About

Gary Benson is an Associate Professor of Biology and Computer Science in the Program in Bioinformatics at Boston University. He earned his PhD from the University of Maryland in 1992. His research focuses on the development of algorithms and software tools for the detection and analysis of novel patterns and repeats in DNA and RNA sequences. His goal is to deliver tools that are effective, efficient, and easy to use, and he maintains ongoing collaborations in this area. He teaches courses including Biological Database Systems, DNA and Protein Sequence Analysis, and Pattern Matching and Pattern Detection Algorithms with Applications in Biological Sequence Analysis. His work combines expertise in computational biology and computer science to advance understanding and analysis of biological sequences.

Research topics

• Genetics
• Biology
• Pediatrics
• Emergency medicine
• Medicine
• Internal medicine
• Intensive care medicine

Selected publications

• A UK-wide analysis of 2265 patients receiving a reversal agent for direct oral anticoagulant–associated bleeding

  Journal of Thrombosis and Haemostasis · 2025-12-03 · 1 citations

  articleOpen access

  BACKGROUND: Reversal agents are used in patients taking direct oral anticoagulants (DOACs) to manage bleeding, but evidence for their effectiveness remains limited. OBJECTIVES: This study assessed the proportion of patients treated with a reversal agent for DOAC-associated bleeding who had major bleeding and evaluated their outcomes. METHODS: This was a retrospective, observational audit across 65 hospitals in the United Kingdom. Adults who received andexanet alfa, idarucizumab, or 4-factor prothrombin complex concentrate (4F-PCC) for DOAC-associated bleeding between October 2020 and June 2023 were included. Data were collected on demographics, medical history, bleed site and severity, reversal agent, thrombosis, and 90-day mortality. A propensity score-matched analysis was performed to estimate the cumulative incidence of thrombosis and death according to reversal agent in gastrointestinal hemorrhage. RESULTS: Of 2265 patients, 875 (38.6%) had gastrointestinal bleeding and 1012 (44.7%) had intracranial hemorrhage. Median age was 81 years. Median time from bleed onset to reversal was 6.5 hours, and that from last anticoagulant dose was 16.0 hours. Of 1253 patients with nonintracranial bleeds, 1001 (79.9%) had major hemorrhage. In a propensity score-matched analysis of 494 patients with gastrointestinal bleeding, there was no significant difference in 90-day-mortality with andexanet alfa compared with that with 4F-PCC (36.4% vs 32.4%), but andexanet alfa was associated with a significantly increased 30-day incidence of stroke (4.5% vs 0%). CONCLUSION: Reversal agents were generally used in patients with clinical evidence of major bleeding but were administered long after the last anticoagulant dose. In gastrointestinal bleeding, andexanet alfa was associated with a higher thrombotic risk than 4F-PCC.

  PublisherOA PDFDOI

• Association between JAK2V617F variable allele frequency and risk of thrombotic events in patients with myeloproliferative neoplasms

  Irish Journal of Medical Science (1971 -) · 2024-08-14 · 7 citations

  articleOpen access

  Abstract Background Myeloproliferative neoplasms (MPNs) are a group of chronic disorders of the bone marrow characterised by the overproduction of clonal myeloid stem cells. The most common driver mutation found in MPNs is a point mutation on exon 14 of the JAK2 gene, JAK2 V617F . Various studies have suggested that measuring the variable allele frequency (VAF) of JAK2 V617F may provide useful insight regarding diagnosis, treatment, risks and outcomes in MPN patients. In particular, JAK2 V617F has been associated with increased risk of thrombotic events, a leading cause of mortality in MPNs. Aims The aim of this study was to determine if JAK2 V617F VAF was associated with clinical outcomes in patients with MPN. Methods JAK2 V617F VAF was determined by quantitative PCR (qPCR) in a cohort of 159 newly diagnosed MPN patients, and the association of JAK2 V617F VAF and risk of thrombosis was examined in this cohort. Results We observed a significantly higher JAK2 V617F VAF in PV and PMF versus ET. A significant association was observed between JAK2 V617F VAF and risk of thrombotic events. When patients were stratified by thrombotic events prior to and post diagnosis, an association with JAK2 V617F VAF was only observed with post diagnosis thrombotic events. Of note, these associations were not observed when looking at each MPN subtype in isolation. Conclusions We have shown that a higher JAK2 V617F VAF is associated with thrombotic events post MPN diagnosis. JAK2 V617F VAF may therefore provide a valuable prognostic indicator for risk of thrombosis in MPNs.

