Hera Vlamakis

Biochemistry, Genetics and Molecular BiologyEnvironmental ScienceMedicineAgricultural and Biological Sciences

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 34 papers. Top paper: “Structure-based protein function prediction using graph convolutional networks”.

Structure-based protein function prediction using graph convolutional networks

Nature Communications(2021)10.1038/s41467-021-23303-9

N/A

10.3DataRank · unranked

937 citations

P. Douglas Renfrew, Tomasz Kościółek, Julia Koehler Leman, Daniel Berenberg, Tommi Vatanen +9 more

Delivery mode impacts newborn gut colonization efficiency

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.01.29.919993

N/A

1.2DataRank · unranked

18 citations

Larson Hogstrom, Allison Bryant, Agnès Bergerat, Avital Cher, Shawna Pochan +9 more

Global chemical effects of the microbiome include new bile-acid conjugations

Nature(2020)10.1038/s41586-020-2047-9

N/A

0.959DataRank · unranked

595 citations

Alexey V. Melnik, Alison Vrbanac, Ting Fu, Kathryn A. Patras, Mitchell P. Christy +53 more

Remodeling of colon plasma cell repertoire within ulcerative colitis patients

Journal of Experimental Medicine(2023)10.1084/jem.20220538

N/A

0.939DataRank · unranked

31 citations

Basak Eraslan, Andrew Hudak, Eric M. Brown, Dallis Sergio, Toni Marie Delorey +13 more

Cytokine-specific autoantibodies shape the gut microbiome in autoimmune polyendocrine syndrome type 1

Journal of Allergy and Clinical Immunology(2021)10.1016/j.jaci.2021.03.025

N/A

0.914DataRank · unranked

19 citations

Martta Jokinen, Damian R. Plichta, Gerhard Liebisch, Wolfram Gronwald, Katja Dettmer +6 more

Akkermansia muciniphila phospholipid induces homeostatic immune responses

Nature(2022)10.1038/s41586-022-04985-7

N/A

0.899DataRank · unranked

400 citations

Chelsi D. Cassilly, Xiaoxi Liu, Sung‐Moo Park, Betsabeh Khoramian Tusi, Xiangjun Chen +10 more

Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin

Genome biology(2022)10.1186/s13059-022-02753-4

N/A

0.765DataRank · unranked

163 citations

Dmitry Shungin, Himel Mallick, Melanie Schirmer, Long H. Nguyen, Raivo Kolde +5 more

Inflammation-associated nitrate facilitates ectopic colonization of oral bacterium Veillonella parvula in the intestine

Nature Microbiology(2022)10.1038/s41564-022-01224-7

N/A

0.749DataRank · unranked

146 citations

Eric M. Brown, Emily R. Temple, Michelle A. Onyekaba, Ahmed M. Mohamed, Kellyanne Duncan +9 more

Alterations in Fecal Microbiomes and Serum Metabolomes of Fatigued Patients With Quiescent Inflammatory Bowel Diseases

Clinical Gastroenterology and Hepatology(2020)10.1016/j.cgh.2020.03.013

N/A

0.628DataRank · unranked

65 citations

Damian R. Plichta, Amit D. Joshi, Gracia Bonilla, Vincent Peng, Francis Colizzo +9 more

A Synthesis-Based Reverse Metabolomics Approach for the Discovery of Chemical Structures from Humans and Animals.

Research Square(2021)10.21203/rs.3.rs-820302/v1

N/A

0.464DataRank · unranked

21 citations

Emily C. Gentry, Stephanie L. Collins, Morgan Panitchpakdi, Pedro Belda‐Ferre, Allison K. Stewart +14 more

Human immunodeficiency virus and antiretroviral therapies exert distinct influences across diverse gut microbiomes

Nature Microbiology(2025)10.1038/s41564-025-02157-7

N/A

0.269DataRank · unranked

5 citations

Sambhawa Priya, Jiawu Xu, Upasana Das Adhikari, Gleb Pishchany, Ahmed M. Mohamed +13 more

Functional modulation of T follicular cells in vivo enhances antigen-specific humoral immunity

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.17.387100

N/A

0DataRank · unranked

0 citations

Hera Vlamakis, Anthony O. Gaca, Ramnik J. Xavier, Robert M. Anthony, Jose D. Pagan

Gut microbiome-mediated metabolism effects on immunity in rural and urban African populations

Nature Communications(2021)10.1038/s41467-021-25213-2

N/A

0DataRank · unranked

93 citations

Godfrey S. Temba, Hera Vlamakis, Vesla Kullaya, Furaha S. Lyamuya, Blandina T. Mmbaga +6 more

Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease

Cell Host & Microbe(2021)10.1016/j.chom.2021.06.019

N/A

0DataRank · unranked

220 citations

Damian R. Plichta, Larson Hogstrom, Nienke Z. Borren, Helena Lau, Sara Gregory +7 more

