Luqman Mushila Hodgkinson

All Publications

• Augmented Reality for medical training in eastern Africa IEEE Conference on Virtual Reality and 3D User Interfaces Oduor, P., Hodgkinson, L. M., Leuze, C., et al 2023
• Dermatomyositis autoantibodies: how can we maximize utility? Annals of Translational Medicine Hodgkinson, L. M., Wu, T. T., Fiorentino, D. F. 2021: 433

  Abstract

  The past 15 years has seen significant advances in the characterization of myositis-specific autoantibodies (MSAs) and their associated phenotypes in patients with dermatomyositis (DM). As more careful studies are performed, it is clear that unique combinations of clinical and pathological phenotypes are associated with each MSA, despite the fact that there is considerable heterogeneity within antibody classes as well as overlap across the groups. Because risk for interstitial lung disease (ILD), internal malignancy, adverse disease trajectory, and, potentially response to therapy differ by DM MSA group, a deeper understanding of MSAs and validation and standardization of assays used for detection are critical for optimizing diagnosis and treatment. Like any test, the diagnostic sensitivity and specificity of assays for various MSAs is not perfect. Currently tests for MSAs are helpful at minimum for a clinician to assess relative risk or contribute to diagnosis and perhaps counsel the appropriate patient about what to expect. With international standardization and larger studies it is likely that more antibody tests will make their way into formal schemata for diagnosis and actionable risk assessment in DM. In this review, we summarize key considerations for interpreting the clinical and pathologic associations with MSA in DM and identify critical gaps in knowledge and practice that will maximize their clinical utility and utility for understanding disease pathogenesis.

  View details for DOI 10.21037/atm-20-5175

  View details for PubMedCentralID PMC8033377

• COVID-19 vaccine distribution strategies in low and middle income countries with implications for global allocation Hodgkinson, L. M., Kim, Y., Memet, S., Rey Malca De Habich, M. M., Rodriguez Silva Santisteban, F. R. Stanford Digital Repository. https://purl.stanford.edu/hp890vk1414. 2021

  Abstract

  On March 11, 2020, the Director-General of the World Health Organization declared the onset of the COVID-19 global pandemic. Countries around the world responded with public health policies including quarantines and mask mandates to combat a rising surge in infections, hospitalizations, and deaths. As of this writing, more than 3 million deaths have been recorded, a staggering number of lives that yet does not capture the total effect of the pandemic on people around the globe. Mass vaccination is viewed as the best way to end this pandemic. This timely and important international report provides evidence of the need for a more equitable global allocation of COVID-19 vaccines to low- and middle-income countries (LMICs). Specifically, this report draws upon public data from five case countries - Haiti, Kenya, Liberia, Peru, and Romania - and develops a framework that policymakers around the world can use when pursuing various vaccine distribution strategies. Using a mixed-method approach including qualitative interviews and a quantitative frequency-dependent dynamic compartmental model, we found that 1) LMICs face many challenges from weakened healthcare infrastructures and economic poverty; 2) the next 12 months are extremely critical to save many lives by vaccinating large percentages of the populations in LMIC; and 3) global support will be essential to implement these large-scale vaccination programs. We were pleased to work closely with Partners in Health (PIH) as our primary client, a global health nonprofit organization with over 18,000 staff across 11 countries in four continents, and the Masinde Muliro School of Medicine in Kakamega County, Kenya. Both helped secure interviews with experts and provided relevant sources of public data. Authors: Hodgkinson, Luqman Mushila (PhD MS), School of Medicine (MD) and the Public Policy Program (MPP), luqman@stanford.edu; Kim, Yoon-Chan, Graduate School of Education (MA) and the Public Policy Program (MPP), ykim47@stanford.edu; Memet, Sevda (MD), Graduate School of Business (MBA) and the Public Policy Program (MPP), sevdam@stanford.edu; Rey Malca De Habich, Maria Marta, School of Humanities & Sciences (BA) and the Public Policy Program (MPP), mmreymdh@stanford.edu; Rodriguez Silva Santisteban, Fernando Rafael, School of Engineering (MS/PhD) and the Public Policy Program (MPP), frodsil@stanford.edu. For media inquiries and questions regarding this publication please contact the publisher: Stanford University Public Policy Program, Stanford, CA 94305, United States, +1 (650) 725-0109, publicpolicy@stanford.edu.

