The disclosure features methods of identifying protein-protein deregulation that include: generating a basal protein-protein interaction network for a plurality of biological samples, the network featuring a set of proteins expressed in the biological samples and concentrations of each member of the set of expressed proteins in each of the biological samples; identifying two associated expressed proteins in the network; for the two associated expressed proteins, comparing correlated relative concentration values of the two proteins in each of the biological samples to identify outliers among a distribution of the relative concentration values; and identifying members of the plurality of biological samples in which deregulation of the two associated expressed proteins occurs based on the outliers.

An intracellular selection system allows screening for peptide bioactivity and stability. Randomized recombinant peptides are screened for bioactivity in a tightly regulated expression system, preferably derived from the wild-type lac operon. Bioactive peptides thus identified are inherently protease- and peptidase-resistant. Also provided are bioactive peptides stabilized by a stabilizing group at the N-terminus, the C-terminus, or both. The stabilizing group can be a small stable protein, such as the Rop protein, glutathione sulfotransferase, thioredoxin, maltose binding protein, or glutathione reductase, an -helical moiety, or one or more proline residues.

Anti-VEGF antibodies and variants thereof, including those having high affinity for binding to VEGF, are disclosed. Also provided are methods of using phage display technology with nave libraries to generate and select the anti-VEGF antibodies with desired binding and other biological activities. Further contemplated are uses of the antibodies in research, diagnostic and therapeutic applications.

This invention provides a method that allows selection of antibodies against cells (e.g., tumor cells) in situ using laser capture microdissection. By restricting antibody selection to binders of internalizing epitopes, a panel of phage antibodies was generated that targets clinically represented prostate cancer antigens.

Triazabutadiene molecules as cleavable cross-linkers adapted to cross-link components with click chemistry, e.g., clickable triazabutadienes. For example, in some embodiments, the triazabutadienes feature alkyne handles attached to the imidazole portion or the aryl portion of the triazabutadienes, wherein the alkyne handles can link to azide handles (e.g., azide handles disposed on other components) via click chemistry. Also described are methods of producing said clickable triazabutadienes and methods of use of said clickable triazabutadienes. The present invention also features methods of cleaving said clickable triazabutadienes, e.g., for liberating the diazonium species for further chemical reactions.

The present invention provides novel microfluidic devices and methods that are useful for performing high-throughput screening assays and combinatorial chemistry. The invention provides for aqueous based emulsions containing uniquely labeled cells, enzymes, nucleic acids, etc., wherein the emulsions further comprise primers, labels, probes, and other reactants. An oil based carrier-fluid envelopes the emulsion library on a microfluidic device, such that a continuous channel provides for flow of the immiscible fluids, to accomplish pooling, coalescing, mixing, sorting, detection, etc., of the emulsion library.

The invention provides a method for detecting one or more biological ligands, where the method generally uses two arrays of biological reagents. The two arrays have two different functionalities: the first array captures the ligands on the array; and the second array delivers detecting reagents to the captured ligands. Use of arrays affords the method high-throughput detection capability; and the use of two different arrays ensures high specificity. The first array has a support structure fixed with a first set of reagents, each at a pre-determined position on the support. The second array has a support structure fixed with a second set of reagents, each at a pre-determined position on the support. The first array contains reagent(s) binding to a ligand, while the second array contains second reagent(s) binding to the same ligand. In preferred embodiments, antibodies are used as reagents, and used in detecting proteins in protein samples.

The present invention provides a system and method for assessing the fidelity of a synthetic peptide population including interrogating a population of peptide features in the presence of a receptor having an affinity for a plurality of binder sequences. A first amino acid is at a defined position within a first one of the binder sequences, and the population of peptide features includes a first control peptide feature synthesized to have an amino acid sequence including the first one of the binder sequences. The system and method further includes detecting a signal output characteristic of an interaction of the receptor with the first control peptide feature. The signal output is indicative of the fidelity of incorporation of the first amino acid into the first control peptide at the defined position within the first one of the binder sequences.

A method for determining past exposure to chemical agents or heavy metals may include coating a capture material with a capture reagent. The capture reagent may be selected based on an ability of the capture reagent to bind with a target antibody, and the target antibody may be an indicator associated with a particular chemical agent or heavy metal. The method may further include interrogating a clinical sample associated with an individual by forming a mixture of the capture material and the clinical sample, and determining an exposure status of the individual to the particular chemical agent or heavy metal based on whether the capture material demonstrates capture of the indicator.

This disclosure relates to single immunoglobulin variable domains with amino substitutions that result in improved thermal stability, cellular expression, and other biophysical properties.