Like just about everyone else with exposure to Wall Street’s woes, university endowments took a big hit during the economic downturn.

According to Bloomberg, Yale’s endowment lost -25% during fiscal 2009. The value of the Harvard endowment dropped by -27.3% over that period.

As is the case at Harvard, Yale’s endowment owns a variety of alternative investments, but it has also disclosed holdings in a handful of U.S.-listed equities. We recently took a look at Harvard’s strategy and noted the prevalence of international-focused ETFs in its portfolio. Yale, meanwhile, appears to have scaled way back on its equity portfolio.

Looking at Yale’s top U.S.-listed holdings at the end of Q3, the endowment’s top positions ware in ETFs iShares MSCI EAFE Index Fund (EFA) and iShares S&P 100 Index (OEF).

Besides the ETFs, Yale’s end-of-Q3 portfolio included stocks like biotech Celgene (Nasdaq: CELG), natural gas firm Crosstex Energy (Nasdaq: XTXI), data center firm Rackspace Hosting (RAX), and big bank JPMorgan Chase (JPM).

Looking at tickerspy.com’s graph charting the performance of the Yale’s end-of-Q3 holdings so far in Q4, one can see that the holdings are ahead of the market. If you want to see how your performance stacks up to Yale’s or see some of the other stocks it’s invested in, visit tickerspy.com to see Yale’s top holdings and a chart of their combined performance.

Pro portfolio performance is based on institutions’ top-15 holdings as disclosed in quarter-end filings with the SEC. Pro performance does not take into account additional holdings beyond the top 15 nor does it include positions that are not required to be disclosed by the SEC. As such, Pro portfolio performance should be considered an approximation and not a precise record of how an institution has performed over time.

With a stated mantra that it is “searching for patterns in financial markets,” hedge fund Zebra Capital Management is among the vanguard of quantitative funds that use complex formulas and brute force computing power to generate returns from volatile markets.

The fund was founded in 2001 by Roger Ibbotson and Zhiwu Chen, a pair of professors of finance at Yale School of Management. Their approach is described on the fund’s website: “Zebra Capital believes that fundamentals drive security prices in the long run, but in the short term price dislocations can occur due to human behavior, fear and emotions. It is our belief that a disciplined quantitative approach, rooted in fundamentals and backed by extensive research, can best realize profits.”

In practice, this likely means that Zebra uses a variety of financial instruments for its investments and likely only holds equity positions for a short period.

Nonetheless, investors can look at Zebra’s recently disclosed, top-15, U.S.-listed equity positions to get a glimpse of the unique funds strategy. At the end of Q3, Zebra was holding a mix of names with positions under $200,000 in value (tiny compared to most big hedge funds). The top holding for the firm at the end of Q3 was in ETF iShares Russell 1000 Index (IWB).

Zebra also disclosed holdings in solar play Energy Conversion Devices (ENER), KFC-parent Yum Brands (YUM), heavy equipment maker Terex (TEX), coffee producer Green Mountain Coffee Roasters (GMCR), oil explorer and producer Brigham Exploration (BEXP), and Sun Microsystems (JAVA), which is set to be acquired by Oracle (ORCL).

Looking at tickerspy.com’s graph charting the performance of Zebra’s end-of-Q3 holdings so far in Q4, one can see that the holdings have kept pace with the market, albeit with a good deal of volatility. If you want to see how your performance stacks up to Zebra’s or see some of the other stocks it’s invested in, visit tickerspy.com to see the hedge fund’s top holdings and a chart of their combined performance.

Pro portfolio performance is based on institutions’ top-15 holdings as disclosed in quarter-end filings with the SEC. Pro performance does not take into account additional holdings beyond the top 15 nor does it include positions that are not required to be disclosed by the SEC. As such, Pro portfolio performance should be considered an approximation and not a precise record of how an institution has performed over time.