  https://purl.stanford.edu/hp890vk1414
• Ten-year survival with analysis of gender difference, risk factors, and causes of death during 13 years of public antiretroviral therapy in rural Kenya: republication Current Opinion in HIV and AIDS Hodgkinson, L. M., Abwalaba, R. A., Arudo, J., Barry, M. 2021; 16 (2): 121-131

  View details for DOI 10.1097/MD.0000000000020328

• Shoshin beriberi in a patient with oral and cutaneous graft-versus-host disease. JAAD case reports Hodgkinson, L. M., Shah, A., Bae, G. H., Novoa, R., Kwong, B. Y. 2020; 6 (5): 420-421

  View details for DOI 10.1016/j.jdcr.2020.02.031

  View details for PubMedID 32382634

  View details for PubMedCentralID PMC7200185

• Ten-year survival with analysis of gender difference, risk factors, and causes of death during 13 years of public antiretroviral therapy in rural Kenya Medicine Hodgkinson, L. M., Abwalaba, R. A., Arudo, J., Barry, M. 2020; 99 (21)

  View details for DOI 10.1097/MD.0000000000020328

• Type I and II interferon signaling differentially associated with histopathologic findings in dermatomyositis skin Journal of Investigative Dermatology Wu, T., Tabata, M., Hodgkinson, L. M., Page, K., Huard, C., Buhlmann, J., Sarin, K., Fiorentino, D. 2020; 140 (7): B17
• Genetic mutations underlying phenotypic plasticity in basosquamous carcinoma Journal of Investigative Dermatology Chiang, A., Tan, C. Z., Kuonen, F., Hodgkinson, L. M., Chiang, F., Cho, R. J., South, A. P., Tang, J. Y., Chang, A. L., Rieger, K. E., Oro, A. E., Sarin, K. Y. 2019

  View details for DOI 10.1016/j.jid.2019.03.1163

• The type 1 interferon signature reflects multiple phenotypic and activity measures in dermatomyositis. Arthritis & rheumatology (Hoboken, N.J.) Tabata, M. M., Hodgkinson, L. M., Wu, T. T., Li, S., Huard, C., Zhao, S., Bennett, D., Johnson, J., Tierney, C., He, W., Buhlmann, J. E., Page, K. M., Johnson, K., Casciola-Rosen, L., Chung, L., Sarin, K. Y., Fiorentino, D. 2023

  Abstract

  The type 1 interferon (IFN1) pathway is upregulated in dermatomyositis (DM). We sought to define how organ-specific disease activity as well as autoantibodies and other clinical factors are independently associated with systemic IFN1 activity in adult patients with DM.RNA sequencing was performed on 355 whole blood samples collected from 202 well-phenotyped DM patients followed during the course of their clinical care. A previously defined 13-gene IFN1 score was modeled as a function of demographic, serologic and clinical variables using both cross-sectional and longitudinal data.The pattern of IFN1-driven transcriptional response was stereotyped across samples with a sequential modular activation pattern strikingly similar to SLE. The median IFN1 score was higher or lower in patients with anti-MDA5 or anti-Mi2 antibodies, respectively, compared to patients without these antibodies. Absolute IFN1 score was independently associated with muscle and skin disease activity, interstitial lung disease, and anti-MDA5 antibodies. Changes in the IFN1 score over time were significantly associated with changes in skin or muscle disease activity. Stratified analysis accounting for heterogeneity in organ involvement and antibody class revealed high correlation (ρ=0.84-0.95) between changes in the IFN1 score and skin disease activity.The IFN1 score independently associates with both skin and muscle disease activity as well as certain clinical and serologic features in DM. Accounting for the effect of muscle disease and anti-MDA5 status reveals that the IFN1 score is strongly correlated with skin disease activity and provides support for IFN1 blockade as a therapeutic strategy for DM. This article is protected by copyright. All rights reserved.

