Jessica M Logan

Dr. Jessica M Logan

orcid

Research Focus & Metrics

Academic Career Length

14Years (2013-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

View All Publications
2 December 2013 in Proceedings of the National Academy of Sciences
Verified
Journal Article
Closed access
PDF file
FVFreek J. Vonk
Freek J. Vonk
NCNicholas Casewell
Nicholas Casewell
CHChristiaan V. Henkel
Christiaan V. Henkel
AHAlysha M. Heimberg
Alysha M. Heimberg
HJHans J. Jansen
Hans J. Jansen
michael richardsonmichael richardson
michael richardson
Snakes are limbless predators, and many species use venom to help overpower relatively large, agile prey. Snake venoms are complex protein mixtures encoded by several multilocus gene families that function synergistically to cause incapacitation. To examine venom evolution, we sequenced and interrogated the genome of a venomous snake, the king cobra (Ophiophagus hannah), and compared it, together with our unique transcriptome, microRNA, and proteome datasets from this species, with data from other vertebrates. In contrast to the platypus, the only other venomous vertebrate with a sequenced genome, we find that snake toxin genes evolve through several distinct co-option mechanisms and exhibit surprisingly variable levels of gene duplication and directional selection that correlate with their functional importance in prey capture. The enigmatic accessory venom gland shows a very different pattern of toxin gene expression from the main venom gland and seems to have recruited toxin-like lectin genes repeatedly for new nontoxic functions. In addition, tissue-specific microRNA analyses suggested the co-option of core genetic regulatory components of the venom secretory system from a pancreatic origin. Although the king cobra is limbless, we recovered coding sequences for all Hox genes involved in amniote limb development, with the exception of Hoxd12. Our results provide a unique view of the origin and evolution of snake venom and reveal multiple genome-level adaptive responses to natural selection in this complex biological weapon system. More generally, they provide insight into mechanisms of protein evolution under strong selection. Significance Snake venoms are toxic protein cocktails used for prey capture. To investigate the evolution of these complex biological weapon systems, we sequenced the genome of a venomous snake, the king cobra, and assessed the composition of venom gland expressed genes, small RNAs, and secreted venom proteins. We show that regulatory components of the venom secretory system may have evolved from a pancreatic origin and that venom toxin genes were co-opted by distinct genomic mechanisms. After co-option, toxin genes important for prey capture have massively expanded by gene duplication and evolved under positive selection, resulting in protein neofunctionalization. This diverse and dramatic venom-related genomic response seemingly occurs in response to a coevolutionary arms race between venomous snakes and their prey.

21 February 2023 in JNCI Cancer Spectrum
Verified
Journal Article
Open access
PDF file
AHAshley Hopkins
Ashley Hopkins
JLJessica M Logan
Jessica M Logan
GKGanessan Kichenadasse
Ganessan Kichenadasse
MSMichael J Sorich
Michael J Sorich
On November 30, 2022, OpenAI enabled public access to ChatGPT, a next-generation artificial intelligence with a highly sophisticated ability to write, solve coding issues, and answer questions. This communication draws attention to the prospect that ChatGPT and its successors will become important virtual assistants to patients and health-care providers. In our assessments, ranging from answering basic fact-based questions to responding to complex clinical questions, ChatGPT demonstrated a remarkable ability to formulate interpretable responses, which appeared to minimize the likelihood of alarm compared with Google’s feature snippet. Arguably, the ChatGPT use case presents an urgent need for regulators and health-care professionals to be involved in developing standards for minimum quality and to raise patient awareness of current limitations of emerging artificial intelligence assistants. This commentary aims to raise awareness at the tipping point of a paradigm shift.