Marty Whitman, the legendary value investor who runs mutual fund firm Third Avenue Management, signaled his confidence in the market (and his own stock-picking abilities) by pouring $3 million into his firm’s flagship Third Avenue Value Fund (TAVFX) during late 2008 and early 2009.

The bet continues to look prescient, with the fund up around 37% year to date. In a recent letter to investors, Third Avenue boiled down its philosophy: “in common stock investing, the sole, or almost sole, focus is on buying into well-financed companies at steep discounts from readily ascertainable NAV where there are reasonable prospects for double digit NAV growth over the next five years or so.”

So, which stocks fit the bill in the minds of Third Avenue’s managers?

Looking at Third Avenue’s top-15, U.S.-listed, equity holdings, which are aggregated across all its funds, one can see that the firm was increasing its holdings in a number of its largest stakes during Q3, including The Bank of New York Mellon (BK), waste management firm Covanta (CVA), independent oil and gas producer Encana (ECA), diversified conglomerate Leucadia (LUK), and drilling contractor Nabors Industries (NBR).

Third Avenue’s largest equity stake at the end of Q3 was in Brookfield Asset Management (BAM), where the firm was trimming shares during Q3. Third Avenue was also trimming stakes in communications equipment maker Sycamore Networks (SCMR), Korean steelmaker Posco (PKX), and independent oil and gas producer Cimarex Energy (XEC).

Looking at tickerspy.com’s graph charting the performance of Third Avenue’s end-of-Q3 holdings during the current quarter, one can see that the holdings have been beating the market. If you want to see how your performance stacks up to Third Avenue’s or see some of its other holdings, visit tickerspy.com to see the firm’s top holdings and a chart of their combined performance.

Pro portfolio performance is based on institutions’ top-15 holdings as disclosed in quarter-end filings with the SEC. Pro performance does not take into account additional holdings beyond the top 15 nor does it include positions that are not required to be disclosed by the SEC. As such, Pro portfolio performance should be considered an approximation and not a precise record of how an institution has performed over time.

The generally bearish outlook of commodity investor Eric Sprott has made for a challenging 2009 for his Canadian investment firm.

Sprott Inc., which debuted in a Canadian-listed IPO over a year ago, saw a wider loss year over year in its Q3 earnings report earlier this month. As might be expected for the commodity-oriented firm, the surging price of gold has been a bright spot. Eric Sprott said, “We continue to believe that gold and other precious metals will be the best store of value for investors over the longer term. As such, several of our larger funds have significant investments in physical gold and silver, as well as mining stocks.”

While Sprott has exposure to many Canadian-listed firms, American investors will be interested in the various U.S.-listed equities it holds, many of them mining stocks.

The largest U.S.-listed position in Sprott’s portfolio is silver miner Silver Wheaton (SLW), where he was increasing his stake during Q3.

Elsewhere, Sprott was adding to a number of stakes, including miners Jaguar Mining (JAG), Yamana Gold (AUY), Kinross Gold (KGC), Exeter Resource (XRA), and Eldorado Gold (EGO).

Meanwhile, he was trimming stakes in miners Golden Star Resources (GSS), IAMGOLD (IAG), Keegan Resources (KGN), and oil sands player Oilsands Quest (BQI).

The rest of Sprott’s top, U.S.-listed, equity holdings from the end of Q3 are available at tickerspy.com, where a performance graph shows that combined holdings have had a volatile but upward trajectory in recent months.

Visit tickerspy.com to see Sprott’s top holdings and a chart of their combined performance.

Pro portfolio performance is based on institutions’ top-15 holdings as disclosed in quarter-end filings with the SEC. Pro performance does not take into account additional holdings beyond the top 15 nor does it include positions that are not required to be disclosed by the SEC. As such, Pro portfolio performance should be considered an approximation and not a precise record of how an institution has performed over time.

Though the market downturn was devastating for the Harvard endowment, 2009’s extend rally has kept the more dire forecasts from being realized.

