Rapid optimization of processes for the integrated purification of biopharmaceuticals by Crowell, Laura E, Rodriguez, Sergio A, Love, Kerry R, Cramer, Steven M, Love, J Christopher

“…Straight-through chromatography, wherein the eluate from one column passes directly onto another column without adjustment, is one strategy to integrate and intensify manufacturing processes for biologics. …”
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Proteogenomic integration reveals therapeutic targets in breast cancer xenografts by Carr, Steven A

“…Here, we employed quantitative proteomics to profile protein expression across 24 breast cancer patient-derived xenograft (PDX) models. Integrated proteogenomic analysis shows positive correlation between expression measurements from transcriptomic and proteomic analyses; further, gene expression-based intrinsic subtypes are largely re-capitulated using non-stromal protein markers. …”
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Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer

“…To provide a detailed analysis of the molecular components and underlying mechanisms associated with ovarian cancer, we performed a comprehensive mass-spectrometry-based proteomic characterization of 174 ovarian tumors previously analyzed by The Cancer Genome Atlas (TCGA), of which 169 were high-grade serous carcinomas (HGSCs). Integrating our proteomic measurements with the genomic data yielded a number of insights into disease, such as how different copy-number alternations influence the proteome, the proteins associated with chromosomal instability, the sets of signaling pathways that diverse genome rearrangements converge on, and the ones most associated with short overall survival. …”
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Identifying Improved Sites for Heterologous Gene Integration Using ATAC-seq by Brady, Joseph R., Tan, Melody C., Whittaker, Charles A., Colant, Noelle A., Dalvie, Neil C., Love, Kerry Routenberg, Love, J. Christopher

“…Constructing efficient cellular factories often requires integration of heterologous pathways for synthesis of novel compounds and improved cellular productivity. …”
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Identification of the transgenic integration site in 2C T cell receptor transgenic mice by Son, Chae-Yeon, Haines, Brian B., Luch, Andreas, Ryu, Chun Jeih

“…Sequence analysis revealed that DC-PCR product contained the probe sequences and the junction sequences of integration site, indicating that 2C TCR α transgene is integrated into chromosome 1. …”
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Report to the President for year ended June 30, 2023, Koch Institute for Integrative Cancer Research at MIT by Vander Heiden, Matthew

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Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1 by Mesirov, Jill P.

“…We describe a robust gene expression-based molecular classification of GBM into Proneural, Neural, Classical, and Mesenchymal subtypes and integrate multidimensional genomic data to establish patterns of somatic mutations and DNA copy number. …”
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Integrated cistromic and expression analysis of amplified NKX2-1 in lung adenocarcinoma identifies LMO3 as a functional transcriptional target by Watanabe, Hideo, Francis, Joshua M., Woo, Michele S., Etemad, Banafsheh, Lin, Wenchu, Fries, Daniel F., Peng, Shouyong, Snyder, Eric, Tata, Purushothama Rao, Izzo, Francesca, Schinzel, Anna C., Cho, Jeonghee, Hammerman, Peter S., Verhaak, Roel G., Hahn, William C., Rajagopal, Jayaraj, Meyerson, Matthew L., Jacks, Tyler E

“…To study the transcriptional impact of NKX2-1 amplification, we generated an expression signature associated with NKX2-1 amplification in human lung adenocarcinoma and analyzed DNA-binding sites of NKX2-1 by genome-wide chromatin immunoprecipitation. Integration of these expression and cistromic analyses identified LMO3, itself encoding a transcription regulator, as a candidate direct transcriptional target of NKX2-1. …”
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Reduction of the therapeutic dose of silencing RNA via its integration into the backbone of a pre-microRNA highly enriched in exosome-like vesicles by Reshke, Ryan, Taylor, James A., Savard, Alexandre, Guo, Huishan, Rhym, Luke Hyunsik, Kowalski, Piotr S, Trung, My Tran, Campbell, Charles, Little, Wheaton, Anderson, Daniel Griffith, Gibbings, Derrick

“…Here, we show that the integration of siRNA sequences into a Dicer-independent RNA stem–loop based on pre-miR-451 microRNA—which is highly enriched in small extracellular vesicles secreted by many cell types—reduces the expression of the genes targeted by the siRNA in the liver, intestine and kidney glomeruli of mice at siRNA doses that are at least tenfold lower than the siRNA doses typically delivered via lipid nanoparticles. …”
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Synthetic Circuit-Driven Expression of Heterologous Enzymes for Disease Detection by He, Jiang, Nissim, Lior, Soleimany, Ava P, Binder-Nissim, Adina, Fleming, Heather E, Lu, Timothy K, Bhatia, Sangeeta N

