Curriculum Vitae
Ben Knowles – Curriculum Vitae
bwknowles@ucla.edu
Professional Preparation
2016 – 2020 Post-doctoral Research Fellow, Department of Marine and Coastal Sciences, Rutgers University
2011 – 2016 Doctorate in Cellular and Molecular Biology, University of California,
San Diego and San Diego State University (UCSD/SDSU Joint Program)
2001 – 2005 Bachelor of Science in Ecology and Marine Biology with Honours in Botany
University of Queensland, Australia
Appointments
2020-current Adjunct Assistant Professor, Department of Ecology and Evolutionary Biology, University of California, Los Angeles
2016 – 2020 Post-doctoral Research Fellow, Institute of Earth, Ocean, and Atmospheric Science, Department of Marine and Coastal Science, Rutgers University
2014 – 2016 Course Co-instructor, Advanced Cell and Molecular Biology, SDSU
2011 – 2014 Teaching Assistant, Introductory Cell and Molecular Biology, SDSU
2011 Research Assistant, Scripps Institution of Oceanography (Mitchell Lab)
2010 – 2011 Research Assistant, University of Queensland (Centre for Water Studies)
2010 Water Quality Monitor, South-East Queensland Water
2009 – 2010 Research Assistant, University of Southern California (Caron Lab)
2009 Research Specialist, Proteus Environmental Technologies
2008 – 2009 Research Assistant, University of Southern California (Manahan Lab)
2007 Ecological Consultant, FRC Environmental Consultancy
2006 – 2007 Technician, Commonwealth Scientific & Industrial Research Organisation
2004 – 2006 Research Assistant, University of Queensland (Marine Botany Group)
Teaching Positions
2020-2021 Course developer and instructor, Viral Ecology and Evolution, UCLA. Designed course to be implemented Spring 2021.
2014 – 2016 Course Co-developer and -instructor, Advanced Cell and Molecular Biology, SDSU
2011 – 2014 Teaching Assistant, Introductory Cell and Molecular Biology Lab, SDSU
Published Work (Google Scholar link)
Knowles B, Bonachela JA, Behrenfeld MJ, Bondoc KG, Cael BB, Carlson CA, Cieslik N*, Diaz BP, Fuchs HL, Graff JR, Grasis J, Halsey H, Haramaty L, Johns CT, Natale F, Nissimov JI, Schieler B, Thamatrakoln K, Thingstad TF, Våge S, Watkins C, Westberry T, and KD Bidle. Temperate infection in a virus-host system previously known for virulent dynamics. Nature Communications 11(4626): 1-13. doi: 0.1038/s41467-020-18078-4
Boling L, Cuevas DA, Kang HS, Knowles B, Maughan H, McNair K, Rojas MI, Sanchez SE, Smurthwaite C, and F Rohwer. Dietary anti-microbials and prophage inducers – towards landscaping of the human gut microbiome. 2020. Gut Microbes. doi: 0.1080/19490976.2019.1701353
Nissimov JI, Talmy D, Haramaty L, Fredricks H, Zelzion E, Knowles B, Eren M, Vandzura R, Laber C, Schieler B, Johns C, More KD, Coolen MJL, Follows MJ, Bhattacharya D, Van Mooy BAS, and K.D. Bidle. 2019. Biochemical diversity of glycosphingolipid biosynthesis as a driver of Coccolithovirus competitive ecology. Environmental Microbiology 21(6):2182-2197
Thamatrakoln K, Talmy D, Haramaty L, Maniscalco C, Latham J, Knowles B, Natale N, Coolen MJL, Follows MJ, and KD Bidle. 2018. Light regulation of coccolithophore host-virus interactions. New Phycologist, doi:10.1111/nph.15459.
Knowles B, Bailey B, Boling L, Breitbart M, Cobián-Güemes A, del Campo J, Edwards R, Felts B, Grasis J, Haas AF, Katira P, Wegley Kelly L, Luque A, Nulton J, Paul L, Peters G, Robinett N, Sandin S, Segall A, Silveira C, Youle M, and F Rohwer. 2017. Variability and host density independence in inductions-based estimates of environmental lysogeny. Nature Microbiology 2, 17064.
Knowles B and F Rohwer. 2017. Reply to Brief Communication Arising: Lysis, lysogeny, and virus-microbe ratios. Nature 549: E3-E4.
Roach T, Abieri M, George E, Knowles B, Smurthwaite C, Haas A, and F Rohwer. 2017. Microbial bioenergetics of coral-algal interactions. PeerJ 5: e3423.
