Ellen has kids with 4 men. Plus she lost one, but I don't remember if he had a name. Add details below.
With Pete
Josh First child to die, died of the virus
Taylor Second child to die, after Dean treated her with the cure, but also succumbed to the virus
With Dean Hayes
Billy Grows up to be a Doctor in the future
Alex, is an artist in the Aragon future that Dean and Ellen visit.
Joey (but Frank is the real Father)
With Frank
Brian (but Dean is the real Father) Brian is frozen after the second plague that George Hadley sent to Beginnings, but still dies when Dean tries to bring him out of the cyrogenics process.
With Henry
Nick
Beginnings Josh, a survivor that Ellen adopts.
Johnny, Franks only child that survived the plague. Ellen treats him as hers.