Provided herein are methods and compositions relating to libraries of optimized antibodies having nucleic acids encoding for an antibody comprising modified sequences. Libraries described herein include variegated libraries comprising nucleic acids each encoding for a predetermined variant of at least one predetermined reference nucleic acid sequence. Further described herein are protein libraries generated when the nucleic acid libraries are translated. Further described herein are cell libraries expressing variegated nucleic acid libraries described herein.

Provided herein are methods and compositions relating to libraries of optimized antibodies having nucleic acids encoding for an antibody comprising modified sequences. Libraries described herein include variegated libraries comprising nucleic acids each encoding for a predetermined variant of at least one predetermined reference nucleic acid sequence. Further described herein are protein libraries generated when the nucleic acid libraries are translated. Further described herein are cell libraries expressing variegated nucleic acid libraries described herein.

Provided herein are methods and compositions relating to libraries of optimized antibodies having nucleic acids encoding for an antibody comprising modified sequences. Libraries described herein include variegated libraries comprising nucleic acids each encoding for a predetermined variant of at least one predetermined reference nucleic acid sequence. Further described herein are protein libraries generated when the nucleic acid libraries are translated. Further described herein are cell libraries expressing variegated nucleic acid libraries described herein.

The present disclosure relates to in vitro experiments and in silico computation and machine-learning based techniques to iteratively improve a process for identifying binders that can bind a target. Particularly, aspects of the present disclosure are directed to obtaining initial sequence data, identifying, by a first machine-learning model having model parameters learned from the initial sequence data, a first set of aptamer sequences, obtaining, using an in vitro binding selection process, subsequent sequence data including sequences from the first set of aptamer sequences, identifying, by a second machine-learning model having model parameters learned from the subsequent sequence data, a second set of aptamer sequences, determining, using one or more in vitro assays, analytical data for aptamers synthesized from the second set of aptamer sequences, and identifying a final set of aptamer sequences from the second set of aptamer sequences based on the analytical data associated with each aptamer.

The present disclosure relates to in vitro experiments and in silico computation and machine-learning based techniques to iteratively improve a process for identifying binders that can bind a target. Particularly, aspects of the present disclosure are directed to obtaining initial sequence data, identifying, by a first machine-learning model having model parameters learned from the initial sequence data, a first set of aptamer sequences, obtaining, using an in vitro binding selection process, subsequent sequence data including sequences from the first set of aptamer sequences, identifying, by a second machine-learning model having model parameters learned from the subsequent sequence data, a second set of aptamer sequences, determining, using one or more in vitro assays, analytical data for aptamers synthesized from the second set of aptamer sequences, and identifying a final set of aptamer sequences from the second set of aptamer sequences based on the analytical data associated with each aptamer.

The present invention relates to a method of whole genome sequencing of a single cell or cell-group for identification of single nucleotide variants, determining chromosome structural variations, or determining phasing information in the genome of the single cell or cell-group. Methods of preparing an indexed DNA library for sequencing of nucleic acid molecules; preparing an indexed DNA library for whole genome sequencing of single cells or cell-groups for the identification of single nucleotide variants, determining chromosome structural variations, or determining phasing information in the genome of the single cells or cell-groups; and whole genome sequencing of a single cell or cell-group to provide data for the identification of single nucleotide variants (SNVs), determining chromosome structural variations, or determining phasing information in the genome of the single cell or cell-group are also described.

The present invention relates to a method of whole genome sequencing of a single cell or cell-group for identification of single nucleotide variants, determining chromosome structural variations, or determining phasing information in the genome of the single cell or cell-group. Methods of preparing an indexed DNA library for sequencing of nucleic acid molecules; preparing an indexed DNA library for whole genome sequencing of single cells or cell-groups for the identification of single nucleotide variants, determining chromosome structural variations, or determining phasing information in the genome of the single cells or cell-groups; and whole genome sequencing of a single cell or cell-group to provide data for the identification of single nucleotide variants (SNVs), determining chromosome structural variations, or determining phasing information in the genome of the single cell or cell-group are also described.

A relevance searching method performed by a computer, the relevance searching method includes generating a combined database by combining a plurality of databases each including a plurality of elements and relevance information indicating direct relevance between two elements in the plurality of elements; and searching for relevance between two elements that do not have direct relevance by using the combined database.

A relevance searching method performed by a computer, the relevance searching method includes generating a combined database by combining a plurality of databases each including a plurality of elements and relevance information indicating direct relevance between two elements in the plurality of elements; and searching for relevance between two elements that do not have direct relevance by using the combined database.

Processes and materials to detect cancer from a biopsy are described. In some cases, cell-free nucleic acids can be sequenced, and the sequencing result can be utilized to detect sequences derived from a neoplasm. Detection of somatic variants occurring in phase can indicate the presence of cancer in a diagnostic scan and a clinical intervention can be performed.