“…The integration of nanotechnology and synthetic biology could lay the framework for new classes of engineered biosensors that produce amplified readouts of disease states. …”
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Toward engineered processes for sequencing-based analysis of single circulating tumor cells by Adalsteinsson, Viktor A, Love, J Christopher

“…Ultimately, technologies should be selected or adapted for optimal performance and compatibility in an integrated process. © 2014 Elsevier Ltd.…”
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On-demand manufacturing of clinical-quality biopharmaceuticals by Crowell, Laura E, Lu, Amos E, Love, Kerry R, Stockdale, Alan, Timmick, Steven M, Wu, Di, Wang, Yu Annie, Doherty, William, Bonnyman, Alexandra, Vecchiarello, Nicholas, Goodwine, Chaz, Bradbury, Lisa, Brady, Joseph R, Clark, John J, Colant, Noelle A, Cvetkovic, Aleksandar, Dalvie, Neil C, Liu, Diana, Liu, Yanjun, Mascarenhas, Craig A, Matthews, Catherine B, Mozdzierz, Nicholas J, Shah, Kartik A, Wu, Shiaw-Lin, Hancock, William S, Braatz, Richard D, Cramer, Steven M, Love, J Christopher

“…Unlike previous systems, InSCyT includes fully integrated modules for sustained production, efficient purification without the use of affinity tags, and formulation to a final dosage form of recombinant biopharmaceuticals. …”
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Producing and Concentrating Lenti-Cre for Mouse Infections by Gierut, J. J., Haigis, K. M., Jacks, Tyler E.

“…They can transduce a wide range of cell types and integrate into the host genome, which results in long-term expression of the transgene (Cre) both in vitro and in vivo. …”
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The redox requirements of proliferating mammalian cells by Hosios, Aaron M, Vander Heiden, Matthew G

“…In this Minireview, we highlight the biosynthetic pathways that involve redox reactions and discuss their integration with metabolism in proliferating mammalian cells.…”
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Single-cell technologies for monitoring immune systems by Chattopadhyay, Pratip K, Gierahn, Todd M, Roederer, Mario, Love, J Christopher

“…We summarize recent approaches to making such computations tractable and discuss challenges for integrating heterogeneous data obtained using these single-cell technologies. © 2014 Nature America, Inc.…”
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LTE1 promotes exit from mitosis by multiple mechanisms by Joyce, K., Whalen, J., Seshan, A., Falk, Jill E., Campbell, Ian Winsten, Amon, Angelika B.

“…In budding yeast, alignment of the anaphase spindle along the mother–bud axis is crucial for maintaining genome integrity. If the anaphase spindle becomes misaligned in the mother cell compartment, cells arrest in anaphase because the mitotic exit network (MEN), an essential Ras-like GTPase signaling cascade, is inhibited by the spindle position checkpoint (SPoC). …”
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Differential selective pressure alters rate of drug resistance acquisition in heterogeneous tumor populations by Sun, Daphne S., Dalin, Simona, Hemann, Michael, Lauffenburger, Douglas A, Zhao, Boyang

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Design and Delivery of Real-Time Adherence Data to Men Who Have Sex with Men Using Antiretroviral Pre-exposure Prophylaxis via an Ingestible Electronic Sensor by Chai, Peter R, Goodman, Georgia, Bustamante, Majo, Mendez, Lizette, Mohamed, Yassir, Mayer, Kenneth H, Boyer, Edward W, Rosen, Rochelle K, O’Cleirigh, Conall

“…Digital pill systems (DPS) utilize an ingestible radiofrequency emitter integrated onto a gelatin capsule, which permits direct, real-time measurement of medication adherence. …”
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Practical considerations for active machine learning in drug discovery by Reker, Daniel

“…Specifically, considerations regarding implementation, infrastructural integration, and expected benefits are discussed. By focusing on these practical aspects of active learning, this review aims at providing insights for scientists planning to implement active learning workflows in their discovery pipelines.…”
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Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq by Li, Bo, Gould, Joshua, Yang, Yiming, Sarkizova, Siranush, Tabaka, Marcin, Ashenberg, Orr, Rosen, Yanay, Slyper, Michal, Kowalczyk, Monika S, Villani, Alexandra-Chloé, Tickle, Timothy, Hacohen, Nir, Rozenblatt-Rosen, Orit, Regev, Aviv

“…Cumulus combines the power of cloud computing with improvements in algorithm and implementation to achieve high scalability, low cost, user-friendliness and integrated support for a comprehensive set of features. …”
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