Knowles B, Silveira C, Bailey B, Barott K, Cantu V, Cobián-Güemes A, Coutinho F, Dinsdale E, Felts B, Furby K, George E, Green K*, Gregoracci G, Haas A, Haggerty J, Hester E, Hisakawa N, Kelly LW, Lim YW, Little M, Luque A, McDole-Somera T, McNair K, de Oliveira L, Quistad S, Robinett N, Sala E, Salamon P, Sanchez S, Sandin S, Silva G, Smith J, Sullivan C, Thompson C, Vermeij M, Youle M, Young C, Zgliczynski B, Brainard R, Edwards R, Nulton J, Thompson F, and F Rohwer. 2016. Lytic to temperate switching of viral communities. Nature 531; 466–470.
Haas A, Fairoz M, Kelly LW, Nelson C, Dinsdale E, Edwards R, Giles S, Hatay M, Hisakawa N, Knowles B, Lim YW, Maughan H, Pantos O, Roach T, Sanchez S, Silveira C, Sandin S, Smith J, and F Rohwer. 2016. Global microbialization of coral reefs. Nature Microbiology 1: 16042.
Roitman S, Flores-Uribe J, Philosof A, Knowles B, Rohwer F, Ignacio-Espinoza J, Sullivan M, Acinas S, Cornejo-Castillo F, Sánchez P, Dupont C, and O Beja. 2015. Closing the gaps on the viral photosystem photosystem-I psaDCAB gene organization. Environmental Microbiology, doi:10.1111/1462-2920.13036.
Haas A, Knowles B, Lim YW, McDole-Somera T, Kelly LW, Hatay M, and F Rohwer. 2014. Unraveling the unseen players in the ocean – a field guide to water chemistry and marine microbiology. Journal of Visualized Experiments (JoVE); e52131, doi:10.3791/52131.
Knowles B. 2014. March from the sea: A brief history of environmental phage ecology from marine to human ecosystems. In Rohwer F, Youle M, Maughan H, and N Hisakawa (Eds.) Life in Our Phage World, Wholon Publishing, San Diego.
Publications in Revision, Review, or Preparation
Diaz B, Knowles B, Johns C, Laber C, Harvey E, Lowenstein D, Hunter J, Haramaty L, Natale F, Bondoc K, Graff J, Haentjens N, Baetge N, Boss E, Carlson C, Behrenfeld M, Van Mooy B, and KD Bidle. Contextualizing phytoplankton accumulation and loss in the North Atlantic with physiological state, virus infection, and mixing dynamics. In revision at Nature Communications.
Silveira CB, Luque A, Haas AF, Roach TNF, George EE, Knowles B, Little M, Sullivan CJ, Kelly LW, Brainard R, Rohwer F, and BA Bailey. Microbial predators governing state transitions in coral reefs. In review at Science.
Knowles B, Bonachela J, Cieslik N*, DellaPenna A, Baetge N, Behrenfeld M, Bondoc K, Boss E, Diaz B, Graff J, Halsey K, Haramaty L, Karp-Boss L, Natale F, and KD Bidle. Many mechanisms operate within dilution-based predator-prey assays. Reviewed at Communications Biology; in revision for resubmission.
Knowles B. An empiricist’s guide to theoretical viral ecology. In preparation for submission to mBio.
Knowles B, Edwards R, Green K*, Haas AF, Hester E, George E, Lim YW, Little M, Kelly LW, Sandin S, Smith J, Young C, Zgliczynski B, F Rohwer, et al. Metagenomic functional profiling of viral communities across the temperate to lytic spectrum. In Preparation for submission to Nature Microbiology.
* Indicates undergraduate authors I mentored.
Awards and Funding
2019 Co-PI. ‘Temperate viral infection as symbiosis in the Emiliania huxleyi-EhV system.’ Submitted to Moore Foundation Symbiosis Model Systems (invited for full submission after pre-submission, not funded).
2019 Co-PI. ‘The landscape of stress, death, and virus infection in the annual North Atlantic bloom across different physical mixing regimes and patterns of carbon accumulation and loss.’ Submitted to Joint Genome Institute Community Science Program (invited for full submission after pre-submission, not funded).
2016 – 2018 PI; ‘Mechanisms of Viral Inhibition of Grazing in the Environment.’ Post-doctoral Research Fellowship from the Institute of Earth, Ocean, and Atmospheric Science (funded).
Professional Service
Reviewer: Current Biology, Environmental Microbiology, FEMS Microbiology Ecology, Frontiers in Microbiology, The ISME Journal, mBio, PLoS One, Science Advances.
