Methods for controlling for non-systematic error in an amplification-based next generation sequencing (NGS) library preparation are described, which method includes using an internal amplification control (IAC) sharing identical priming sites to a native nucleic acid target template of interest in a NGS library preparation.

The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.

The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.

A method for implementing deep reinforcement learning with T-cell receptor (TCR) mutation policies to generate binding TCRs for immunotherapy includes extracting peptides to identify a virus or tumor cells, collecting a library of TCRs from patients, predicting interaction scores between the extracted peptides and the TCRs from the patients, developing a deep reinforcement learning framework with TCR mutation policies to generate TCRs with maximum binding scores, defining reward functions, outputting mutated TCRs, ranking the outputted TCRs to utilize top-ranked TCR candidates to target the virus or the tumor cells, and for each top-ranked TCR candidate, repeatedly identifying a set of self-peptides that the top-ranked TCR candidate binds to and further optimizing it greedily by maximizing a sum of its interaction scores with a given set of peptide antigens while minimizing a sum of its interaction scores with the set of self-peptides until stopping criteria of efficacy and safety are met.

A method for implementing deep reinforcement learning with T-cell receptor (TCR) mutation policies to generate binding TCRs for immunotherapy includes extracting peptides to identify a virus or tumor cells, collecting a library of TCRs from patients, predicting interaction scores between the extracted peptides and the TCRs from the patients, developing a deep reinforcement learning framework with TCR mutation policies to generate TCRs with maximum binding scores, defining reward functions, outputting mutated TCRs, ranking the outputted TCRs to utilize top-ranked TCR candidates to target the virus or the tumor cells, and for each top-ranked TCR candidate, repeatedly identifying a set of self-peptides that the top-ranked TCR candidate binds to and further optimizing it greedily by maximizing a sum of its interaction scores with a given set of peptide antigens while minimizing a sum of its interaction scores with the set of self-peptides until stopping criteria of efficacy and safety are met.

Disclosed herein are polynucleotide adaptors and methods of use thereof for identifying and analyzing nucleic adds, including cell-free nucleic acids from a patient sample. Also disclosed herein are methods of using the adaptors to detect, diagnose, or determine prognosis of cancers.

Cell-stored barcoded viral protein deep mutational scanning libraries are described. The libraries can be used to map resistance mutations to therapeutic treatments. The libraries can be used to predict viruses that become resistant to therapeutic compounds and/or may more easily evolve to infect new species. The libraries can also be used to more safely study dangerous viruses that normally require high safety biocontainment facilities. The libraries include features that allow efficient collection and assessment of informative data, obviating many bottlenecks of previous approaches.

Provided are antibodies that include amino acid sequences of SEQ ID NOs: 2, 4, and 6-12, or amino acid sequences that are about 95% identical thereto, and fragments thereof Also provided are scFv peptides that include a V.sub.H segment having a first amino acid sequence of amino acids 4-113 of any one of SEQ ID NOs: 2 and 8-12, a V.sub.L segment having a second amino acid sequence having amino acids 113-237 of SEQ ID NOs. 2 and 8-12, or both; nucleic acids encoding the same; methods for using the same to detect and/or target conformational states of FN in samples; methods for treating diseases and/or disorders and/or for meliorating at least one symptom of consequence of a disease or disorder associated with abnormal expression of a force-induced conformational state of FN in subjects; and methods for screening for compounds having selective binding activities for conformational states of FN.

Provided are antibodies that include amino acid sequences of SEQ ID NOs: 2, 4, and 6-12, or amino acid sequences that are about 95% identical thereto, and fragments thereof Also provided are scFv peptides that include a V.sub.H segment having a first amino acid sequence of amino acids 4-113 of any one of SEQ ID NOs: 2 and 8-12, a V.sub.L segment having a second amino acid sequence having amino acids 113-237 of SEQ ID NOs. 2 and 8-12, or both; nucleic acids encoding the same; methods for using the same to detect and/or target conformational states of FN in samples; methods for treating diseases and/or disorders and/or for meliorating at least one symptom of consequence of a disease or disorder associated with abnormal expression of a force-induced conformational state of FN in subjects; and methods for screening for compounds having selective binding activities for conformational states of FN.

The present disclosure provides shuttle vectors for editing exogenous polynucleotides in heterologous live cells, as well as automated methods, modules, and multi-module cell editing instruments and systems for performing the editing methods.