Additional file 1: Supplementary Materials. The file contains derivation of edge cost formula (2) and EM algorithm, example of read graph construction and analysis of 454 pyrosequencing data. Ebola Virion Attachment and Entry into Human Macrophages Profoundly Effects Early Cellular Gene Expression Zaire ebolavirus (ZEBOV) infections are associated with high lethality in primates. ZEBOV primarily targets mononuclear phagocytes, which are activated upon infection and secrete mediators believed to trigger initial stages of pathogenesis. The characterization of the responses of target cells to ZEBOV infection may therefore not only further understanding of pathogenesis but also suggest possible points of therapeutic intervention. Gene expression profiles of primary human macrophages exposed to ZEBOV were determined using DNA microarrays and quantitative PCR to gain insight into the cellular response immediately after cell entry. Significant changes in mRNA concentrations encoding for 88 cellular proteins were observed. Most of these proteins have not yet been implicated in ZEBOV infection. Some, however, are inflammatory mediators known to be elevated during the acute phase of disease in the blood of ZEBOV-infected humans. Interestingly, the cellular response occurred within the first hour of Ebola virion exposure, i.e. prior to virus gene expression. This observation supports the hypothesis that virion binding or entry mediated by the spike glycoprotein (GP(1,2)) is the primary stimulus for an initial response. Indeed, ZEBOV virions, LPS, and virus-like particles consisting of only the ZEBOV matrix protein VP40 and GP(1,2) (VLP(VP40-GP)) triggered comparable responses in macrophages, including pro-inflammatory and pro-apoptotic signals. In contrast, VLP(VP40) (particles lacking GP(1,2)) caused an aberrant response. This suggests that GP(1,2) binding to macrophages plays an important role in the immediate cellular response. Zaire ebolavirus (ZEBOV) is a member of the family Filoviridae within the order Mononegavirales [1] . It was discovered in 1976 in what is now the Democratic Republic of the Congo [2] as the etiological agent of a severe human viral hemorrhagic fever known as Ebola Hemorrhagic Fever (EHF). Infection with ZEBOV typically results in a rapidly fatal illness associated with high-level viremia, lack of an effective immune response, drastic lymphopenia, a severe coagulation disorder including disseminated intravascular coagulation and limited hemorrhages, widespread focal tissue necroses, systemic shock and multiorgan failure (reviewed in detail in [3] ). While the pathogenesis of ZEBOV infection has been relatively well described in experimental animals [4, 5] , only a few studies were reported that shed light on the molecular events following infection in humans. Unfortunately, these studies are partially contradictory. For instance, higher serum cytokine concentrations (IFN-a, IFN-c, IL-2, IL-6, and TNF-a) were measured in seven fatally infected patients compared to two survivors in one study, suggesting that a hyperactive immune responses may contribute to fatal outcome [6] . Other studies, describing the responses of eight fatally infected patients and four survivors, did not reveal significant concentration differences of IFN-a, IL-2, and TNF-a. On the other hand, that study suggested that fatal infections are due to generalized immunosuppression, including decreased IFN-c, IL-2, and IL-4 concentrations, lymphocyte apoptosis, and diminished IgG synthesis [7, 8, 9, 10] . The largest study to date included 42 fatally infected patients and 14 survivors. Hypersecretion of proinflammatory cytokines, chemokines and growth factors (IL-1b, IL-1RA, IL-6, IL-8, IL-15, IL-16, CXCL1 (GROa), CXCL10 (IP-10), eotaxin, M-CSF, MIP-1a, MIP-1b, MCP-1, MIF) and decreased concentrations of T lymphocyte-derived cytokines (IL-2, IL-3, IL-4, IL-5, IL-9, IL-13) concomitant to apoptotic loss of CD4 and CD8 T lymphocytes were typical for fatal cases [11] . Unfortunately, all these data reveal only the extent of homeostatic disarray in ZEBOV-infected individuals, but not its origin or genesis. It is therefore important to measure the responses of individual human cell types to infection, ideally in chronological order of their infection in vivo. Mononuclear phagocytes are very early, if not initial, targets of ZEBOV in humans and experimentally infected animals [12, 13, 14, 15] . In vitro, human and nonhuman primate macrophages are highly susceptible to ZEBOV infection with subsequent robust virus production [16, 17] , suggesting they may be the major source of the high viremia observed during the critical stages of infection. Studies performed in vitro are also strongly indicative that macrophages play a major role in inducing cytokine/chemokine dysregulation. For instance, human monocytes and macrophages infected with ZEBOV react with increased expression of MCP-1, CXCL1, IL-1b, IL-6, IL-8, MIP-1a, RANTES and TNF-a [16, 18] . Previous studies revealed that similar increased levels of expression of some of these cytokines were triggered by incubation of human macrophages with Ebola virus-like particles (VLPs) consisting of the ZEBOV matrix protein VP40 and the spike glycoprotein (GP 1,2 ) [19] or with UV-inactivated ZEBOV [16] . These findings indicated that virus replication might not be required for the activation of macrophages.