Bogdan Knezevic

Bogdan Knezevic

New York, New York, United States
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About

I'm passionate about findings ways in which tech can be leveraged to push other fields…

Activity

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Experience

  • Kaleidoscope.bio Graphic

    Kaleidoscope.bio

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    Toronto, Ontario, Canada

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    Toronto, Canada Area

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    Oxford, United Kingdom

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    Oxford, United Kingdom

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    Greater Boston Area

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Education

  • University of Oxford Graphic

    University of Oxford

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    Activities and Societies: Rhodes Scholar (Prairies & Trinity 2015)

    My project investigated the ways in which rich and diverse genomic datasets can be used to inform pre-clinical drug target discovery. Specifically, I used data-mining and machine learning techniques in order to aggregate and integrate various predictors which can then be manipulated to yield a prioritized list of promising candidate gene targets. The project also had a focus on gene network interactions and their importance in understanding the complexity of disease. Example methods include SQL…

    My project investigated the ways in which rich and diverse genomic datasets can be used to inform pre-clinical drug target discovery. Specifically, I used data-mining and machine learning techniques in order to aggregate and integrate various predictors which can then be manipulated to yield a prioritized list of promising candidate gene targets. The project also had a focus on gene network interactions and their importance in understanding the complexity of disease. Example methods include SQL (for database exploration) and R (for implementing machine learning).

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    Activities and Societies: Varsity swim team

    Graduated with a First Class Honours degree (B.Sc), majoring in Neuroscience.

    My thesis project was titled "The behavioural effects and mechanism behind epicatechin, a plant flavonoid, with respect to learning and memory."

    I received a Rhodes Scholarship in my last year of undergrad, which I used towards a DPhil in Clinical Medicine, starting in October of 2015.

    My other awards include: Canadian Interuniversity Sport Scholar Athlete Community Service Award (2015), Calgary…

    Graduated with a First Class Honours degree (B.Sc), majoring in Neuroscience.

    My thesis project was titled "The behavioural effects and mechanism behind epicatechin, a plant flavonoid, with respect to learning and memory."

    I received a Rhodes Scholarship in my last year of undergrad, which I used towards a DPhil in Clinical Medicine, starting in October of 2015.

    My other awards include: Canadian Interuniversity Sport Scholar Athlete Community Service Award (2015), Calgary Booster Club Scholar Athlete Award (2011, 2014, 2015), Capital-One Academic All-Americas Scholar Athlete of the Year (2014), Canada West Student Athlete Community Service Award (2014), Dean’s List, Faculty of Science (2010-2015), Academic All-Canadian Scholar Athlete (2010-2014).

Volunteer Experience

  • Webber Academy Graphic

    Keynote Speaker

    Webber Academy

    - 2 months

    Education

    Spoke at a President's Club breakfast to 400 students and teachers, ranging from elementary to high school age, about the importance of balance in life for success.

  • Chief Organizer, Committee Chair

    TEDx

    - 5 months

    Held a TEDx conference at the University of Calgary campus, with the theme "Blueprint". A blueprint is a guide for making something, a design or pattern that can be followed. A blueprint is also a map and a plan. A person can have a “blueprint for success”, or a blueprint that guides his/her life rooted in a particular religion or philosophy. There are “genetic blueprints”, recipes for making living things. Blueprints guide us through unfamiliar terrain, help TV characters in devising an escape…

    Held a TEDx conference at the University of Calgary campus, with the theme "Blueprint". A blueprint is a guide for making something, a design or pattern that can be followed. A blueprint is also a map and a plan. A person can have a “blueprint for success”, or a blueprint that guides his/her life rooted in a particular religion or philosophy. There are “genetic blueprints”, recipes for making living things. Blueprints guide us through unfamiliar terrain, help TV characters in devising an escape plan from prison, but blueprints may also be outdated and lead us astray. They can be restricting, confusing, difficult to decipher. With so many ways to interpret a blueprint, we challenged our speakers to present their take on the theme while drawing from personal and professional experiences.

  • University of Calgary Graphic

    Master of Ceremony

    University of Calgary

    - Present 10 years 3 months

    Served as an MC for the University of Calgary Hall of Fame induction ceremony.

