenko, A. V., … & Nasyrova, R. F.
  Microbiome, 5(1), 141.

• Data on gut metagenomes of the patients with alcoholic dependence syndrome and alcoholic liver cirrhosis.
  Tyakht, A. V., Dubinkina, V. B.,, Odintsova, V. Y., Yarygin, K. S., Kovarsky, B. A., Pavlenko, A. V., … & Nasyrova, R. F.
  Data in Brief, 11, 98-102.

2016

• MetaFast: fast reference free graph-based comparison of shotgut metagenomic data.
  Ulyantsev, V. I., Kazakov S. V., Dubinkina, V. B., Tyakht, A. V., & Alexeev, D. G.
  Bioinformatics, 1-9.

• Assessment of k-mer spectrum applicability for metagenomic dissimilarity analysis. Dubinkina, V. B., Ischenko, D. S., Ulyantsev, V. I., Tyakht, A. V., & Alexeev, D. G. (2016).
  BMC bioinformatics, 17(1), 1.