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If there were a biggest-loser competition for stocks, Valeant Pharmaceuticals (BHC 3.14%) and Ionis Pharmaceuticals (IONS -1.13%) would definitely be contenders. Ionis has lost nearly 60% of its market cap in 2016, while Valeant's stock is down over 75% this year.

After these enormous drops in their share prices, are these stocks worth taking a look at now? If so, which is the better pick for investors? Here's how Valeant and Ionis stack up against each other.

The case for Valeant

If every cloud has a silver lining, Valeant should be awash in silver linings. The company has been vilified by politicians over its drug pricing. It severed ties with a major distributor amid controversy. It had to restate financial results for several quarters, missing some SEC filing deadlines in the process. It lowered the revenue and earnings outlook for 2016. It has nearly $32 billion in debt. And it underwent a change in CEO. Valeant has had plenty of clouds, so where are the silver linings?

First, despite slashing its financial outlook for the year, Valeant's revenue is growing. One primary driver behind that growth came from acquisitions, especially Salix Pharmaceuticals. 

Second, Valeant's pipeline looks solid. The company has 18 drugs in late-stage development that should launch within the next two and a half years. Of those candidates, plaque psoriasis drug brodalumab has probably received the most attention. Valeant bought commercialization rights for the drug for markets outside Asia from AstraZeneca last year but recently sold European rights back to the big drugmaker.

Third, Valeant has a capable new CEO at the helm. The company lured Joseph Papa away from Perrigo in April, with Papa starting on the job in early May. During Papa's stint at Perrigo, which began in October 2006, shares of the generic drugmaker increased over 450%.

Fourth, Valeant's stock is dirt cheap. Shares are trading at just under three times forward earnings. If Joseph Papa is able to execute on his vision for the company and the pipeline's potential is realized, earnings should grow and drive the stock higher.

The case for Ionis

Ionis Pharmaceuticals' stock price was hammered in April as a result of GlaxoSmithKline's decision to delay a planned phase 3 clinical study of IONIS-TTRRx for the treatment of familial amyloid neuropathy. However, Ionis has more in its arsenal than just the one drug -- and the fat lady hasn't sung over IONIS-TTRRx yet, either. 

Antisense technology is Ionis' specialty. This approach involves preventing disease-causing proteins from being produced by keeping messenger RNA instructions from reaching the ribosome. Ionis' first antisense drug, Kynamro, is now being marketed by privately held Kastle Therapeutics. 

Several other antisense drugs might not be far away from reaching the market. Spinal muscular atrophy drug nusinersen is in two phase 3 studies. The same is true for volanesorsen. Cancer drug custirsen and bacterial infection drug plazomicin are also in phase 3 studies. And alicaforsen, which treats pouchitis, is being sold in Europe via Named Patient Supply protocols while it is finishing up late-stage testing.

Also, while Glaxo is waiting on moving forward with IONIS-TTRRx, Ionis is forging ahead. The company is evaluating the drug in a phase 3 study of patients with transthyretin (TTR) familial amyloid polyneuropathy.

Better buy

Both of these stocks come with considerable risks. They also both have opportunities to rebound.

For Valeant, the biggest questions revolve around the company's huge debt load. Valeant appears likely to sell off some of its assets, particularly dermatology units and perhaps its Bausch & Lomb division, to raise some cash.

Ionis faces the prospects of pipeline failures. A lot of the company's valuation was linked to IONIS-TTRRx. Ionis must overcome the safety concerns that led Glaxo to suspend its plans for phase 3 testing of the drug.

So which is the better buy? I'm cautiously optimistic about a turnaround for Valeant. Joseph Papa will probably make smart moves in righting the ship for the troubled drugmaker. However, I'm not sure the company will get as much from selling off assets as it might hope. As I mentioned earlier, Valeant has some silver linings, but its debt is one huge dark cloud.

I think Ionis is the better call right now. My view is that the stock was oversold after the Glaxo decision. There seems to be a pretty good chance that the safety concerns for IONIS-TTRRx will be satisfactorily addressed. Ionis' pipeline should make this stock more of a winner for investors with a long-term perspective.