  • University of Calgary Graphic

    Social Media Strategist, Office of Sustainability

    University of Calgary

    - 4 months

    Environment

    Led a team of students to work with the University of Calgary's Office of Sustainability on their annual report. We focused on drawing student awareness and opinions on matters relating to sustainability, through Twitter and Facebook.

  • The Alex Community Health Centre Graphic

    Event Co-Organizer, Guest Speaker

    The Alex Community Health Centre

    - 7 months

    Health

    Organized an educational initiative with a chain of local community health centres on the topic of chronic and acute stress. Communicated causes and health implications, as well as management techniques. Presented to the clinics’ staff (20 people), “Dark Chocolate, Green Tea, and Stress: From Snails to Humans”.

  • The Triple Helix, Inc. Graphic

    Editor-in-Chief; President

    The Triple Helix, Inc.

    - 1 year 9 months

    Science and Technology

    Assisted establishment of the founding executive board of the University of Calgary’s Triple Helix chapter, an online, student-run forum for the publication and discussion of topics relating to science, technology, and society. Interacted with and assisted writers in the writing and editing process. Guided associate editors in their work with writers. Supervised the publication process; within the first year, the chapter was third overall in terms of article publication numbers (23 articles…

    Assisted establishment of the founding executive board of the University of Calgary’s Triple Helix chapter, an online, student-run forum for the publication and discussion of topics relating to science, technology, and society. Interacted with and assisted writers in the writing and editing process. Guided associate editors in their work with writers. Supervised the publication process; within the first year, the chapter was third overall in terms of article publication numbers (23 articles published), out of 22 international chapters, thetriplehelix.org. Took over as President in September of 2014.

Publications

  • Genomic insights into myasthenia gravis identify distinct immunological mechanisms in early and late onset disease

    Annals of Neurology

    We used a novel genomic methodology to integrate genomewide association study (GWAS) findings in myasthenia gravis with cell-type specific information, such as gene expression patterns and promotor-enhancer interactions, in order to identify disease-relevant genes. Subsequently, we conducted additional genomic investigations, including an expression quantitative analysis of 313 healthy people to provide mechanistic insights. The disease-relevant genes identified in this study are a unique…

    We used a novel genomic methodology to integrate genomewide association study (GWAS) findings in myasthenia gravis with cell-type specific information, such as gene expression patterns and promotor-enhancer interactions, in order to identify disease-relevant genes. Subsequently, we conducted additional genomic investigations, including an expression quantitative analysis of 313 healthy people to provide mechanistic insights. The disease-relevant genes identified in this study are a unique resource for many disciplines, including clinicians, scientists, and the pharmaceutical industry. The distinct immunological pathways linked to early and late onset myasthenia gravis carry important implications for drug repurposing opportunities and for future studies of drug development.

    See publication

  • Identifying collagen VI as a target of fibrotic diseases regulated by CREBBP/EP300

    PNAS

    Fibrotic diseases remain a major cause of morbidity and mortality, yet there are few effective therapies. The underlying pathology of all fibrotic conditions is the activity of myofibroblasts. Using cells from freshly excised disease tissue from patients with Dupuytren's disease (DD), a localized fibrotic disorder of the palm, we sought to identify new therapeutic targets for fibrotic disease. We hypothesized that the persistent activity of myofibroblasts in fibrotic diseases might involve…

