Focus areas

  • Title

    An epidemiological modeling investigation of the long-term changing dynamics of the plague epidemics in Hong Kong.

    AUTHORS
    Musa S, Zhao S, Mkandawire W, Colubri A, He D.
    PUBLICATION
    Submitted to Mathematical Biosciences and Engineering.
  • Title

    Investigating the etiologies of non-malarial febrile illness in Senegal using metagenomic sequencing.

    AUTHORS
    Levine ZC, Sene A, Mkandawire W, Deme AB, Ndiaye T, Sy M, Gaye A, Diedhiou Y, Mbaye AM, Ndiaye IM, Gomis J, Ndiop M, Sene D, Faye Paye M, MacInnis BL, Schaffner SF, Park DJ, Badiane AS, Colubri A, Ndiaye M, Sy N, Sabeti PC, Ndiaye D, Siddle KJ.
    PUBLICATION
    Nat Commun. 2024 Jan 25;15(1):747.
    LINKS
    PUBMEDDOI
  • Title

    Evaluating the spike in the symptomatic proportion of SARS-CoV-2 in China in December 2022 considering variolation effects: a modeling analysis.

    AUTHORS
    Musa SS, Zhao S, Abdulrashid I, Qureshi S, Colubri A, Abu-Odah H, He D.
    PUBLICATION
    Under review at Infectious Disease Modeling.
  • Title

    Unveiling the Complexity and Evolution of Brain-Active Regulatory Elements: Insights from a Comprehensive Atlas and Predictive Models.

    AUTHORS
    Pratt HE, Andrews G, Shedd N, Phalke N, Li T, Pampari A, Jensen M, Wen C, PsychENCODE Consortium, Gandal MJ, Geschwind DH, Gerstein M, Moore J, Kundaje A, Colubri A, Weng Z.
    PUBLICATION
    Under review at Science Advances.
  • Title

    Derivation and Internal Validation of a Mortality Prognostication Machine Learning Model in Ebola Virus Disease Using Iterative Point-of-Care Biomarkers.

    AUTHORS
    Bearnot CJ, Laghari R, Mbong EN, Muhayangabo RF, Butler K, Gainey M, Perera SM, Michelow IC, Tang OY, Levine AC, Colubri A, Aluisio AR.
    PUBLICATION
    Accepted for publication Open Forum Infectious Diseases.
  • Title

    Performance of Screening for SARS-CoV-2 using Rapid Antigen Tests to Detect Incidence of Symptomatic and Asymptomatic SARS-CoV-2 Infection: findings from the Test Us at Home prospective cohort study.

    AUTHORS
    Soni A, Herbert C, Lin H, Yan Y, Pretz C, Stamegna P, …, Colubri A, O'Connor L, Lemon SC, Fahey N, Luzuriaga KL, Hafer N, Roth K, Lowe T, Stenzel T, Heetderks W, Broach J, McManus DD.
    PUBLICATION
    Annals of Internal Medicine. 2023 Jul 4
    LINKS
    PUBMED
  • Title

    Knowledge, Attitudes and Practices Regarding the Use of Mobile Travel Health Apps.

    AUTHORS
    Machoko MMP, Dong Y, Grozdani A, Hong H, Oliver E, Hyle EP, Ryan ET, Walker AT, Colubri A, LaRocque RC.
    PUBLICATION
    J Travel Med. 2023 Jul 6:taad089.
    LINKS
    PUBMEDDOI
  • Title

    Analyzing the impact of a real-life outbreak simulator on pandemic mitigation: An epidemiological modeling study.

    AUTHORS
    Specht I, Sani K, Loftness BC, Hoffman C, Gionet G, Bronson A, Marshall J, Decker C, Bailey L, Siyanbade T, Kemball M, Pickett BE, Hanage WP, Brown T, Sabeti PC, Colubri A.
    PUBLICATION
    Patterns (N Y). 2022 Aug 12;3(8):100572.
    LINKS
    PUBMEDDOI
  • Title

    Using machine learning to predict survival in children with Ebola Virus Disease.

    AUTHORS
    Genisca AE, Butler K, Gainey M, Chu TC, Huang L, Mbong EN, Kennedy SB, Laghari R, Nganga F, Muhayangabo RF, Vaishnav H, Perera SM, Adeniji M, Levine AC, Michelow IC, Colubri A.
    PUBLICATION
    PLOS Neglected Tropical Diseases. 2022 Oct 12;16(10):e0010789.
    LINKS
    PUBMEDDOI
  • Title

    Multimodal surveillance of SARS-CoV-2 at a university enables development of a robust outbreak response framework.

    AUTHORS
    Petros BA, Paull JS, Tomkins-Tinch CH, Loftness B, ..., Colubri A.; MacInnis BL, Ozsoy AZ, Parrie E, Sholtes K, Siddle KJ, Fry B, Luban J, Park DJ, Marshall J, Bronson A, Schaffner SF, Sabeti PC.
    PUBLICATION
    Cell Med. 2022 Dec 9;3(12):883-900.e13.
    LINKS
    PUBMEDDOI
  • Title

    Risk Prediction Score for Pediatric Patients with Suspected Ebola Virus Disease.

    AUTHORS
    Genisca AE, Chu TC, Huang L, Gainey M, Adeniji M, Mbong EN, Kennedy SB, Laghari R, Nganga F, Muhayangabo RF, Vaishnav H, Perera SM, Colubri A, Levine AC, Michelow IC.
    PUBLICATION
    Emerg Infect Dis. 2022 Jun;28(6):1189-1197.
    LINKS
    PUBMEDDOI
  • AUTHORS
    Morrill K, Hekman J, Li X, McClure J, Logan B, Goodman L, Gao M, Dong Y, Alonso M, Carmichael E, Snyder-Mackler N, Alonso J, Noh HJ, Johnson J, Koltookian M, Lieu C, Megquier K, Swofford R, Turner-Maier J, White ME, Weng Z, Colubri A, Genereux DP, Lord KA, Karlsson EK.
    PUBLICATION
    Science. 2022 Apr 29;376(6592):eabk0639.
    LINKS
    PUBMEDDOI
  • Title

    Containing the spread of mumps on college campuses.

    AUTHORS
    Shah M, Ferra G, Fitzgerald S, Barreira PJ, Sabeti PC, Colubri A.
    PUBLICATION
    R Soc Open Sci. 2022 Jan 26;9(1):210948.
    LINKS
    PUBMEDDOI
  • Title

    The case for altruism in institutional diagnostic testing.

    AUTHORS
    Specht I, Sani K, Botti-Lodovico Y, Hughes M, Heumann K, Bronson A, Marshall J, Baron E, Parrie E, Glennon O, Fry B, Colubri A, Sabeti PC.
    PUBLICATION
    Sci Rep. 2022 Feb 3;12(1):1857.
    LINKS
    PUBMEDDOI
  • Title

    Sciviewer enables interactive visual interrogation of single-cell RNA-Seq data from the python programming environment.

    AUTHORS
    Kotliar D, Colubri A.
    PUBLICATION
    Bioinformatics. 2021 Oct 2:btab689.
    LINKS
    PUBMEDDOI
  • Title

    The Origins and Future of Sentinel: An Early-Warning System for Pandemic Preemption and Response.

    AUTHORS
    Botti-Lodovico Y, Nair P, Nosamiefan D, Stremlau M, Schaffner S, Agignoae SV, Aiyepada JO, Ajogbasile FV, Akpede GO, Alhasan F, Andersen KG, Asogun DA, Ayodeji OO, Badiane AS, Barnes K, Bauer MR, Bell-Kareem A, Benard ME, Benevolence EO, Blessing O, Boehm CK, Boisen ML, Bond NG, Branco LM, Butts MJ, Carter A, Colubri A, Deme AB, DeRuff KC, Diédhiou Y, Edamhande AP, Elhamoumi S, Engel EJ, Eromon P, Fallah M, Folarin OA, Fry B, Garry R, Gaye A, Gbakie M, Gevao SM, Gionet G, Gladden-Young A, Goba A, Gomis JF, Happi AN, Houghton M, Ihekwuazu C, Iruolagbe CO, Jackson J, Jalloh S, Johnson J, Kanneh L, Kayode A, Kemball M, Kingsley OC, Koroma V, Kotliar D, Mehta S, Metsky HC, Michael A, Mirhashemi ME, Modjarrad K, Momoh M, Myhrvold CA, Naregose OG, Ndiaye T, Ndiaye M, Ndiaye A, Normandin E, Odia I, Oguzie JU, Okogbenin SA, Okokhere PO, Okolie J, Olawoye IB, Olumade TJ, Oluniyi PE, Omoregie O, Park DJ, Paye MF, Petros B, Philippakis AA, Priscilla A, Ricks A, Rimoin A, Sandi JD, Schieffelin JS, Schreiber M, Seck MC, Siddiqui S, Siddle K, Smither AR, Sy M, Sy N, Tomkins-Tinch CH, Tomori O, Ugwu C, Uwanibe JN, Uyigue EA, Victoria DI, Vinzé A, Vodzak ME, Welch N, Wurie HI, Zoumarou D, Grant DS, Ndiaye D, MacInnis B, Sabeti PC, Happi C.
    PUBLICATION
    Viruses. 2021 Aug 13;13(8):1605.
    LINKS
    PUBMEDDOI
  • Title