According to Bloomberg, the value of Harvard’s investments fell by -27.3% in the year ended June 30, not as bad as the -30% decline that had been predicted and not as bad as the hits that other institutional investors took.

Though the endowment has substantial investments in alternative assets like real estate and private equity, investors can get a sense of Harvard’s strategy by looking at its U.S.-listed, equity holdings. They turn out to be quite diversified, with an international bias that makes ample use of a variety of ETFs.

Looking at Harvard’s top U.S.-listed holdings at the end of Q3, which were recently disclosed to the SEC, the largest U.S.-listed, equity holding by a wide margin was ETF iShares MSCI Emerging Markets Index (EEM), where Harvard was adding its stake during the quarter.

Meanwhile, Harvard was upping its exposure to individual emerging and overseas markets via increased stakes in a variety of ETFs, including iShares FTSE/Xinhua China 25 Index (FXI), iShares MSCI Brazil Index (EWZ), iPath MSCI India Index ETN (INP), iShares MSCI Taiwan Index (EWT), iShares MSCI Malaysia Index (EWM), and iShares MSCI South Africa Index (EZA).

Harvard also trimmed its stake in mobile telecom firm China Mobile (CHL), increased its stake in Israeli pharmaceutical company Teva Pharmaceutical Industries (TEVA), and opened a new stake in recent IPO Starwood Property Trust (STWD).

Looking at tickerspy.com’s graph charting the performance of the Harvard’s end-of-Q3 holdings so far in Q4, one can see that the holdings have outperformed the rising market. If you want to see how your performance stacks up to Harvard’s or see some of the other stocks and ETFs it’s invested in, visit tickerspy.com to see Harvard’s top holdings and a chart of their combined performance.

Pro portfolio performance is based on institutions’ top-15 holdings as disclosed in quarter-end filings with the SEC. Pro performance does not take into account additional holdings beyond the top 15 nor does it include positions that are not required to be disclosed by the SEC. As such, Pro portfolio performance should be considered an approximation and not a precise record of how an institution has performed over time.

A year after what some feared might be the end for the venerable investment bank, Goldman Sachs (GS) now appears to be on much firmer footing. Certainly, the market thinks so, with the stock having more than doubled thus far in 2009.

Even as confidence in Wall Street has been shaken, thanks to its pedigree, Goldman Sachs’ investments are closely watched.

Looking at Goldman Sachs’ top U.S.-listed holdings at the end of Q3, which include the aggregated holdings of its internal hedge funds as well as other investments, one can see a laundry list of blue chip stocks.

The top holding, however, is an ETF, SPDR S&P 500 Index (SPY), where the firm was adding to its stake during the quarter. Goldman was also adding to its stake in the iShares Russell 2000 Index (IWM), while trimming shares of the iShares MSCI Emerging Markets Index ETF (EEM).

During the quarter, Goldman also added to its stakes in tech giants Cisco (CSCO) and Qualcomm (QCOM), as well as in consumer products blue chip Procter & Gamble (PG)

Elsewhere, the firm was trimming its holdings in rival financials Bank of America (BAC) and JPMorgan Chase (JPM), tech firms Apple (AAPL) and Microsoft (MSFT), and energy multinational Exxon Mobil (XOM).

Looking at tickerspy.com’s graph charting the performance of Goldman Sachs’ end-of-Q3 holdings so far in Q4, one can see that its blue chip focus has helped it keep pace with the market. If you want to see how your performance stacks up to Goldman Sachs’ or see some of the other stocks it’s invested in, visit tickerspy.com to see Goldman Sachs’ top holdings and a chart of their combined performance.

Pro portfolio performance is based on institutions’ top-15 holdings as disclosed in quarter-end filings with the SEC. Pro performance does not take into account additional holdings beyond the top 15 nor does it include positions that are not required to be disclosed by the SEC. As such, Pro portfolio performance should be considered an approximation and not a precise record of how an institution has performed over time.

