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Lana X. Garmire
University of Michigan
GeneCancerGeneticsBioinformaticsBiology
59Publications
20H-index
1,855Citations
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Publications 84
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Computational methods have reshaped the landscape of modern biology. While the biomedical community is increasingly dependent on computational tools, the mechanisms ensuring open data, open software, and reproducibility are variably enforced by academic institutions, funders, and publishers. Publications may describe the software for which source code is unavailable, documentation is incomplete or unmaintained, and analytical source code is missing. Publications that lack this information compro...
#1Bing HeH-Index: 1
#2Lana X. Garmire (UM: University of Michigan)H-Index: 20
Coronavirus disease (COVID-19) is an infectious disease discovered in 2019 and currently in outbreak across the world. Lung injury with severe respiratory failure is the leading cause of death in COVID-19, brought by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, there still lacks efficient treatment for COVID-19 induced lung injury and acute respiratory failure. Inhibition of Angiotensin-converting enzyme 2 (ACE2) caused by spike protein of SARS-CoV-2 is the most plausib...
Lung injury with severe respiratory failure is the leading cause of death in COVID-19. Inhibition of ACE2 caused by spike protein of (SARS)-CoV-2 is the most plausible mechanism of lung injury in COVID-19. We proposed six candidate drugs, including geldanamycin, panobinostat, trichostatin A, narciclasine, COL-3 and CGP-60474, that could best reverse abnormal gene expression caused by (SARS)-CoV-2-induced inhibition of ACE2 in lung cells, for the promise of treating lung injuries in COVID-19.
#1Yuheng Du (UM: University of Michigan)
#2Qianhui Huang (UM: University of Michigan)
Last. Lana X. Garmire (UM: University of Michigan)H-Index: 20
view all 4 authors...
Alignment of scRNA-Seq data is the first and one of the most critical steps of the scRNA-Seq analysis workflow, and thus the choice of proper aligners is of paramount importance. Recently, STAR an alignment method and Kallisto a pseudoalignment method have both gained a vast amount of popularity in the single cell sequencing field. However, an unbiased third-party comparison of these two methods in scRNA-Seq is lacking. Here we conduct a systematic comparison of them on a variety of Drop-seq, Fl...
1 CitationsSource
#1Bin Chen (MSU: Michigan State University)
#2Lana X. Garmire (UM: University of Michigan)H-Index: 20
Last. Xin Chen (UCSF: University of California, San Francisco)H-Index: 48
view all 6 authors...
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#1Lana X. Garmire (UM: University of Michigan)H-Index: 20
#2Zhucheng Zhan (CUHK: The Chinese University of Hong Kong)
Last. Travers ChingH-Index: 14
view all 7 authors...
Pathological images are easily accessible data type with potential as prognostic biomarkers. Here we extend Cox-nnet, a neural network based prognosis method previously used for transcriptomics data, to predict patient survival using hepatocellular carcinoma (HCC) pathological images. Cox-nnet based imaging predictions are more robust and accurate than Cox-PH. Moreover, using a novel two-stage Cox-nnet complex model, we are able to combine pathology image and transcriptomics RNA-Seq data to make...
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Maternal obesity has become a growing global health concern that may predispose the offspring to medical conditions later in life. However, the metabolic link between maternal pre-pregnant obesity and healthy offspring has not yet been fully elucidated. In this study, we conducted a case-control study using coupled untargeted and targeted metabolomics approach, from the newborn cord blood metabolomes associated with a matched maternal pre-pregnant obesity cohort of 28 cases and 29 controls. The ...
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#2Fadhl M. Al-AkwaaH-Index: 5
Last. Lana X. GarmireH-Index: 20
view all 5 authors...
Abstract Preeclampsia is a medical condition affecting 5–10% of pregnancies. It has serious effects on the health of the pregnant mother and developing fetus. While possible causes of preeclampsia are speculated, there is no consensus on its etiology. The advancement of big data and high-throughput technologies enables to study preeclampsia at the new and systematic level. In this review, we first highlight the recent progress made in the field of preeclampsia research using various omics techno...
1 CitationsSource
Computational methods have reshaped the landscape of modern biology. While the biomedical community is increasingly dependent on computational tools, the mechanisms ensuring open data, open software, and reproducibility are variably enforced. Publications may describe the software for which source code is unavailable, documentation is incomplete or unmaintained, and analytical source code is missing. Publications that lack this information compromise the role of peer review in evaluating technic...
#1Bin Chen (MSU: Michigan State University)
#2Lana X. Garmire (UM: University of Michigan)
Last. Xin Chen (UCSF: University of California, San Francisco)H-Index: 48
view all 6 authors...
Hepatocellular carcinoma (HCC) is the most common form of primary adult liver cancer. After nearly a decade with sorafenib as the only approved treatment, multiple new agents have demonstrated efficacy in clinical trials, including the targeted therapies regorafenib, lenvatinib and cabozantinib, the anti-angiogenic antibody ramucirumab, and the immune checkpoint inhibitors nivolumab and pembrolizumab. Although these agents offer new promise to patients with HCC, the optimal choice and sequence o...
2 CitationsSource
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