Virginia Savova
Harvard University
GeneNatural language processingComputer scienceGeneticsBiology
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Publications 36
#1Rapolas Zilionis (Harvard University)H-Index: 9
#2Camilla Engblom (Harvard University)H-Index: 16
Last. Allon M. Klein (Harvard University)H-Index: 32
view all 18 authors...
Summary Tumor-infiltrating myeloid cells (TIMs) comprise monocytes, macrophages, dendritic cells, and neutrophils, and have emerged as key regulators of cancer growth. These cells can diversify into a spectrum of states, which might promote or limit tumor outgrowth but remain poorly understood. Here, we used single-cell RNA sequencing (scRNA-seq) to map TIMs in non-small-cell lung cancer patients. We uncovered 25 TIM states, most of which were reproducibly found across patients. To facilitate tr...
26 CitationsSource
#1Sébastien Vigneau (Harvard University)H-Index: 10
#2S. V. Vinogradova (Harvard University)H-Index: 4
Last. Alexander A. Gimelbrant (Harvard University)H-Index: 20
view all 4 authors...
8 CitationsSource
#1Lindsey W. Plasschaert (Novartis)H-Index: 2
#2Rapolas Žilionis (Harvard University)H-Index: 1
Last. Aron B. Jaffe (Novartis)H-Index: 16
view all 8 authors...
The functions of epithelial tissues are dictated by the types, abundance and distribution of the differentiated cells they contain. Attempts to restore tissue function after damage require knowledge of how physiological tasks are distributed among cell types, and how cell states vary between homeostasis, injury–repair and disease. In the conducting airway, a heterogeneous basal cell population gives rise to specialized luminal cells that perform mucociliary clearance1. Here we perform single-cel...
99 CitationsSource
#1Indira Krishnan (BIDMC: Beth Israel Deaconess Medical Center)H-Index: 2
#2Giorgia Maroni (BIDMC: Beth Israel Deaconess Medical Center)H-Index: 3
Last. Elena Levantini (BIDMC: Beth Israel Deaconess Medical Center)H-Index: 20
view all 24 authors...
Lung cancer represents one of the most significant and lethal diseases worldwide. Advances in treatment protocols, the development of targeted agents, and our comprehensive understanding of the genetics and mechanisms driving this disease, have helped identify novel agents with therapeutic promise, yet mortality remains high. Thus, there is a real need to identify new therapeutic options that can target this disease to improve patient outcome. BMI-1 (B cell-specific Moloney murine leukemia virus...
#1Camilla Engblom (Harvard University)H-Index: 16
#2Christina Pfirschke (Harvard University)H-Index: 18
Last. Mikael J. Pittet (Harvard University)H-Index: 66
view all 33 authors...
INTRODUCTION Myeloid cells have emerged as key regulators of cancer growth because of their abundance in the tumor stroma in a broad range of cancers, their association with clinical outcome, and their ability to modulate tumor progression. Most tumor-infiltrating myeloid cells derive from circulating precursors, which are produced in distant tissues, and some tumors amplify myeloid cell activity by skewing hematopoiesis toward the myeloid lineage or increasing myeloid cell populations in the pe...
59 CitationsSource
#1Camilla EngblomH-Index: 16
#2Christina PfirschkeH-Index: 18
Last. Mikael J. PittetH-Index: 66
view all 33 authors...
2 Citations
#1Virginia Savova (Harvard University)H-Index: 16
#2S. V. Vinogradova (Harvard University)H-Index: 4
Last. Lauren A. Weiss (UCSF: University of California, San Francisco)H-Index: 29
view all 5 authors...
Risk alleles of genes with monoallelic expression are enriched in gain-of-function variants and depleted in loss-of-function variants for neurodevelopmental disorders
4 CitationsSource
#1Virginia Savova (Harvard University)H-Index: 16
#2Esther J. Pearl (MBL: Marine Biological Laboratory)H-Index: 6
Last. Leonid Peshkin (Harvard University)H-Index: 31
view all 7 authors...
We characterize the genetic diversity of Xenopus laevis strains using RNA-seq data and allele-specific analysis. This data provides a catalogue of coding variation, which can be used for improving the genomic sequence, as well as for better sequence alignment, probe design, and proteomic analysis. In addition, we paint a broad picture of the genetic landscape of the species by functionally annotating different classes of mutations with a well-established prediction tool (PolyPhen-2). Further, we...
1 CitationsSource
#1Rapolas ZilionisH-Index: 9
#2Juozas NainysH-Index: 9
Last. Linas MazutisH-Index: 18
view all 7 authors...
Zilionis et al. describe a protocol for the inDrops platform, which is a high-throughput droplet microfluidics system that allows for single-cell barcoding of over 15,000 cells in 1 h.
182 CitationsSource
#2David R. KargerH-Index: 83
Last. Leonid PeshkinH-Index: 31
view all 4 authors...
This paper formulates a novel problem on graphs: find the minimal subset of edges in a fully connected graph, such that the resulting graph contains all spanning trees for a set of specifed sub-graphs. This formulation is motivated by an un-supervised grammar induction problem from computational linguistics. We present a reduction to some known problems and algorithms from graph theory, provide computational complexity results, and describe an approximation algorithm.