This is a 2-day workshop on Mathematical Challenges in Biological Big Data. The workshop especially focuses on three themes: 1) Single Cell Genomics, 2) Population Dynamics, and 3) Neural Representation and Information Processing. For each theme, a group of experts from biological sciences, mathematics, and statistics will come together to discuss and possibly address the emerging challenges created by big data problems in biology. The first day of the workshop is open to the public and includes a series of talks describing these challenges. We hope these talks inspire early-career researchers (PhD students, postdocs, and junior faculty). On the second day (by invitation only), cross-disciplinary scientific teams are formed to address these challenges and to come up with potential solutions.