    Fibrotic diseases remain a major cause of morbidity and mortality, yet there are few effective therapies. The underlying pathology of all fibrotic conditions is the activity of myofibroblasts. Using cells from freshly excised disease tissue from patients with Dupuytren's disease (DD), a localized fibrotic disorder of the palm, we sought to identify new therapeutic targets for fibrotic disease. We hypothesized that the persistent activity of myofibroblasts in fibrotic diseases might involve epigenetic modifications. Using a validated genetics-led target prioritization algorithm (Pi) of genome wide association studies (GWAS) data and a broad screen of epigenetic inhibitors, we found that the acetyltransferase CREBBP/EP300 is a major regulator of contractility and extracellular matrix production via control of H3K27 acetylation at the profibrotic genes, ACTA2 and COL1A1 Genomic analysis revealed that EP300 is highly enriched at enhancers associated with genes involved in multiple profibrotic pathways, and broad transcriptomic and proteomic profiling of CREBBP/EP300 inhibition by the chemical probe SGC-CBP30 identified collagen VI (Col VI) as a prominent downstream regulator of myofibroblast activity. Targeted Col VI knockdown results in significant decrease in profibrotic functions, including myofibroblast contractile force, extracellular matrix (ECM) production, chemotaxis, and wound healing. Further evidence for Col VI as a major determinant of fibrosis is its abundant expression within Dupuytren's nodules and also in the fibrotic foci of idiopathic pulmonary fibrosis (IPF). Thus, Col VI may represent a tractable therapeutic target across a range of fibrotic disorders.

    See publication

  • A genetics-led approach defines the drug target landscape of 30 immune-related traits.

    Nature Genetics

    Most candidate drugs currently fail later-stage clinical trials, largely due to poor prediction of efficacy on early target selection. Drug targets with genetic support are more likely to be therapeutically valid, but the translational use of genome-scale data such as from genome-wide association studies for drug target discovery in complex diseases remains challenging. Here, we show that integration of functional genomic and immune-related annotations, together with knowledge of network…

    Most candidate drugs currently fail later-stage clinical trials, largely due to poor prediction of efficacy on early target selection. Drug targets with genetic support are more likely to be therapeutically valid, but the translational use of genome-scale data such as from genome-wide association studies for drug target discovery in complex diseases remains challenging. Here, we show that integration of functional genomic and immune-related annotations, together with knowledge of network connectivity, maximizes the informativeness of genetics for target validation, defining the target prioritization landscape for 30 immune traits at the gene and pathway level. We demonstrate how our genetics-led drug target prioritization approach (the priority index) successfully identifies current therapeutics, predicts activity in high-throughput cellular screens (including L1000, CRISPR, mutagenesis and patient-derived cell assays), enables prioritization of under-explored targets and allows for determination of target-level trait relationships. The priority index is an open-access, scalable system accelerating early-stage drug target selection for immune-mediated disease.

    See publication

  • XGR software for enhanced interpretation of genomic summary data, illustrated by application to immunological traits

    Genome Medicine

    XGR provides a single integrated solution to enhance interpretation of genomic summary data for downstream biological discovery. XGR is released as both an R package and a web-app, freely available at http://galahad.well.ox.ac.uk/XGR.

    Other authors
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  • A flavanoid component of chocolate quickly reverses an imposed memory deficit.

    Journal of Experimental Biology

    The ability to remember is influenced by environmental and lifestyle factors, such as stress and diet. A flavanol contained in chocolate, epicatechin (Epi), has been shown to enhance long-term memory (LTM) formation in Lymnaea. Combining two stressors (low calcium pond water and crowding) block learning and all forms of memory. That is, this combination of environmentally relevant stressors creates a memory-unfriendly state. We tested the hypothesis that Epi will immediately reverse the…

    The ability to remember is influenced by environmental and lifestyle factors, such as stress and diet. A flavanol contained in chocolate, epicatechin (Epi), has been shown to enhance long-term memory (LTM) formation in Lymnaea. Combining two stressors (low calcium pond water and crowding) block learning and all forms of memory. That is, this combination of environmentally relevant stressors creates a memory-unfriendly state. We tested the hypothesis that Epi will immediately reverse the memory-unfriendly state. Thus, snails in the memory-deficit state when trained in Epi will immediately become competent to learn and form memory. We found that Epi not only reverses the memory-deficit state but further enhance LTM formation. Thus, a naturally occurring bioactive plant compound can overcome a memory unfriendly state. This supports the idea that bioactive substances may mitigate memory-making deficits that, for example, occur with ageing.

    Other authors
    • Yoshimasa Komatsuzaki
    • Emily de Freitas
    • Ken Lukowiak
    See publication

  • The flavonol epicatechin reverses the suppressive effects of a stressor on long-term memory formation.

