Collaborative antisense drug developer Isis Pharmaceuticals (NASDAQ:IONS) touted the maturation of its pipeline during its first-quarter earnings results today, but it couldn't hide the fact that both its top and bottom lines reversed course from the prior-year period.

For the quarter, Isis reported revenue of $28.2 million, down 35% from the $43.4 million reported in the year-ago quarter. The timing and nature of certain milestone payments was mostly to blame, with milestone and development revenue down from $41.7 million to $19.6 million in Q1 2014. Licensing and royalty revenue, however, soared to $8.6 million from just $1.7 million,

As you might imagine, with the company planning on ending the year with three drugs in phase 3 trials and nine in phase 2, operating expenses are going up. As Isis noted, operating expenses rose 39% to $57.8 million, primarily as a result of increased research and development spending which rose to $53.4 million from $38.3 million in the year-ago quarter.

Net loss for the quarter widened considerably in the wake of less recognized milestone revenue, landing at $31.3 million, or $0.27 per share, from $1.7 million, or $0.02 per share, in Q1 2013. Most importantly, Isis ended the quarter with a healthy $631.3 million in cash and cash equivalents, down from the $656.8 million that it ended 2013 with. For biopharmaceutical companies currently losing money, cash remaining and cash burn are two important factors to monitor.

Looking ahead, Isis pegged its full-year revenue figure at $160 million, on track with its previous guidance, with an expectation that $110 million of that total will come from milestone and development payments from its partners. It also reaffirmed its expectation for a net operating loss in the low $50 million range, and expects to end the year with more than $575 million in cash and cash equivalents.

Sean Williams has no material interest in any companies mentioned in this article. You can follow him on CAPS under the screen name TMFUltraLong, track every pick he makes under the screen name TrackUltraLong, and check him out on Twitter, where he goes by the handle @TMFUltraLong.

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