Personal information

Glycobiology, Bioinformatics, Systems Biology, Transcriptomics

Activities

Education and qualifications (1)

University of California San Diego: La Jolla, California, US

2013 to 2020 | Ph.D. Student/Candidate (Pediatrics; Bioengineering)
Qualification
Source: Self-asserted source
Ben Kellman

Works (25)

Joint linear modeling of transcriptomics and proteomics is predictive of cancer metastasis

2025-02-20 | Preprint
Contributors: Ronit Sharma; Nikolaos Meimetis; Arjana Begzati; Shashwat Depali Nagar; Benjamin Kellman; Hratch M. Baghdassarian
Source: check_circle
Crossref

Decoding glycosylation potential from protein structure across human glycoproteins with a multi-view recurrent neural network

2024-05-15 | Preprint
Contributors: Benjamin P. Kellman; Julien Mariethoz; Yujie Zhang; Sigal Shaul; Mia Alteri; Daniel Sandoval; Mia Jeffris; Erick Armingol; Bokan Bao; Frederique Lisacek et al.
Source: check_circle
Crossref

Protein structure, a genetic encoding for glycosylation

2024-05-15 | Preprint
Contributors: Benjamin P. Kellman; Daniel Sandoval; Olga O. Zaytseva; Kelly Brock; Sabyasachi Baboo; Daniela Nachmanson; Edward B. Irvine; Erick Armingol; Nathan Mih; Yujie Zhang et al.
Source: check_circle
Crossref

Boosting with adjuvanted SCB-2019 elicits superior Fcγ-receptor engagement driven by IgG3 to SARS-CoV-2 spike

npj Vaccines
2024-01-05 | Journal article
Contributors: Wonyeong Jung; Dansu Yuan; Benjamin Kellman; Isabela Garrido da Silva Gonzalez; Ralf Clemens; Eveline Pipolo Milan; Eduardo Sprinz; José Cerbino Neto; Igor Smolenov; Galit Alter et al.
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Crossref

Preparing glycomics data for robust statistical analysis with GlyCompareCT

2022-06-01 | Preprint
Contributors: Yujie Zhang; Sridevi Krishnan; Bokan Bao; Austin W.T. Chiang; James T. Sorrentino; Song-Min Schinn; Benjamin P. Kellman; Nathan E. Lewis
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Crossref

Multiplex genome editing of mammalian cells for producing recombinant heparin

Metabolic Engineering
2022-03 | Journal article
Contributors: Bryan E. Thacker; Kristen J. Thorne; Colin Cartwright; Jeeyoung Park; Kimberly Glass; Annie Chea; Benjamin P. Kellman; Nathan E. Lewis; Zhenping Wang; Anna Di Nardo et al.
Source: check_circle
Crossref

Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing

BMC Genomics
2021 | Journal article
EID:

2-s2.0-85099917920

Part of ISSN: 14712164
Contributors: Kellman, B.P.; Baghdassarian, H.M.; Pramparo, T.; Shamie, I.; Gazestani, V.; Begzati, A.; Li, S.; Nalabolu, S.; Murray, S.; Lopez, L. et al.
Source: Self-asserted source
Ben Kellman via Scopus - Elsevier

Correcting for sparsity and interdependence in glycomics by accounting for glycan biosynthesis

Nature Communications
2021-08-17 | Journal article
Contributors: Bokan Bao; Benjamin P. Kellman; Austin W. T. Chiang; Yujie Zhang; James T. Sorrentino; Austin K. York; Mahmoud A. Mohammad; Morey W. Haymond; Lars Bode; Nathan E. Lewis
Source: check_circle
Crossref

Simple and practical sialoglycan encoding system reveals vast diversity in nature and identifies a universal sialoglycan-recognizing probe derived from AB5 toxin B subunits

2021-05-29 | Preprint
Contributors: Aniruddha Sasmal; Naazneen Khan; Zahra Khedri; Benjamin P. Kellman; Saurabh Srivastava; Andrea Verhagen; Hai Yu; Anders Bech Bruntse; Sandra Diaz; Nissi Varki et al.
Source: check_circle
Crossref