    The Journal of Experimental Biology

    Learning and subsequent memory formation are influenced by both environmental and lifestyle factors, such as stress and diet. Epicatechin, a plant flavonol found in cocoa, red wine and green tea enhances long-term memory (LTM) formation in Lymnaea. By contrast, an ecologically relevant stressor, low-calcium pond water, suppresses LTM formation. We tested the hypothesis that epicatechin overcomes the suppressive effects of the stressor on LTM formation in the continued presence of the stressor…

    Learning and subsequent memory formation are influenced by both environmental and lifestyle factors, such as stress and diet. Epicatechin, a plant flavonol found in cocoa, red wine and green tea enhances long-term memory (LTM) formation in Lymnaea. By contrast, an ecologically relevant stressor, low-calcium pond water, suppresses LTM formation. We tested the hypothesis that epicatechin overcomes the suppressive effects of the stressor on LTM formation in the continued presence of the stressor. Snails trained in low calcium pond water exhibit learning but not LTM. Epicatechin (15 mg l−1) in control pond water enhances LTM formation. When epicatechin was added to the low-calcium pond water an enhanced LTM similar to that seen in control pond water was observed. Thus, a naturally occurring bioactive plant compound was able to overcome the suppressive effects of an ecologically relevant stressor on LTM formation.

    Other authors
    • Ken Lukowiak
    See publication

  • Low external environmental calcium levels prevent forgetting in Lymnaea.

    The Journal of Experimental Biology

    Forgetting may allow an animal to react more appropriately to current conditions, rather than continuing to exhibit a previously learned, possibly maladaptive behaviour based on previous experience. One theory is that forgetting is an active process, whereby the previously learnt response is replaced by new learning that interferes with the older memory. Hence, we hypothesized that an appropriately timed environmental stressor that blocks long-term memory (LTM) formation would also block…

    Forgetting may allow an animal to react more appropriately to current conditions, rather than continuing to exhibit a previously learned, possibly maladaptive behaviour based on previous experience. One theory is that forgetting is an active process, whereby the previously learnt response is replaced by new learning that interferes with the older memory. Hence, we hypothesized that an appropriately timed environmental stressor that blocks long-term memory (LTM) formation would also block forgetting. Lymnaea stagnalis (L.) is a freshwater snail, which requires environmental calcium of at least 20 mg l 1 to meet its requirements. Low environmental Ca2+ (i.e. 20mgl–1) in their environment acts as a stressor, and prevents LTM formation. Here, we asked whether a low Ca2+ environment would also prevent forgetting, concordant with the retrograde interference model of Jenkins and Dallenbach. Snails were operantly conditioned to reduce aerial respiration in hypoxia. When maintained in standard conditions (80 mg l–1 Ca2+), snails demonstrated LTM following training lasting 24 h, but not 72 h; however, when trained in standard conditions then exposed to a low Ca2+ environment (20mgl–1) immediately following training, they retained memory for at least 96 h, indicating that forgetting had been blocked. Thus, when exposed to low environmental Ca2+, Lymnaea will fail to form new memories, but will also continue to retain information previously learned and remembered as the low calcium blocks forgetting.

    Other authors
    • Sarah Dalesman
    • Vikram Karnik
    • Jovita Byzitter
    • Ken Lukowiak
    See publication

Honors & Awards

  • 2021 Arch Award for Early Career Achievement

    University of Calgary Alumni Association

    The Arch Awards are the highest honour awarded by the UCalgary Alumni Association. Since 1985, they have celebrated bold alumni who’ve transformed business and community, art and technology, sport and health, for the betterment of all.

  • Rhodes Scholarship

    The Rhodes Trust

    Selected as a Canadian Rhodes Scholar (Prairies & Trinity, 2015).

  • Capital-One Academic All-Americas Athlete of the Year

    CoSIDA

    Selected as one of four student athletes to hold the ‘at-large’ title (15 sports included), across all universities and colleges in USA and Canada.

Languages

  • English

    Native or bilingual proficiency

  • Bosnian

    Professional working proficiency

  • Croatian

    Professional working proficiency

  • Serbian

    Native or bilingual proficiency

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