The two Phase III trials in question looked at using a drug called alfimeprase to treat blood clots in the periphery of the body (peripheral arterial occlusion, PAO) and to unblock catheters.
Although the catheter trial will now be restarted with a higher dose, it's back to the drawing board for PAO, with the California-based company looking for a new delivery method in this indication.
Nuvelo has also decided to restart patient enrolment in a Phase II study designed to test the effectiveness of alfimeprase at preventing strokes.
This last indication is perhaps the most important in terms of reinvigorating the company.
When the trials failed last December, Nuvelo's stock price plummeted from around $20 (€15) to just $4, and has since dropped further to level out at around $3.34 today.
Although, Nuvelo only began trading in 2006 at $8 and the major jump up in price came when the original Bayer deal was signed.
Although the CEO of Nuvelo, Dr Ted Love, said he is "committed" to the drug's development, Bayer is not so dedicated.
The German based big pharma firm has pulled out of its $385m collaboration deal with Nuvelo with immediate effect.
As part of the original collaboration, Bayer was supposed to give Nuvelo 12 months notice if it wanted to terminate the partnership.
However, Nuvelo has agreed to waive this notice period in return for a one off payment of $15m.
The drug itself is a recombinant analogue of fibrolase - a zinc-containing enzyme originally isolated from snake venom by Professor Frank Markland, currently of the University of Southern California, and later developed by Amgen (Nuvelo then bought the rights off the biotech giant).
The drug directly degrades fibrin and was designed to be delivered via a catheter to the site of a blood clot.
Dr Love said: "Therapeutic options for stroke patients are limited, and stroke remains the third leading cause of death in the United States and a leading cause of severe, long-term disability."
"We believe that a safer, more efficacious intra-arterial therapy can change the treatment paradigm for these patients and that a product candidate such as alfimeprase holds the potential to rapidly restore flow and expand the treatment window beyond the current three-hour time frame."
Despite a less than successful year for Nuvelo, the board controversially received large bonus packages at the end of January.
The CEO's target bonus was set at 40 per cent of his base salary and at the senior vice president level the target bonus was 35 per cent of their base.
The board decided to fund this bonus pool at 92 per cent of its target level and the executives received bonuses at between 100 and 140 per cent of their target levels.
In effect this meant, for example, that Dr Love got $289,248 and Dr Michael Levy, head of R&D got $184,828.
In a scathing write-up on inelegantinvestor.com, Neal Shanske described this decision as "rather unseemly... in a year which saw the stock drop 50 per cent and in which the value of the company's pipeline evaporated" .
Although the PAO trial will be scrapped, Nuvelo will be hoping that by restarting clinical development in one major indication, it might be able to recapture some of that pipeline value, albeit in a condensed form.