  PublisherOA PDFDOI

• A consensus viewpoint on the role of direct factor Xa inhibitors in the management of cancer-associated venous thromboembolism in the UK

  Current Medical Research and Opinion · 2023-01-11 · 1 citations

  reviewOpen access

  OBJECTIVE: Cancer patients are at high risk of venous thromboembolism (VTE), a significant cause of cancer-related death. Historically, low molecular weight heparins (LMWH) were the gold standard therapy for cancer-associated VTE, but recent evidence supports the use of direct factor Xa inhibitors in cancer-associated VTE and this is now reflected in many guidelines. However, uptake of direct factor Xa inhibitors varies and guidance on the use of direct factor Xa inhibitors in specific cancer sub-populations and clinical situations is lacking. This review presents consensus expert opinion alongside evaluation of evidence to support healthcare professionals in the use of direct factor Xa inhibitors in cancer-associated VTE. METHODS: Recent guidelines, meta-analyses, reviews and clinical studies on anticoagulation therapy for cancer-associated VTE were used to direct clinically relevant topics and evidence to be systematically discussed using nominal group technique. The consensus manuscript and recommendations were developed based on these discussions. RESULTS: Considerations when prescribing anticoagulant therapy for cancer-associated VTE include cancer site and stage, systemic anti-cancer therapy (including vascular access), drug-drug interactions, length of anticoagulation, quality of life and needs during palliative care. Treatment of patients with kidney or liver impairment, gastrointestinal disorders, extremes of bodyweight, elevated bleeding or recurrence risk, VTE recurrence and COVID-19 is discussed. CONCLUSION: Anticoagulant therapy for cancer-associated VTE patients should be carefully selected with consideration given to the relative benefits of specific drugs when individualizing care. Direct factor Xa inhibitors are typically the treatment of choice for preventing VTE recurrence in non-cancer patients and should also be considered as such for cancer-associated VTE in most situations.

  PublisherDOI

• Supplementary Data from Mutations in the Hepatitis C Virus <i>core</i> Gene Are Associated with Advanced Liver Disease and Hepatocellular Carcinoma

  2023-03-31

  preprintOpen access

  Supplementary Data from Mutations in the Hepatitis C Virus <i>core</i> Gene Are Associated with Advanced Liver Disease and Hepatocellular Carcinoma

  PublisherOA PDFDOI

• Data from Mutations in the Hepatitis C Virus <i>core</i> Gene Are Associated with Advanced Liver Disease and Hepatocellular Carcinoma

  2023-03-31

  preprintOpen access

  <div>Abstract<p><b>Purpose:</b> Hepatitis C virus (HCV) infection can promote the development of hepatocellular carcinoma (HCC). Published data implicate the HCV <i>core</i> gene in oncogenesis. We tested the hypothesis that <i>core</i> gene sequences from HCC patients differ from those of patients without cirrhosis/HCC.</p><p><b>Experimental Design:</b> Full-length HCV sequences from HCC patients and controls were obtained from the investigators and GenBank and compared with each other. A logistic regression model was developed to predict the HCC risk of individual point mutations and other sequence features. Mutations in partial sequences (bases 36-288) from HCC patients and controls were also analyzed. The first base of the AUG start codon was designated position 1.</p><p><b>Results:</b> A logistic regression model developed through analysis of full-length <i>core</i> gene sequences identified seven polymorphisms significantly associated with increased HCC risk (36G/C, 209A, 271U/C, 309A/C, 435A/C, 481A, and 546A/C) and an interaction term (for 209A-271U/C) that had an odds ratio <1.0. Three of these polymorphisms could be analyzed in the partial sequences. Two of them, 36G/C and 209A, were again associated with increased HCC risk, but 271U/C was not. The odds ratio of 209A-271U/C was not significant.</p><p><b>Conclusions:</b> HCV <i>core</i> genes from patients with and without HCC differ at several positions. Of interest, 209A has been associated with IFN resistance and HCC in previous studies. Our findings suggest that HCV <i>core</i> gene sequence data might provide useful information about HCC risk. Prospective investigation is needed to establish the temporal relationship between appearance of the viral mutations and development of HCC.</p></div>

  PublisherDOI

• Data from Mutations in the Hepatitis C Virus <i>core</i> Gene Are Associated with Advanced Liver Disease and Hepatocellular Carcinoma

  2023-03-31

  preprintOpen access

  <div>Abstract<p><b>Purpose:</b> Hepatitis C virus (HCV) infection can promote the development of hepatocellular carcinoma (HCC). Published data implicate the HCV <i>core</i> gene in oncogenesis. We tested the hypothesis that <i>core</i> gene sequences from HCC patients differ from those of patients without cirrhosis/HCC.</p><p><b>Experimental Design:</b> Full-length HCV sequences from HCC patients and controls were obtained from the investigators and GenBank and compared with each other. A logistic regression model was developed to predict the HCC risk of individual point mutations and other sequence features. Mutations in partial sequences (bases 36-288) from HCC patients and controls were also analyzed. The first base of the AUG start codon was designated position 1.</p><p><b>Results:</b> A logistic regression model developed through analysis of full-length <i>core</i> gene sequences identified seven polymorphisms significantly associated with increased HCC risk (36G/C, 209A, 271U/C, 309A/C, 435A/C, 481A, and 546A/C) and an interaction term (for 209A-271U/C) that had an odds ratio <1.0. Three of these polymorphisms could be analyzed in the partial sequences. Two of them, 36G/C and 209A, were again associated with increased HCC risk, but 271U/C was not. The odds ratio of 209A-271U/C was not significant.</p><p><b>Conclusions:</b> HCV <i>core</i> genes from patients with and without HCC differ at several positions. Of interest, 209A has been associated with IFN resistance and HCC in previous studies. Our findings suggest that HCV <i>core</i> gene sequence data might provide useful information about HCC risk. Prospective investigation is needed to establish the temporal relationship between appearance of the viral mutations and development of HCC.</p></div>