After slashing his hedge fund’s stock portfolio by -97% to end to 2008, legendary oilman T. Boone Pickens was dipping his toe back into equities during Q3. The moves come after a brutal 2008 for BP Capital, Pickens’ energy-focused hedge fund.

Pickens is still a bull on the energy complex. Bloomberg reported last week that Pickens now sees oil hitting $100 a barrel next year.

Looking at Pickens’ top, U.S.-listed, equity positions at the end of Q3, it appears he may be ramping up his buying of energy-oriented equities, with new positions in oil refiner Hess (HES), oil and natural gas producers SandRidge Energy (SD) and McMoRan Exploration (MMR), and oil equipment and services company Wetherford International (WFT).

Elsewhere, Pickens was accumulating shares in natural gas producer Chesapeake Energy (CHK), offshore drilling contractor Transocean (RIG), oil services giant Schlumberger (SLB), and oil and natural gas producers XTO Energy (XTO) and Devon Energy (DVN).

Looking at tickerspy.com’s graph charting the performance of Pickens’ end-of-Q3 holdings so far in Q4, one can see that the top holdings have stayed ahead of the market. If you want to see how your performance stacks up to Pickens’ or see some of his other holdings, visit tickerspy.com to see his fund’s top positions and a chart of their combined performance.

Pro portfolio performance is based on institutions’ top-15 holdings as disclosed in quarter-end filings with the SEC. Pro performance does not take into account additional holdings beyond the top 15 nor does it include positions that are not required to be disclosed by the SEC. As such, Pro portfolio performance should be considered an approximation and not a precise record of how an institution has performed over time.

The endowment of the Bill and Melinda Gates Foundation, closely watched because of its value focus and close association with Warren Buffett, was incrementally adding to positions in its portfolio during the third quarter of 2009.

Bill Gates has famously set aside a major portion of the substantial wealth he accrued as Microsoft’s (Nasdaq: MSFT) founder for his Bill and Melinda Gates Foundation, which, with assets of nearly $30.2 billion as of June 30, 2009, is the largest transparently operated charitable foundation in the world. It aims, among other things, to combat poverty and address a number of global health issues.

The Foundation counts Gates’ friend and fellow billionaire Warren Buffett among its trustees. Buffett made headlines in 2006 when he pledged $30 billion in Berkshire Hathaway (NYSE: BRK-A, BRK-B) stock to the Gates’ charitable efforts. While Gates’ money is managed by his investment officer, Michael Larson, his proximity to Buffett leads many to believe that he may be privy to the thinking of the world’s most famous investor. In June, Gates told Fortune Magazine “I’ve gotten a lot of great advice from Warren.”

Looking at the Gates Foundation’s holdings from the end of Q3, one can see that the endowment was adding to its massive Berkshire Hathaway stake. Elsewhere, Gates was making limited moves, adding shares of fast food chain McDonald’s (MCD), beverage maker Coca-Cola (KO), heavy equipment maker Caterpillar (CAT), and waste services firm Waste Management (WM).

The Gates Foundation also held steady with large stakes in energy giants Exxon Mobil (XOM) and BP (BP) and discount retailer Wal-Mart (WMT).

Looking at tickerspy.com’s graph charting the performance of the Gates Foundation’s end-of-Q3 top holdings so far this quarter, one can see that they are keeping pace with the market. If you want to see how your performance stacks up to the Gates Foundation’s or see some of his other holdings, visit tickerspy.com to see the endowment’s top positions and a chart of their combined performance.

Pro portfolio performance is based on institutions’ top-15 holdings as disclosed in quarter-end filings with the SEC. Pro performance does not take into account additional holdings beyond the top 15 nor does it include positions that are not required to be disclosed by the SEC. As such, Pro portfolio performance should be considered an approximation and not a precise record of how an institution has performed over time.

Warren Buffett was in a buying mood during Q3, but he also held steady with an array of blue chips that are at the center of his investing strategy.