  View details for DOI 10.1002/art.42526

  View details for PubMedID 37096447

• Community outreach programs and major adherence lapses with antiretroviral therapy in rural Kakamega, Kenya. AIDS care Hodgkinson, L. M., Makori, J., Okwiri, J., Tsisiche, C., Arudo, J., Barry, M. 2018; 30 (6): 696-700

  Abstract

  We investigated features of major adherence lapses in antiretroviral therapy (ART) at public Emusanda Health Centre in rural Kakamega County, Kenya using medical records from 2008 to 2015 for all 306 eligible patients receiving ART. Data were modelled using survival analysis. Patients were more likely to lapse if they received stavudine (hazard ratio (HR) 2.54, 95% confidence interval (95%CI):1.44-4.47) or zidovudine (HR 1.64, 95%CI:1.02-2.63) relative to tenofovir. Each day a patient slept hungry per month increased risk of major adherence lapse by 3% (95%CI:0-7%). Isolated home visits by community health workers (CHWs) were more effective to assist patients to return to the health centre than isolated phone calls (HR 2.52, 95%CI:1.02-6.20).

  View details for DOI 10.1080/09540121.2017.1391987

  View details for PubMedID 29058457

• Optimization criteria and biological process enrichment in homologous multiprotein modules PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Hodgkinson, L., Karp, R. M. 2013; 110 (26): 10872-10877

  Abstract

  Biological process enrichment is a widely used metric for evaluating the quality of multiprotein modules. In this study, we examine possible optimization criteria for detecting homologous multiprotein modules and quantify their effects on biological process enrichment. We find that modularity, linear density, and module size are the most important criteria considered, complementary to each other, and that graph theoretical attributes account for 36% of the variance in biological process enrichment. Variations in protein interaction similarity within module pairs have only minor effects on biological process enrichment. As random modules increase in size, both biological process enrichment and modularity tend to improve, although modularity does not show this upward trend in modules with size at most 50 proteins. To adjust for these trends, we recommend a size correction based on random sampling of modules when using biological process enrichment or other attributes to evaluate module boundaries. Characteristics of homologous multiprotein modules optimized for each of the optimization criteria are examined.

  View details for DOI 10.1073/pnas.1308621110

  View details for Web of Science ID 000321503700088

  View details for PubMedID 23757502

  View details for PubMedCentralID PMC3696829

• Algorithms to Detect Multiprotein Modularity Conserved during Evolution IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS Hodgkinson, L., Karp, R. M. 2012; 9 (4): 1046-1058

  Abstract

  Detecting essential multiprotein modules that change infrequently during evolution is a challenging algorithmic task that is important for understanding the structure, function, and evolution of the biological cell. In this paper, we define a measure of modularity for interactomes and present a linear-time algorithm, Produles, for detecting multiprotein modularity conserved during evolution that improves on the running time of previous algorithms for related problems and offers desirable theoretical guarantees. We present a biologically motivated graph theoretic set of evaluation measures complementary to previous evaluation measures, demonstrate that Produles exhibits good performance by all measures, and describe certain recurrent anomalies in the performance of previous algorithms that are not detected by previous measures. Consideration of the newly defined measures and algorithm performance on these measures leads to useful insights on the nature of interactomics data and the goals of previous and current algorithms. Through randomization experiments, we demonstrate that conserved modularity is a defining characteristic of interactomes. Computational experiments on current experimentally derived interactomes for Homo sapiens and Drosophila melanogaster, combining results across algorithms, show that nearly 10 percent of current interactome proteins participate in multiprotein modules with good evidence in the protein interaction data of being conserved between human and Drosophila.

  View details for DOI 10.1109/TCBB.2011.125

  View details for Web of Science ID 000304147000013

  View details for PubMedID 21968956

• Parallel software architecture for experimental workflows in computational biology on clouds Lecture Notes in Computer Science Hodgkinson, L., Rosa, J., Brewer, E. A. 2012

  View details for DOI 10.1007/978-3-642-31500-8_29

• Algorithms to detect multiprotein modularity conserved during evolution Lecture Notes in Bioinformatics Hodgkinson, L., Karp, R. M. 2011

  View details for DOI 10.1007/978-3-642-21260-4_14