  PublisherDOI

• Supplementary Data from Mutations in the Hepatitis C Virus <i>core</i> Gene Are Associated with Advanced Liver Disease and Hepatocellular Carcinoma

  2023-03-31

  preprintOpen access

  Supplementary Data from Mutations in the Hepatitis C Virus <i>core</i> Gene Are Associated with Advanced Liver Disease and Hepatocellular Carcinoma

  PublisherDOI

• Bernard-Soulier syndrome in pregnancy with retinal detachment: a rare phenomenon

  BMJ Case Reports · 2022-08-01

  articleOpen access

  Bernard-Soulier syndrome (BSS) is a rare congenital bleeding disorder of the platelet, and it is mainly inherited as an autosomal recessive trait. It is caused by both qualitative and quantitative deficiency of the platelet membrane glycoprotein (GP) Ib-IX-V receptor complex, thereby causing abnormal platelets adhesion.We report a case of a primigravida in her 20s with history of BSS diagnosed in childhood due to family history. Her preconception period was challenging as she suffered from severe menorrhagia often requiring hospital admission, blood and platelet transfusions.At 35 weeks gestation, she developed temporal crowded retinal detachment of the left eye and had a successful left scleral buckling surgery under general anaesthesia (GA).She had a multidisciplinary team care with a successful elective GA caesarean section at 39+3 weeks gestation with peridelivery platelet transfusion and intravenous recombinant factor VIIa. Regional anaesthesia, intramuscular injections and anticoagulation were avoided.

  PublisherOA PDFDOI

• Diagnostic uncertainty presented barriers to the timely management of acute thrombotic thrombocytopenic purpura in the United Kingdom between 2014 and 2019

  Journal of Thrombosis and Haemostasis · 2022 · 22 citations

  • Medicine
  • Pediatrics
  • Internal medicine
  PublisherOA PDFDOI

• Genome-wide characterization of human minisatellite VNTRs: population-specific alleles and gene expression differences

  Nucleic Acids Research · 2021 · 35 citations

  Senior authorCorresponding
  • Biology
  • Genetics

  Variable Number Tandem Repeats (VNTRs) are tandem repeat (TR) loci that vary in copy number across a population. Using our program, VNTRseek, we analyzed human whole genome sequencing datasets from 2770 individuals in order to detect minisatellite VNTRs, i.e., those with pattern sizes ≥7 bp. We detected 35 638 VNTR loci and classified 5676 as commonly polymorphic (i.e. with non-reference alleles occurring in >5% of the population). Commonly polymorphic VNTR loci were found to be enriched in genomic regions with regulatory function, i.e. transcription start sites and enhancers. Investigation of the commonly polymorphic VNTRs in the context of population ancestry revealed that 1096 loci contained population-specific alleles and that those could be used to classify individuals into super-populations with near-perfect accuracy. Search for quantitative trait loci (eQTLs), among the VNTRs proximal to genes, indicated that in 187 genes expression differences correlated with VNTR genotype. We validated our predictions in several ways, including experimentally, through the identification of predicted alleles in long reads, and by comparisons showing consistency between sequencing platforms. This study is the most comprehensive analysis of minisatellite VNTRs in the human population to date.

  PublisherOA PDFDOI

Recent grants

• III:Small:Algorithms for Tandem Repeat Variant Discovery Using Next Generation Sequencing Data

  NSF · $500k · 2010–2015

• III: Small: Bit-Parallel Algorithms for Sequence Alignment and Applications in Detecting Human Genetic Variation and Bacterial Strain Typing

  NSF · $561k · 2014–2019

• SEI(BIO): DNA Inverted Repeats: Sensitive Detection Methods and Research Database

  NSF · $669k · 2006–2010

• REU Site: Bioinformatics Research and Interdisciplinary Training Experience in Analysis and Interpretation of Information-Rich Biological Data Sets (REU-BRITE)

  NSF · $292k · 2016–2019

Frequent coauthors

• Yevgeniy Gelfand

  Multidisciplinary Association for Psychedelic Studies

  39 shared

• Kar-Wai Ng

  Howard Hughes Medical Institute

  25 shared

• Jeffrey Laidlaw

  Biocom

  25 shared

• Rama Ranganathan

  University of Chicago

  25 shared

• Harold R. Garner

  AtlantiCare

  25 shared

• John W. Fondon

  The University of Texas at Arlington

  25 shared

• Yözen Hernández

  Rockefeller University

  21 shared

• Martı́n Farach-Colton

  18 shared