Ad-hoc Reviewer: NSF Dimensions of Biodiversity
Synergistic Activities
2015 – 2016 Bioinformatic Breakfast: founded an ongoing working group of biologists and computational scientists to improve inter-disciplinary communication.
2015 Bioinformatics for Ecologists: using my expertise in both ecology and computational science, I initiated and conducted a workshop teaching basic bioinformatics to traditional ecologists and oceanographers.
2013 – 2016 Coral Club: coordinated monthly informal outreach meetings and talks from coral reef researchers from across institutions in San Diego, covering and integrating across a broad range of disciplines and interests.
2011 – 2016 BioMath Group: contributed to weekly interdisciplinary fusion of biological and mathematic approaches and problem-solving for projects across viral ecology, metagenomics, proteomics, metabolomics, thermodynamics, evolution, theoretical modeling, and coral reef biology.
Mentoring
2020 ASLO Multicultural Program Mentor and Career and Research Advice Mentorship; Ocean Sciences Meeting Feb 2020
2019 Meeting Mentor at ASLO 2019 Aquatic Sciences
2017-2020 Nicole Cieslik* Undergraduate Aresty Research Assistant (Rutgers)
Physiology- vs. density-dependence of viral predation; now lab tech at Gingko BioWorks. *see publications
2016 Kevin Green* Undergraduate student ; now Master student (SDSU)
Microbial metagenomic sequencing; *see publications
2015 – 2016 Group leader, Holobiont Evolution Group, Rohwer Lab (SDSU): mentored a group with differing experience levels and backgrounds probing symbiotic biological interactions over evolutionary time.
2012 Undergraduate Research Program Judge; San Diego State University
Invited Talks
Nov 2020 Oregon State University (virtual) Host: Kimberly Halsey
Oct 2020 Weizmann Institute, Israel (virtual) Host: Assaf Vardi
Feb 2020 San Diego State University Host: Forest Rohwer
Oct 2019 University of Maine Host: Lee Karp-Boss
Oct 2018 University of California, Santa Barbara Host: Craig Carlson
July 2018 Oregon State University Host: Mike Behrenfeld
June 2018 NIOZ, Netherlands Host: Andreas Haas
May 2017 University of Bergen, Norway Host: Frede Thingstad
April 2016 University of Exeter, UK Host: Tom Richards
Feb 2014 Scripps Institution of Oceanography Host: Stuart Sandin
Conferences and Workshops
2020 Association for the Sciences of Limnology and Oceanography (San Deigo 2020, San Juan 2019, Portland 2018).
2019 American Society for Microbiology ASM Microbe conference, San Francisco, USA.
2018 Gordon Research Conference and Seminar on Marine Microbes, Lucca, Italy.
2017 – 2019 NASA North Atlantic Atmospheric and Marine Ecosystem Study Science Team Meetings (annual meetings in 2017, 2018, and 2019), Langley Research Center, Virginia and Corvallis, Oregon, USA.
2016 International Coral Reef Symposium, Honolulu, USA.
2015 Canadian Institute for Advanced Research Integrative Microbiology Workshop, Victoria, Canada.
2015 Single Cell Genomics Workshop, Bigelow Laboratory for Ocean Sciences, USA.
2015 Year of the Phage Conference, San Diego, USA.
2013 Environmental Virology Workshop, Tucson, USA.
2012 International Coral Reef Symposium, Cairns, Australia.
Relevant Research Cruises and Field Work
Over 1000 Scientific SCUBA dives logged, hundreds of hours in small boats.
2017 – 2018 Characterizing viral mortality terms as drivers in the annual bloom cycle of the North Atlantic Ocean, (R/V Atlantis, Aug-Sept, 2017, Mar-Apr, 2018); NASA NAAMES project.
2017 Emiliania huxleyi – virus mesocosm experiments, Bergen, Norway (shore-based, May-June, 2017).
2015 Microbial virus- and protist-predation dynamics along a disturbance gradient in the near-shore waters of Curaçao, South Caribbean Sea (shore-based, April 2015).
2012 – 2015 Characterizing coral reef viral and microbial communities in the Manu’a Islands group (2015), North-West Hawaiian Islands (2013), and from Hawai’i to American Samoa (2012) collaborating with NOAA Coral Reef Ecosystem Division (NOAA RV Hi’ialakai; 3 cruises, 4 months at sea).
2011 Characterizing biological and optical properties of the Bering and Chukchi Seas to develop remote sensing algorithms (USCG Cutter Healy, June-August 2011); NASA Icescape project.
2003- 2010 Extensive small boating and Scientific SCUBA diving work in the Great Barrier Reef (especially Heron Island) and Moreton Bay, Australia, and Catalina Island, California, USA.