23 December 2021 in Cells
Verified
Journal Article
Open access
PDF file
Shane HickeyShane Hickey
Shane Hickey
BUBenjamin Ung
Benjamin Ung
CBChristie Bader
Christie Bader
Robert Douglas BrooksRobert Douglas Brooks
Robert Douglas Brooks
JLJoanna Lazniewska
Joanna Lazniewska
Doug BrooksDoug Brooks
Doug Brooks
Fluorescence microscopy has become a critical tool for researchers to understand biological processes at the cellular level. Micrographs from fixed and live-cell imaging procedures feature in a plethora of scientific articles for the field of cell biology, but the complexities of fluorescence microscopy as an imaging tool can sometimes be overlooked or misunderstood. This review seeks to cover the three fundamental considerations when designing fluorescence microscopy experiments: (1) hardware availability; (2) amenability of biological models to fluorescence microscopy; and (3) suitability of imaging agents for intended applications. This review will help equip the reader to make judicious decisions when designing fluorescence microscopy experiments that deliver high-resolution and informative images for cell biology.

3 September 2024 in JAMA Network Open
Verified
Journal Article
Open access
PDF file
BMBradley D. Menz
Bradley D. Menz
NKNicole M. Kuderer
Nicole M. Kuderer
BCBenjamin Chin-Yee
Benjamin Chin-Yee
JLJessica M Logan
Jessica M Logan
ARAndrew Rowland
Andrew Rowland
AHAshley Hopkins
Ashley Hopkins
Importance: With the growing use of large language models (LLMs) in education and health care settings, it is important to ensure that the information they generate is diverse and equitable, to avoid reinforcing or creating stereotypes that may influence the aspirations of upcoming generations.Objective: To evaluate the gender representation of LLM-generated stories involving medical doctors, surgeons, and nurses and to investigate the association of varying personality and professional seniority descriptors with the gender proportions for these professions.Design, Setting, and Participants: This is a cross-sectional simulation study of publicly accessible LLMs, accessed from December 2023 to January 2024. GPT-3.5-turbo and GPT-4 (OpenAI), Gemini-pro (Google), and Llama-2-70B-chat (Meta) were prompted to generate 500 stories featuring medical doctors, surgeons, and nurses for a total 6000 stories. A further 43 200 prompts were submitted to the LLMs containing varying descriptors of personality (agreeableness, neuroticism, extraversion, conscientiousness, and openness) and professional seniority.Main Outcomes and Measures: The primary outcome was the gender proportion (she/her vs he/him) within stories generated by LLMs about medical doctors, surgeons, and nurses, through analyzing the pronouns contained within the stories using χ2 analyses. The pronoun proportions for each health care profession were compared with US Census data by descriptive statistics and χ2 tests.Results: In the initial 6000 prompts submitted to the LLMs, 98% of nurses were referred to by she/her pronouns. The representation of she/her for medical doctors ranged from 50% to 84%, and that for surgeons ranged from 36% to 80%. In the 43 200 additional prompts containing personality and seniority descriptors, stories of medical doctors and surgeons with higher agreeableness, openness, and conscientiousness, as well as lower neuroticism, resulted in higher she/her (reduced he/him) representation. For several LLMs, stories focusing on senior medical doctors and surgeons were less likely to be she/her than stories focusing on junior medical doctors and surgeons.Conclusions and Relevance: This cross-sectional study highlights the need for LLM developers to update their tools for equitable and diverse gender representation in essential health care roles, including medical doctors, surgeons, and nurses. As LLMs become increasingly adopted throughout health care and education, continuous monitoring of these tools is needed to ensure that they reflect a diverse workforce, capable of serving society’s needs effectively.

7 December 2022 in Molecular Diagnosis & Therapy
Verified
Journal Article
Closed access
PDF file
GIANG THUY LAMGIANG THUY LAM
GIANG THUY LAM
SPSarita Prabhakaran
Sarita Prabhakaran
ASAlexandra Sorvina
Alexandra Sorvina
CMCarmela Martini
Carmela Martini
BUBen S.-Y. Ung
Ben S.-Y. Ung
JLJessica M Logan
Jessica M Logan

1 April 2020 in Critical Reviews in Oncology/Hematology
Verified
Journal Article
Closed access
NMNatansh D. Modi
Natansh D. Modi
MSMichael Sorich
Michael Sorich
ARAndrew Rowland
Andrew Rowland
JLJessica M Logan
Jessica M Logan
RMRoss McKinnon
Ross McKinnon
AHAshley Hopkins
Ashley Hopkins