Systems & Computational Biology

Research output

Research output per year 2003 2009 2013 2014 2015 2016 2017 2018 2019 2020 2021 2022 2024

• 275 Article
• 22 Review article
• 6 Comment/debate
• 5 Chapter
• 9 More
  • 4 Conference contribution
  • 2 Conference article
  • 2 Short survey
  • 1 Editorial

Research output per year

Research output per year

Search results

• 2022

  Cell fate decisions, transcription factors and signaling during early retinal development

  Diacou, R., Nandigrami, P., Fiser, A., Liu, W., Ashery-Padan, R. & Cvekl, A., Nov 2022, In: Progress in Retinal and Eye Research. 91, 101093.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Transcription Factors 100%
  • Eye 82%
  • Organoids 34%
  • Retinal Diseases 32%
  • Otx Transcription Factors 25%
  24 Scopus citations
• 2021

  Engineering the Microbiome to Prevent Adverse Events: Challenges and Opportunities

  Khan, S., Hauptman, R. & Kelly, L., Jan 6 2021, In: Annual Review of Pharmacology and Toxicology. 61, p. 159-179 21 p.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Microbiota 100%
  • Drug 53%
  • Pharmacological Metabolism 39%
  • Application 15%
  • Pharmaceutical Preparations 9%
  16 Scopus citations

• Residue-based pharmacophore approaches to study protein–protein interactions

  Shrestha, R., Fajardo, J. E. & Fiser, A., Apr 2021, In: Current Opinion in Structural Biology. 67, p. 205-211 7 p.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Molecular Dynamics Simulation 100%
  • Proteins 99%
  • Drug Discovery 92%
  • Ligands 63%
  4 Scopus citations
• 2020

  Microbial transformation of widely used pharmaceutical and personal care product compounds

  Porter, A. W., Wolfson, S. J., Häggblom, M. & Youn, L. Y., 2020, In: F1000Research. 9, 130.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Pharmaceutical Services 100%
  • Cosmetics 94%
  • Pharmaceutical 58%
  • Chemical Transformation 50%
  • Waste Water 25%
  9 Scopus citations

• The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View

  Xavier, J. B., Young, V. B., Skufca, J., Ginty, F., Testerman, T., Pearson, A. T., Macklin, P., Mitchell, A., Shmulevich, I., Xie, L., Caporaso, J. G., Crandall, K. A., Simone, N. L., Godoy-Vitorino, F., Griffin, T. J., Whiteson, K. L., Gustafson, H. H., Slade, D. J., Schmidt, T. M., Walther-Antonio, M. R. S., & 10 othersKorem, T., Webb-Robertson, B. J. M., Styczynski, M. P., Johnson, W. E., Jobin, C., Ridlon, J. M., Koh, A. Y., Yu, M., Kelly, L. & Wargo, J. A., Mar 2020, In: Trends in Cancer. 6, 3, p. 192-204 13 p.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Microbiota 100%
  • Neoplasms 32%
  • Ecology 20%
  • Systems Biology 20%
  • Allergy and Immunology 17%
  150 Scopus citations
• 2019

  Bringing microbiome-drug interaction research into the clinic

  Guthrie, L. & Kelly, L., Jun 2019, In: EBioMedicine. 44, p. 708-715 8 p.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Microbiota 100%
  • Drug Interactions 98%
  • Drug 53%
  • Safety 34%
  • Gastrointestinal Microbiome 28%
  44 Scopus citations

• Predicting and Understanding the Human Microbiome's Impact on Pharmacology

  Hitchings, R. & Kelly, L., Jul 2019, In: Trends in Pharmacological Sciences. 40, 7, p. 495-505 11 p.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Microbiota 100%
  • Pharmacology 67%
  • Drug 53%
  • Pharmaceutical Preparations 41%
  • Pharmacokinetics 21%
  37 Scopus citations
• 2017

  Adaptation in the visual cortex: A case for probing neuronal populations with natural stimuli

  Schwartz, O., Snow, M. & Coen-Cagli, R., 2017, In: F1000Research. 6, 1246.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Visual Cortex 100%
  • Neurons 58%
  • Environment 53%
  • Population 37%
  • Direction compound 22%
  15 Scopus citations

• Postinfection Irritable Bowel Syndrome: The Links between Gastroenteritis, Inflammation, the Microbiome, and Functional Disease

  Downs, I. A., Aroniadis, O. C., Kelly, L. & Brandt, L. J., 2017, In: Journal of clinical gastroenterology. 51, 10, p. 869-877 9 p.

