Provided are methods and compositions for preparing nucleic acid fragments for sequencing by synthesis on a flow cell. The methods and compositions described herein introduce nucleotide diversity into a sample preparation that would otherwise lack nucleotide diversity due to homogeneity of the sequencing target.

Provided are methods and compositions for preparing nucleic acid fragments for sequencing by synthesis on a flow cell. The methods and compositions described herein introduce nucleotide diversity into a sample preparation that would otherwise lack nucleotide diversity due to homogeneity of the sequencing target.

Methods for preparing enriched sequencing libraries from test samples that contain double-stranded deoxyribonucleic acid (dsDNA) are provided.

Methods for preparing enriched sequencing libraries from test samples that contain double-stranded deoxyribonucleic acid (dsDNA) are provided.

The present disclosure relates to a method of protein structure and amino acid residue interaction prediction based on saturation suppressor mutagenesis screening of a protein of interest. The method of the instant disclosure can be adapted for multi-protein complexes, and is useful where crystal structure of a protein of interest is not available.

A method for identifying highly-skewed classes using an imperfect annotation of every instance together with a set of features for all instances. The imperfect annotations designate a plurality of instances as belonging to the target rare class and others to the majority class. First, a classifier is trained on the set of features using the imperfect annotation as supervision, to designate each instance to either the rare class or majority class. A combination of the predictions from the trained classifier and the imperfect annotations is then used to classify each instance to either the rare class or majority class. In particular, an instance is classified to the rare class only when both the trained classifier and the imperfect annotation classify the instance to the rare class. Finally, for each instance assigned as a rare class instance by the combination stage, all instances in its neighborhood are re-classified as either rare class or majority class.

Provided herein are polypeptides that bind to a transferrin receptor, methods of generating such polypeptides, and methods of using the polypeptides to target a composition to a transferrin receptor-expressing cell.

The present disclosure is directed to methods and kits for identifying, enriching, and evaluating templated assembly reactants. Some embodiments disclose methods for identifying templated assembly targets by synthesizing templated assembly reactants, hybridizing the templated assembly reactants to target nucleic acids, performing a templated assembly reaction, and identifying the target nucleic acids that hybridized to the templated assembly reactants. Libraries of templated assembly reactants, a kit for identifying templated assembly targets, and a pair of templated assembly targets enriched from a library of chemically-ligated oligonucleotides spatially elicited (CLOSE) products are also disclosed.

Provided herein are polypeptides that bind to a transferrin receptor, methods of generating such polypeptides, and methods of using the polypeptides to target a composition to a transferrin receptor-expressing cell.

Described are methods for selecting an amount of a critical parameter (such as an amount of a sequencing library, amount of a capture probe library, or a number of amplification cycles) for direct targeted sequencing. The methods include hybridizing capture probes in a capture probe library to surface-bound oligonucleotides; extending the surface-bound oligonucleotides using the hybridized capture probes as a template; hybridizing nucleic acid molecules from a sequencing library to the surface-bound capture probes; extending the surface-bound capture probes using the hybridized nucleic acid molecules as a template; amplifying the surface-bound complements of the nucleic acid molecules by bridge amplification for a number of amplification cycles; sequencing the amplified surface-bound complements of the nucleic acid molecules to determine an average cluster density after a predetermined number of sequencing cycles; repeating these steps at a plurality of different amounts of the critical parameter; and selecting an amount of the critical parameter.