Integrated semiconductor bioarray

1. An integrated biosensor array, comprising,

in order,

a molecular recognition layer,

an optical layer, and

a sensor layer integrated in a sandwich configuration, wherein:

(a) the molecular recognition layer comprises a plurality of different probes attached at different independently addressable locations, each of said independently addressable locations configured to receive an excitation photon flux directly from a single source located on a single side of said molecular recognition layer, wherein the molecular recognition layer transmits light to the optical layer;

(b) the optical layer comprises an optical filter layer, wherein the optical layer transmits light from the molecular recognition layer to the sensor layer, whereby the transmitted light is filtered; and

(c) the sensor layer comprises an array of optical sensors that detect the filtered light transmitted through the optical layer, said sensor layer comprising sensor elements fabricated using a CMOS fabrication process; wherein said molecular recognition layer, said optical layer and said sensor layer comprise an integrated structure in which said molecular layer is in contact with said optical layer and said optical layer is in contact with said sensor layer.

2. The biosensor array of claim 1 wherein the optical layer further comprises an optical coupling layer between the optical filter layer and the molecular recognition layer.

3. The biosensor array of claim 2 wherein the optical coupling layer comprises a plurality of optical waveguides.

4. The biosensor array of claim 2 wherein the optical coupling layer comprises a fiber-optic faceplate.

5. The biosensor array of claim 1 wherein the optical layer is 2 μm to 20 cm thick.

6. The biosensor array of claim 1 wherein the optical layer is 5 μm to 1 cm thick.

7. The biosensor array of claim 1 wherein the optical layer provides thermal insulation between the array of optical sensors and the molecular recognition layer.

8. The biosensor array of claim 1 wherein the sensor layer comprises a photodiode array.

9. The biosensor array of claim 1 wherein the sensor layer comprises embedded detection circuitry connected to the optical sensors.

10. The biosensor array of claim 1 wherein the sensor layer comprises embedded detection and signal processing circuitry connected to the optical sensors.

11. The biosensor array of claim 1 , wherein the integrated biosensor array comprises a digital signal processor.

12. The biosensor array of claim 1 , wherein the integrated biosensor array comprises an integrated in-pixel photocurrent detector.

13. The biosensor array of 12 wherein the integrated in-pixel photocurrent detector comprises a capacitive transimpedance amplifier (CTIA).

14. The biosensor array of claim 1 , wherein the integrated biosensor array has an in-pixel analog to digital converter.

15. The biosensor array of claim 1 wherein the optical filter layer comprises a multilayer dielectric.

16. The biosensor array of claim 15 wherein the optical filter layer has a passband or a stopband with a bandwidth of about 10 nm to 20 nm.

17. The biosensor array of claim 16 wherein the passband or stopband is in the range of 400 nm to 800 nm.

18. The biosensor array of claim 1 wherein the optical filter layer attenuates fluorescent excitation light by 10 2 to 10 7 .

19. The biosensor array of claim 1 wherein the optical filter layer attenuates fluorescent excitation light by 10 3 to 10 5 .

20. The biosensor array of claim 1 wherein at least one optical sensor corresponds to one independently addressable location comprising a probe.

21. The biosensor array of claim 1 wherein more than one optical sensor corresponds to one independently addressable location.

22. The biosensor array of claim 1 wherein about 10 to about 1000 optical sensors correspond to one independently addressable location.

23. The biosensor array of claim 1 wherein different optical sensors corresponding to one independently addressable location measure different wavelengths of light.

24. The biosensor array of claim 1 wherein the molecular recognition layer comprises 2 to 1,000,000 probes.

25. The biosensor array of claim 1 wherein the independently addressable locations comprise probes comprising fluorescent moieties.

26. The biosensor array of claim 25 wherein the fluorescent moieties are capable of being quenched upon binding of an analyte comprising a quencher.

27. The biosensor array of claim 25 wherein the fluorescent moieties are bound to the probes.

28. The biosensor array of claim 25 wherein the fluorescent moieties are bound to the surface of the array, but are not covalently bound to the probes.

29. The biosensor array of claim 1 wherein the probes comprise nucleic acids.

30. The biosensor array of claim 1 wherein the probes comprise proteins.