  Research output: Contribution to journal › Review article › peer-review

  • Irritable Bowel Syndrome 100%
  • Gastroenteritis 97%
  • Microbiota 86%
  • Inflammation 51%
  • Bacteroidetes 15%
  30 Scopus citations
• 2016

  The origin and evolution of cell types

  Arendt, D., Musser, J. M., Baker, C. V. H., Bergman, A., Cepko, C., Erwin, D. H., Pavlicev, M., Schlosser, G., Widder, S., Laubichler, M. D. & Wagner, G. P., Dec 1 2016, In: Nature Reviews Genetics. 17, 12, p. 744-757 14 p.

  Research output: Contribution to journal › Review article › peer-review

  • Transcription Factors 100%
  • Animals 66%
  424 Scopus citations
• 2015

  Niche construction game cancer cells play

  Bergman, A. & Gligorijevic, B., Oct 1 2015, In: European Physical Journal Plus. 130, 10, 203.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • games 100%
  • Cells 78%
  • cancer 75%
  • Environment 45%
  • Modification 45%
  4 Scopus citations
• 2014

  Crk at the quarter century mark: Perspectives in signaling and cancer

  Kumar, S., Fajardo, J. E., Birge, R. B. & Sriram, G., May 2014, In: Journal of Cellular Biochemistry. 115, 5, p. 819-825 7 p.

  Research output: Contribution to journal › Review article › peer-review

  • src Homology Domains 100%
  • Signal Transduction 35%
  • Protein 34%
  • Biochemical Role 27%
  • Neoplasms 26%
  26 Scopus citations

• Smotifs as structural local descriptors of supersecondary elements: Classification, completeness and applications

  Bonet, J., Fiser, A., Oliva, B. & Fernandez-Fuentes, N., Dec 1 2014, In: Bio-Algorithms and Med-Systems. 10, 4, p. 195-212 18 p.

  Research output: Contribution to journal › Review article › peer-review

  • Proteins 100%
  • Protein Structure 53%
  • Protein 45%
  • Application 34%
  • Conformations 19%
  3 Scopus citations
• 2013

  Not to be suppressed? Rethinking the host response at a root-parasite interface

  Goto, D. B., Miyazawa, H., Mar, J. C. & Sato, M., Dec 2013, In: Plant Science. 213, p. 9-17 9 p.

  Research output: Contribution to journal › Review article › peer-review

  • root-knot nematodes 100%
  • Parasites 73%
  • Plant Development 70%
  • Sustainable Development 62%
  • parasites 60%
  18 Scopus citations
• 2010

  Template-based protein structure modeling.

  Fiser, A., 2010, In: Methods in molecular biology (Clifton, N.J.). 673, p. 73-94 22 p.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Proteins 100%
  168 Scopus citations
• 2009

  Toxoplasma gondii proteomics

  Weiss, L. M., Fiser, A., Angeletti, R. H. & Kim, K., Jun 2009, In: Expert Review of Proteomics. 6, 3, p. 303-313 11 p.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Toxoplasma 100%
  • Proteomics 81%
  • Protein 36%
  • Strain 30%
  • Infectious Encephalitis 26%
  29 Scopus citations
• 2008