A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR)

Beilstein Journal of Organic Chemistry
2020 | Journal article
EID:

2-s2.0-85098284567

Part of ISSN: 18605397
Contributors: Kellman, B.P.; Zhang, Y.; Logomasini, E.; Meinhardt, E.; Godinez-Macias, K.P.; Chiang, A.W.T.; Sorrentino, J.T.; Liang, C.; Bao, B.; Zhou, Y. et al.
Source: Self-asserted source
Ben Kellman via Scopus - Elsevier
grade
Preferred source (of 2)‎

Big-Data Glycomics: Tools to Connect Glycan Biosynthesis to Extracellular Communication

Trends in Biochemical Sciences
2020 | Journal article
EID:

2-s2.0-85098136318

Part of ISSN: 13624326 09680004
Contributors: Kellman, B.P.; Lewis, N.E.
Source: Self-asserted source
Ben Kellman via Scopus - Elsevier

SARS-CoV-2 Infection Depends on Cellular Heparan Sulfate and ACE2

Cell
2020 | Journal article
EID:

2-s2.0-85091607317

Part of ISSN: 10974172 00928674
Contributors: Clausen, T.M.; Sandoval, D.R.; Spliid, C.B.; Pihl, J.; Perrett, H.R.; Painter, C.D.; Narayanan, A.; Majowicz, S.A.; Kwong, E.M.; McVicar, R.N. et al.
Source: Self-asserted source
Ben Kellman via Scopus - Elsevier

Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor

Cell Host and Microbe
2020 | Journal article
EID:

2-s2.0-85090566044

Part of ISSN: 19346069 19313128
Contributors: Zhao, P.; Praissman, J.L.; Grant, O.C.; Cai, Y.; Xiao, T.; Rosenbalm, K.E.; Aoki, K.; Kellman, B.P.; Bridger, R.; Barouch, D.H. et al.
Source: Self-asserted source
Ben Kellman via Scopus - Elsevier

ZNF263 is a transcriptional regulator of heparin and heparan sulfate biosynthesis

Proceedings of the National Academy of Sciences of the United States of America
2020 | Journal article
EID:

2-s2.0-85084149768

Part of ISSN: 10916490 00278424
Contributors: Weiss, R.J.; Spahn, P.N.; Toledo, A.G.; Chiang, A.W.T.; Kellman, B.P.; Li, J.; Benner, C.; Glass, C.K.; Gordts, P.L.S.M.; Lewis, N.E. et al.
Source: Self-asserted source
Ben Kellman via Scopus - Elsevier

Elucidating Human Milk Oligosaccharide biosynthetic genes through network-based multiomics integration

2020-09-03 | Preprint
Contributors: Benjamin P. Kellman; Anne Richelle; Jeong-Yeh Yang; Digantkumar Chapla; Austin W. T. Chiang; Julia Najera; Bokan Bao; Natalia Koga; Mahmoud A. Mohammad; Anders Bech Bruntse et al.
Source: check_circle
Crossref

A consensus-based and readable extension ofLinearCode forReactionRules (LiCoRR)

2020-06-01 | Preprint
Contributors: Benjamin P. Kellman; Yujie Zhang; Emma Logomasini; Eric Meinhardt; Austin W. T. Chiang; James T. Sorrentino; Chenguang Liang; Bokan Bao; Yusen Zhou; Sachiko Akase et al.
Source: check_circle
Crossref

Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing

2020-04-03 | Preprint
Contributors: Benjamin P. Kellman; Hratch M. Baghdassarian; Tiziano Pramparo; Isaac Shamie; Vahid Gazestani; Arjana Begzati; Shengzhong Li; Srinivasa Nalabolu; Sarah Murray; Linda Lopez et al.
Source: check_circle
Crossref