Capsular polysaccharide correlates with immune response to the human gut microbe Ruminococcus gnavus

Proceedings of the National Academy of Sciences(2021)10.1073/pnas.2007595118

N/A

0DataRank · unranked

131 citations

Eric M. Brown, Chelsi D. Cassilly, Hera Vlamakis, Ramnik J. Xavier, Jon Clardy +1 more

Population study of the gut microbiome: associations with diet, lifestyle, and cardiometabolic disease

Genome Medicine(2021)10.1186/s13073-021-01007-5

N/A

0DataRank · unranked

83 citations

Hera Vlamakis, Jonathan Lee, Luke A. Besse, Vanessa Xanthakis, Ramachandran S. Vasan +3 more

Congruent microbiome signatures in fibrosis-prone autoimmune diseases: IgG4-related disease and systemic sclerosis

Genome Medicine(2021)10.1186/s13073-021-00853-7

N/A

0DataRank · unranked

59 citations

Juhi Somani, Matthieu Pichaud, Zachary S. Wallace, Ana D. Fernandes, Cory A. Perugino +8 more

The influence of the gut microbiome on BCG-induced trained immunity

Genome biology(2021)10.1186/s13059-021-02482-0

N/A

0DataRank · unranked

51 citations

Vera P. Mourits, Valerie A. C. M. Koeken, L. Charlotte J. de Bree, Simone J.C.F.M. Moorlag, Leo A. B. Joosten +5 more

Gut microbiome ADP-ribosyltransferases are widespread phage-encoded fitness factors

Cell Host & Microbe(2021)10.1016/j.chom.2021.07.011

N/A

0DataRank · unranked

50 citations

Hugo Arellano-Santoyo, Emily R. Temple, Zachary A. Costliow, Matthieu Pichaud, A. Brantley Hall +9 more

Gut bacterial metabolites modulate endoplasmic reticulum stress

Genome biology(2021)10.1186/s13059-021-02496-8

N/A

0DataRank · unranked

47 citations

Kwontae You, Matthieu Pichaud, Henry J. Haiser, Daniel B. Graham, Hera Vlamakis +3 more

Multi-“-Omics” Profiling in Patients With Quiescent Inflammatory Bowel Disease Identifies Biomarkers Predicting Relapse

Inflammatory Bowel Diseases(2020)10.1093/ibd/izaa183

N/A

0DataRank · unranked

54 citations

Damian R. Plichta, Amit D. Joshi, Gracia Bonilla, Ruslan I. Sadreyev, Hera Vlamakis +3 more

Linking Strain Engraftment in Fecal Microbiota Transplantation With Maintenance of Remission in Crohn’s Disease

Gastroenterology(2020)10.1053/j.gastro.2020.08.045

N/A

0DataRank · unranked

68 citations

Jason Lloyd‐Price, Tommi Vatanen, Philippe Seksik, Laurent Beaugerie, Tabassome Simon +4 more

Human gut bacteria produce T H 17-modulating bile acid metabolites

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.01.08.425913

N/A

0DataRank · unranked

10 citations

Lina Yao, Yancong Zhang, Sena Bae, Gabriel D. D’Agostino, Eunha Kim +14 more

Longitudinal disease-associated gut microbiome differences in infants with early food allergic manifestations

Research Square(2021)10.21203/rs.3.rs-654476/v1

N/A

0DataRank · unranked

0 citations

Yamini V. Virkud, Ehud Dahan, Hannah Seay, Hera Vlamakis, Ramnik J. Xavier +4 more

Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease

Nature Microbiology(2020)10.1038/s41564-019-0655-7

N/A

0DataRank · unranked

104 citations

Eric A. Franzosa, Jason Bishai, John W. Annand, Akihiko Oka, Jason Lloyd‐Price +12 more

Delivery Mode Affects Stability of Early Infant Gut Microbiota

Cell Reports Medicine(2020)10.1016/j.xcrm.2020.100156

N/A

0DataRank · unranked

235 citations

Chiara Mazzoni, Larson Hogstrom, Allison Bryant, Agnès Bergerat, Avital Cher +10 more

Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level

Cell Host & Microbe(2020)10.1016/j.chom.2020.05.013

N/A

0DataRank · unranked

309 citations

Damian R. Plichta, Dmitry Shungin, Nitzan Koppel, A. Brantley Hall, Beverly Fu +6 more

The CD4+ T cell response to a commensal-derived epitope transitions from a tolerant to an inflammatory state in Crohn’s disease

Immunity(2022)10.1016/j.immuni.2022.08.016

N/A

0DataRank · unranked

58 citations

Eric M. Brown, Damian R. Plichta, Joachim Johansen, Shaina W. Twardus, Toni Marie Delorey +6 more

Longitudinal disease-associated gut microbiome differences in infants with food protein-induced allergic proctocolitis

Microbiome(2022)10.1186/s40168-022-01322-y

N/A

0DataRank · unranked

50 citations

Yamini V. