This is a prospective pilot study evaluating the effect of omalizumab on the small airways of moderate to severe asthmatic individuals who are not fully controlled on fluticasone/salmeterol 250/50 or 500/50 mcg 1 puff bid. After screening, all subjects will be placed on fluticasone/salmeterol 250/50 or 500/50 mcg 1 puff bid for a 6-week run-in. Subjects will then be evaluated for level of asthma control. Individuals with total control of their asthma (no daytime or nighttime symptoms, no rescue use of short-acting inhaled beta-agonist, normal PEF, no unscheduled office visits, no ER visits) will be excluded from the study. Subjects without total asthma control will then have baseline studies performed to include HRCT of the chest before and after a methacholine challenge test (MCT), spirometry, closing volume, inspiratory capacity, symptom scores, asthma questionnaires, exhaled NO (performed at different expiratory flow rates to estimate alveolar NO) and blood work for evaluation of eosinophils and ECP, and banked serum. Subjects who meet acceptable criteria for omalizumab dosing based on serum IgE levels and body weight and the presence of atopy (at least one positive skin test to a common environmental allergen) will then receive omalizumab in addition to fluticasone/salmeterol 250/50 or 500/50 mcg 1 puff bid for sixteen weeks. Subjects will be seen every 2-4 weeks during the sixteen-week treatment phase to receive injections as prescribed and every 4 weeks to measure spirometry, inspiratory capacity, and to evaluate the level of compliance. After the sixteen-week treatment phase subjects will again undergo HRCT of the chest before and after a MCT [in the case where the follow-up methacholine responsiveness is diminished (improved) a mid-scan will be performed at the prior (target) methacholine dose and the challenge then continued to a maximum dose of 16 mg/ml and a third scan done], spirometry, closing volume, inspiratory capacity, exhaled NO at different expiratory flow rates (to estimate alveolar NO) and blood work for evaluation of eosinophils and ECP and banked serum.