A perturbed gene network containing PI3K–AKT, RAS–ERK and WNT–β-catenin pathways in leukocytes is linked to ASD genetics and symptom severity

Nature Neuroscience
2019 | Journal article
EID:

2-s2.0-85072615268

Part of ISSN: 15461726 10976256
Contributors: Gazestani, V.H.; Pramparo, T.; Nalabolu, S.; Kellman, B.P.; Murray, S.; Lopez, L.; Pierce, K.; Courchesne, E.; Lewis, N.E.
Source: Self-asserted source
Ben Kellman via Scopus - Elsevier
grade
Preferred source (of 2)‎

Combating viral contaminants in CHO cells by engineering innate immunity

Scientific Reports
2019 | Journal article
EID:

2-s2.0-85067641246

Part of ISSN: 20452322
Contributors: Chiang, A.W.T.; Li, S.; Kellman, B.P.; Chattopadhyay, G.; Zhang, Y.; Kuo, C.-C.; Gutierrez, J.M.; Ghazi, F.; Schmeisser, H.; Ménard, P. et al.
Source: Self-asserted source
Ben Kellman via Scopus - Elsevier
grade
Preferred source (of 2)‎

Evolution of the exclusively human pathogen Neisseria gonorrhoeae: Human-specific engagement of immunoregulatory Siglecs

Evolutionary Applications
2019 | Journal article
EID:

2-s2.0-85060527973

Part of ISSN: 17524571 17524563
Contributors: Landig, C.S.; Hazel, A.; Kellman, B.P.; Fong, J.J.; Schwarz, F.; Agarwal, S.; Varki, N.; Massari, P.; Lewis, N.E.; Ram, S. et al.
Source: Self-asserted source
Ben Kellman via Scopus - Elsevier

NCBI’s Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements

Genes
2019-09 | Journal article | Author
Contributors: Ryan Connor; Rodney Brister; Jan Piotr Buchmann; Ward Deboutte; Rob Edwards; Joan Martí-Carreras; Mike Tisza; Vadim Zalunin; Juan Andrade-Martínez; Adrian Cantu et al.
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Multidisciplinary Digital Publishing Institute
grade
Preferred source (of 2)‎

Correcting for sparsity and non-independence in glycomic data through a systems biology framework

2019-07-05 | Preprint
Contributors: Bokan Bao; Benjamin P. Kellman; Austin W.T. Chiang; Austin K. York; Mahmoud A. Mohammad; Morey W. Haymond; Lars Bode; Nathan E. Lewis
Source: check_circle
Crossref

Human milk oligosaccharide composition predicts risk of necrotising enterocolitis in preterm infants

Gut
2018 | Journal article
EID:

2-s2.0-85050283090

Part of ISSN: 14683288
Contributors: Autran, C.A.; Kellman, B.P.; Kim, J.H.; Asztalos, E.; Blood, A.B.; Spence, E.C.H.; Patel, A.L.; Hou, J.; Lewis, N.E.; Bode, L.
Source: Self-asserted source
Ben Kellman via Scopus - Elsevier

Optimization of carbon and energy utilization through differential translational efficiency

Nature Communications
2018 | Journal article
EID:

2-s2.0-85055613437

Part of ISSN: 20411723
Contributors: Al-Bassam, M.M.; Kim, J.-N.; Zaramela, L.S.; Kellman, B.P.; Zuniga, C.; Wozniak, J.M.; Gonzalez, D.J.; Zengler, K.
Source: Self-asserted source
Ben Kellman via Scopus - Elsevier
grade
Preferred source (of 2)‎

A Systematic Evaluation of Methods for Tailoring Genome-Scale Metabolic Models

Cell Systems
2017 | Journal article
EID:

2-s2.0-85012870351

Part of ISSN: 24054720 24054712
Contributors: Opdam, S.; Richelle, A.; Kellman, B.; Li, S.; Zielinski, D.C.; Lewis, N.E.
Source: Self-asserted source
Ben Kellman via Scopus - Elsevier