    Deployable CRISPR-Cas13a diagnostic tools to detect and report Ebola and Lassa virus cases in real-time.

    AUTHORS
    Barnes KG, Lachenauer AE, Nitido A, Siddiqui S, Gross R, Beitzel B, Siddle KJ, Freije CA, Dighero-Kemp B, Mehta SB, Carter A, Uwanibe J, Ajogbasile F, Olumade T, Odia I, Sandi JD, Momoh M, Metsky HC, Boehm CK, Lin AE, Kemball M, Park DJ, Branco L, Boisen M, Sullivan B, Amare MF, Tiamiyu AB, Parker ZF, Iroezindu M, Grant DS, Modjarrad K, Myhrvold C, Garry RF, Palacios G, Hensley LE, Schaffner SF, Happi CT, Colubri A, Sabeti PC.
    PUBLICATION
    Nature Communications. 2020 Aug 17;11(1):4131.
    LINKS
    PUBMEDDOI
  • Title

    Caseload and Case Fatality of Lassa Fever in Nigeria, 2001-2018: A Specialist Center's Experience and Its Implications.

    AUTHORS
    Akpede GO, Asogun DA, Okogbenin SA, Dawodu SO, Momoh MO, Dongo AE, Ike C, Tobin E, Akpede N, Ogbaini-Emovon E, Adewale AE, Ochei O, Onyeke F, Okonofua MO, Atafo RO, Odia I, Adomeh DI, Odigie G, Ogbeifun C, Muebonam E, Ihekweazu C, Ramharter M, Colubri A, Sarbeti PC, Happi CT, Günther S, Agbonlahor DE.
    PUBLICATION
    Front Public Health 7: 170 (2019).
  • Title

    Retrospective Cohort Study of Lassa Fever in Pregnancy, Southern Nigeria.

    AUTHORS
    Okogbenin S, Okoeguale J, Akpede G, Colubri A, Barnes KG, Mehta S, Eifediyi R, Okogbo F, Eigbefoh J, Momoh M, Rafiu M, Adomeh D, Odia I, Aire C, Atafo R, Okonofua M, Pahlman M, Becker-Ziaja B, Asogun D, Okokhere P, Happi C, Günther S, Sabeti PC, Ogbaini-Emovon E.
    PUBLICATION
    Emerging Infectious Diseases 25: 1494–1500 (2019).
  • Title

    Machine-learning Prognostic Models from the 2014–16 Ebola Outbreak: Data-harmonization Challenges, Validation Strategies, and mHealth Applications.

    AUTHORS
    Colubri A, Hartley MA, Siakor M, Wolfman V, Sesay T, Felix A, Sesay T, Shaffer JG, Garry RF, Grant DS, Levine AC, Sabeti PC.
    PUBLICATION
    EClinicalMedicine 11: 54–64 (2019).
  • Title

    NX4: A web-based visualization of large multiple sequence alignments.

    AUTHORS
    Solano-Román JA, Cruz-Castillo C, Offenhuber D, Colubri A.
    PUBLICATION
    Bioinformatics 35: 4800–4802 (2019).
  • Title

    Clinical and laboratory predictors of Lassa fever outcome in a dedicated treatment facility in Nigeria: a retrospective, observational cohort study.

    AUTHORS
    Okokhere P, Colubri A, Azubike C, Iruolagbe C, Osazuwa O, Tabrizi S, Chin E, Asad S, Ediale E, Rafiu M, Adomeh D, Odia I, Atafo R, Aire C, Okogbenin S, Pahlman M, Becker-Ziaja B, Asogun D, Fradet T, Fry B, Schaffner SF, Happi C, Akpede G, Günther S, Sabeti PC.
    PUBLICATION
    Lancet Infect Dis. 2018 Jun;18(6):684-695.
    LINKS
    PUBMEDDOI
  • Title

    Transforming clinical data into actionable Ebola prognosis models.