  Protein production and purification

  Gräslund, S., Nordlund, P., Weigelt, J., Hallberg, B. M., Bray, J., Gileadi, O., Knapp, S., Oppermann, U., Arrowsmith, C., Hui, R., Ming, J., dhe-Paganon, S., Park, H. W., Savchenko, A., Yee, A., Edwards, A., Vincentelli, R., Cambillau, C., Kim, R., Kim, S. H., & 64 othersRao, Z., Shi, Y., Terwilliger, T. C., Kim, C. Y., Hung, L. W., Waldo, G. S., Peleg, Y., Albeck, S., Unger, T., Dym, O., Prilusky, J., Sussman, J. L., Stevens, R. C., Lesley, S. A., Wilson, I. A., Joachimiak, A., Collart, F., Dementieva, I., Donnelly, M. I., Eschenfeldt, W. H., Kim, Y., Stols, L., Wu, R., Zhou, M., Burley, S. K., Emtage, J. S., Sauder, J. M., Thompson, D., Bain, K., Luz, J., Gheyi, T., Zhang, F., Atwell, S., Almo, S. C., Bonanno, J. B., Fiser, A., Swaminathan, S., Studier, F. W., Chance, M. R., Sali, A., Acton, T. B., Xiao, R., Zhao, L., Ma, L. C., Hunt, J. F., Tong, L., Cunningham, K., Inouye, M., Anderson, S., Janjua, H., Shastry, R., Ho, C. K., Wang, D., Wang, H., Jiang, M., Montelione, G. T., Stuart, D. I., Owens, R. J., Daenke, S., Schütz, A., Heinemann, U., Yokoyama, S., Büssow, K. & Gunsalus, K. C., Feb 2008, In: Nature Methods. 5, 2, p. 135-146 12 p.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Research Personnel 100%
  • Purification 96%
  • Recombinant Proteins 70%
  • Protein 59%
  • Decision Making 59%
  699 Scopus citations
• 2007

  Genetic determinants of human health span and life span: Progress and new opportunities

  Martin, G. M., Bergman, A. & Barzilai, N., Jul 2007, In: PLoS genetics. 3, 7, p. 1121-1130 10 p.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • gerontology 100%
  • human health 93%
  • Longevity 91%
  • Geriatrics 64%
  • Health 49%
  97 Scopus citations

• Head and neck cancer: Reduce and integrate for optimal outcome

  Belbin, T. J., Bergman, A., Brandwein-Gensler, M., Chen, Q., Childs, G., Garg, M., Haigentz, M., Hogue-Angeletti, R., Moadel, R., Negassa, A., Owen, R., Prystowsky, M. B., Schiff, B., Schlecht, N. F., Shifteh, K., Smith, R. V. & Zheng, X., Nov 2007, In: Cytogenetic and Genome Research. 118, 2-4, p. 92-109 18 p.

  Research output: Contribution to journal › Review article › peer-review
  8 Scopus citations

• Structural genomics of protein phosphatases

  Almo, S. C., Bonanno, J. B., Sauder, J. M., Emtage, S., Dilorenzo, T. P., Malashkevich, V., Wasserman, S. R., Swaminathan, S., Eswaramoorthy, S., Agarwal, R., Kumaran, D., Madegowda, M., Ragumani, S., Patskovsky, Y., Alvarado, J., Ramagopal, U. A., Faber-Barata, J., Chance, M. R., Sali, A., Fiser, A., & 3 othersZhang, Z. Y., Lawrence, D. S. & Burley, S. K., Sep 2007, In: Journal of Structural and Functional Genomics. 8, 2-3, p. 121-140 20 p.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Phosphoprotein Phosphatases 100%
  • Genomics 86%
  • National Institute of General Medical Sciences (U.S.) 40%
  • Protein 35%
  • African Trypanosomiasis 30%
  127 Scopus citations
• 2006

  Pentapeptide repeat proteins

  Vetting, M. W., Hegde, S. S., Fajardo, J. E., Fiser, A., Roderick, S. L., Takiff, H. E. & Blanchard, J. S., Jan 10 2006, In: Biochemistry. 45, 1, p. 1-10 10 p.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Pentapeptide 100%
  • Proteins 30%
  • Protein 25%
  • DNA Gyrase 19%
  • Amino Acid Sequence 18%
  140 Scopus citations
• 2004

  Protein structure modeling in the proteomics era

  Fiser, A., 2004, In: Expert Review of Proteomics. 1, 1, p. 97-110 14 p.

  Research output: Contribution to journal › Review article › peer-review

  • Protein Structure 100%
  • Proteomics 94%
  • Proteins 37%
  • Explosions 31%
  • Protein 21%
  59 Scopus citations