Benjamin P Kellman
Cambridge
Bioinformatics PhD @ UCSD | Research Fellow @ Ragon Institute at MGH, MIT, and Harvard | glycan metabolism, gene expression, NGS, pathology (he/him)
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Articles by Benjamin P Kellman
Antithrombin-binding heparan sulfate is ubiquitously expressed in epithelial cells and suppresses pancreatic tumorigenesis
Abstract 3-O-sulfation of heparan sulfate (HS) is the key determinant for binding and activation of antithrombin III (AT). This interaction is the basis of heparin treatment to prevent thrombotic events and excess coagulation. Antithrombin-binding HS (HSAT) is expressed in human tissues but is thought to be expressed in the subendothelial space, mast cells, and follicular fluid. Here, we show that HSAT is ubiquitously expressed in the basement membranes of epithelial cells in multiple tissues.
"Elucidating Human Milk Oligosaccharide Biosynthetic Genes Through Netw" by Benjamin P Kellman, Anne Richelle et al.
Keywords Glycosyltransferases, Humans, Infant, Milk, Human, Oligosaccharides, Glycomics, Polysaccharides, Biochemical networks Abstract Human Milk Oligosaccharides (HMOs) are abundant carbohydrates fundamental to infant health and development. Although these oligosaccharides were discovered more than half a century ago, their biosynthesis in the mammary gland remains largely uncharacterized.
Boosting with adjuvanted SCB-2019 elicits superior Fcγ-receptor engagement driven by IgG3 to SARS-CoV-2 spike - npj Vaccines
Abstract With the continued emergence of variants of concern, the global threat of COVID-19 persists, particularly in low- and middle-income countries with limited vaccine access. Protein-based vaccines, such as SCB-2019, can be produced on a large scale at a low cost while antigen design and adjuvant use can modulate efficacy and safety.
Optimal balancing of clinical factors in large scale clinical RNA-Seq studies
New Results doi: https://doi.org/10.1101/2021.06.30.450639 Abstract Omics technologies are ubiquitous in biomedical research. However, improper sample selection is an often-overlooked complication with large omics studies, resulting in confounding effects that can disrupt the internal validity of a study and lead to false conclusions.
Systems glycobiology for discovering drug targets, biomarkers, and rational designs for glyco-immunotherapy
Austin W. T. Chiang ORCID: orcid.org/0000-0001-6514-56121,2 na1, 1,2,3 na1, Benjamin P. Kellman1,2,3, Bokan Bao1,2,3, James T. Sorrentino1,2,3, Chenguang Liang1,4, Chih-Chung Kuo1,2,4, Helen O. Masson1,4 & Nathan E. Lewis1,2,4,5 Journal of Biomedical Science volume 28, Article number: 50 (2021) Cite this article Abstract Cancer immunotherapy has revolutionized treatment and led to an unprecedented wave of immuno-oncology research during the past two decades.
Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing
Research article Open Access Published: 21 January 2021 Benjamin P. Kellman1,2 na1, 1,2 na1, Tiziano Pramparo3, Isaac Shamie1,2, Vahid Gazestani1,3, Arjana Begzati4, Shangzhong Li1,5, Srinivasa Nalabolu3, Sarah Murray6, Linda Lopez3, Karen Pierce3, Eric Courchesne3 & Nathan E.
Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity
Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity Cameron Martino, Benjamin P. Kellman, Daniel R. Sandoval, Thomas Mandel Clausen, Clarisse A. Marotz, Se Jin Song, Stephen Wandro, Livia S. Zaramela, Rodolfo Antonio Salido Benítez, Qiyun Zhu, Erick Armingol, Yoshiki Vázquez-Baeza, Daniel McDonald, James T. Sorrentino, Bryn Taylor, Pedro Belda-Ferre, Chenguang Liang, Yujie Zhang, Luca Schifanella, Nichole R. Klatt, Aki S.
ZNF263 is a transcriptional regulator of heparin and heparan sulfate biosynthesis
Recent research raises the prospect that such activity should be taken into account in order to better tailor therapies.
A perturbed gene network containing PI3K-AKT, RAS-ERK and WNT-β-catenin pathways in leukocytes is linked to ASD genetics and symptom severity
Abstract Hundreds of genes are implicated in autism spectrum disorder (ASD), but the mechanisms through which they contribute to ASD pathophysiology remain elusive. Here we analyzed leukocyte transcriptomics from 1- to 4-year-old male toddlers with ASD or typical development from the general population. We discovered a perturbed gene network that includes highly expressed genes during fetal brain development.
Optimization of carbon and energy utilization through differential translational efficiency
We carried out RNA-seq and Ribo-seq experiments for autotrophic cultures of C. ljungdahlii grown either on CO or H :CO and heterotrophic cultures grown on fructose. To enable direct comparison between transcription and translation, strand-specific RNA-seq libraries were prepared from the same lysates used for Ribo-seq experiments in biological duplicates. RNA-seq and Ribo-seq libraries were deeply sequenced (Supplementary Fig.
Human milk oligosaccharide composition predicts risk of necrotising enterocolitis in preterm infants
Objective Necrotising enterocolitis (NEC) is one of the most common and often fatal intestinal disorders in preterm infants. Markers to identify at-risk infants as well as therapies to prevent and treat NEC are limited and urgently needed. NEC incidence is significantly lower in breast-fed compared with formula-fed infants. Infant formula lacks human milk oligosaccharides (HMO), such as disialyllacto-N-tetraose (DSLNT), which prevents NEC in neonatal rats.
Human milk oligosaccharide composition predicts risk of necrotising enterocolitis in preterm infants
Objective Necrotising enterocolitis (NEC) is one of the most common and often fatal intestinal disorders in preterm infants. Markers to identify at-risk infants as well as therapies to prevent and treat NEC are limited and urgently needed. NEC incidence is significantly lower in breast-fed compared with formula-fed infants. Infant formula lacks human milk oligosaccharides (HMO), such as disialyllacto-N-tetraose (DSLNT), which prevents NEC in neonatal rats.
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