We outlined where Buffett was putting his money to work in yesterday’s article, but the Oracle of Omaha also retained huge stakes many of his long-time favorite stocks that reside at the top of the Berkshire Hathaway (NYSE: BRK-A, BRK-B) portfolio. He was also trimming stakes in a handful of names.

The top stock in Buffett’s holdings from the start of Q3 is beverage giant Coca-Cola (KO). Also among Buffett’s top holdings are several of America’s best-known brands, including Kraft Foods (KFT), American Express (AXP), Costco (COST), and Nike (NKE), and General Electric (GE). For years, Buffett has looked to steady, well-known brands like these as places to stash his cash.

He also, of course, also maintains significant exposure to Goldman Sachs (GS) (not listed among Berkshire’s publicly traded holdings) via the special investment he made in the firm late last year.

Elsewhere, Buffett was trimming stakes in credit rating firm Moody’s (MCO), health insurer Wellpoint (WLP), power wholesaler NRG Energy (NRG), SunTrust Banks (STI), and ConocoPhillips (COP), an investment that he said was ill-timed in his annual letter earlier this year. And Buffett exited stakes in hydraulics manufacturer Eaton (ETN) and vehicle control systems maker Wabco Holdings (WBC).

Looking at tickerspy.com’s graph charting the performance of Berkshire’s end-of-Q3 holdings so far during Q4, Buffett’s holdings have kept pace with the broader market during the recent rally. If you want to see how your performance stacks up to Warren Buffett’s, visit tickerspy.com to see the Oracle of Omaha’s top holdings and a chart of their combined performance.

Pro portfolio performance is based on institutions’ top-15 holdings as disclosed in quarter-end filings with the SEC. Pro performance does not take into account additional holdings beyond the top 15 nor does it include positions that are not required to be disclosed by the SEC. As such, Pro portfolio performance should be considered an approximation and not a precise record of how an institution has performed over time.

After a harrowing 2008, highly regarded hedge fund manager Mohnish Pabrai shifted strategy and put together an impressive 2009.

Though 2008 saw Pabrai’s funds slide by as much as -60%, he was boasting returns of 120% in 2009 through September, according to an October letter to investors.

Once well known for keeping a very concentrated portfolio of ten positions or fewer, Pabrai took his funds’ struggles as an opportunity to diversify his holdings somewhat, expanding his portfolio in late 2008 and early 2009. In addition, according to a recent letter to investors, as redemptions accelerated at the end of 2008, Pabrai sold the worst performing names in his portfolio to free up funds. According to Pabrai, the “portfolio ended up stronger as a result.

Looking at Pabrai’s holdings as of the end of Q3, one can see that he continues to look for new winners, opening a fresh position in automated electronic broker Interactive Brokers Group (IBKR) and upping stakes in real estate development firm Brookfield Properties (BPO), Argentinean agricultural company Cresud (Nasdaq: CRESY), fertilizer firm Potash (POT), heavy equipment maker Terex (TEX), bank Wells Fargo (WFC), and Warren Buffett’s Berkshire Hathaway (NYSE: BRK-A, BRK-B). Pabrai, a former IT consulting exec, models himself after Warren Buffett and in 2007 paid over $650,000 in a charity auction to have lunch with the Oracle of Omaha.

Elsewhere during Q3, Pabrai was trimming stakes in Harvest Natural Resources (HNR) and diversified conglomerate Leucadia (LUK).

Looking at tickerspy.com’s graph charting the performance of Pabrai’s end-of-Q3 holdings so far in Q4, one can see that Pabrai’s moves appear to be paying off. If you want to see how your performance stacks up to Pabrai’s or see some other Pabrai holdings, visit tickerspy.com to see the fund’s top positions and a chart of their combined performance.

Pro portfolio performance is based on institutions’ top-15 holdings as disclosed in quarter-end filings with the SEC. Pro performance does not take into account additional holdings beyond the top 15 nor does it include positions that are not required to be disclosed by the SEC. As such, Pro portfolio performance should be considered an approximation and not a precise record of how an institution has performed over time.