I remember glancing at an article saying that exercise can counteract the negative effects of diet. I was wondering if anyone has the links to that body of research.
Even if such a research exists, you should discard it because it's likely based on inaccurate data. While exercises can counteract the negative effects of diet on the short term, it cannot do so on the long run. This is because
Caveat: If you're young (14 - 22), it's possible to counteract bad diet with exercises because your body's still developing and your metabolism is high; however, it still won't be sustainable over time. Although there are articles about ectomorphs that claim they can eat anything without gaining weight, many are being debunked.
Excerise absoultely cannot counteract a "bad diet".
A bad diet is more than just consuming more calories than required. Yes, in that single case exercise would be beneficial. However, a bad diet can also include not consuming enough of the right foods. Chronically low intake of good foods, or chronically high intake of bad foods will lead to health issues, and exercise cannot counter act this.
Not consuming enough fresh fruit and vegetables, leads to poor vitamin C levels. Chronically, this would result in scurvey, and surprisingly, this has happened in recent times. Exercise cannot counter act this.
Same with low calcium levels leading to brittle bones. Chronically low-fat consumption would lead to decreased absoption of fat-soluble vitamins. A diet low in protein (or complete proteins) would lead to slower muscle growth. A diet very high in apex fish such as tuna can lead to mercury build-up. None of these are health states to be in.
A good diet, based on a varied intake of whole foods is fundamental to good health and fitness. Where required supplements help, but should be just that, supplementary to a good diet.