    AUTHORS
    Colubri A, Silver T, Fradet T, Retzepi K, Fry BW, Sabeti PC.
    PUBLICATION
    PLOS Neglected Tropical Diseases 10: e0004549 (2016).
  • Title

    KGH Lassa Fever Program; Viral Hemorrhagic Fever Consortium; WHO Clinical Response Team. Clinical Illness and Outcomes in Patients with Ebola in Sierra Leone.

    AUTHORS
    Schieffelin JS, Shaffer JG, Goba A, Gbakie M, Gire SK, Colubri A, Sealfon RS, Kanneh L, Moigboi A, Momoh M, Fullah M, Moses LM, Brown BL, Andersen KG, Winnicki S, Schaffner SF, Park DJ, Yozwiak NL, Jiang PP, Kargbo D, Jalloh S, Fonnie M, Sinnah V, French I, Kovoma A, Kamara FK, Tucker V, Konuwa E, Sellu J, Mustapha I, Foday M, Yillah M, Kanneh F, Saffa S, Massally JL, Boisen ML, Branco LM, Vandi MA, Grant DS, Happi C, Gevao SM, Fletcher TE, Fowler RA, Bausch DG, Sabeti PC, Khan SH, Garry RF
    PUBLICATION
    The New England Journal of Medicine 371: 2092-2100 (2014).
  • Title

    Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak.

    AUTHORS
    Gire SK, Goba A, Andersen KG, Sealfon RS, Park DJ, Kanneh L, Jalloh S, Momoh M, Fullah M, Dudas G, Wohl S, Moses LM, Yozwiak NL, Winnicki S, Matranga CB, Malboeuf CM, Qu J, Gladden AD, Schaffner SF, Yang X, Jiang PP, Nekoui M, Colubri A, Coomber MR, Fonnie M, Moigboi A, Gbakie M, Kamara FK, Tucker V, Konuwa E, Saffa S, Sellu J, Jalloh AA, Kovoma A, Koninga J, Mustapha I, Kargbo K, Foday M, Yillah M, Kanneh F, Robert W, Massally JL, Chapman SB, Bochicchio J, Murphy C, Nusbaum C, Young S, Birren BW, Grant DS, Scheiffelin JS, Lander ES, Happi C, Gevao SM, Gnirke A, Rambaut A, Garry RF, Khan SH, Sabeti PC.
    PUBLICATION
    Science 345: 1369-1372 (2014).
  • Title

    Mimicking the folding pathway to improve homology-free protein structure prediction.

    AUTHORS
    DeBartolo J, Colubri A, Jha AK, Fitzgerald JE, Freed KF, Sosnick TR.
    PUBLICATION
    Proceedings of the National Academy of Sciences 106: 3734-3739 (2009).
  • Title

    Reduced Cβ statistical potentials can outperform all‐atom potentials in decoy identification.

    AUTHORS
    Fitzgerald JE, Jha AK, Colubri A, Sosnick TR, Freed KF.
    PUBLICATION
    Protein Science 16: 2123-2139 (2007).
  • Title

    Minimalist representations and the importance of nearest neighbor effects in protein folding simulations.

    AUTHORS
    Colubri A, Jha AK, Shen M-y, Sali A, Berry RS, Sosnick TR, et al.
    PUBLICATION
    Journal of Molecular Biology 363: 835-857 (2006).
  • Title

    Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library.

    AUTHORS
    Jha AK, Colubri A, Zaman MH, Koide S, Sosnick TR, Freed KF.
    PUBLICATION
    Biochemistry 44: 9691-9702 (2005).
  • Title

    Statistical coil model of the unfolded state: resolving the reconciliation problem.

    AUTHORS
    Jha AK, Colubri A, Freed KF, Sosnick TR.
    PUBLICATION
    Proceedings of the National Academy of Sciences 102: 13099-13104 (2005).
  • Title

    Prediction of protein structure by simulating coarse-grained folding pathways: a preliminary report.

    AUTHORS
    Colubri A.
    PUBLICATION
    Journal of Biomolecular Structure and Dynamics 21: 625-638 (2004).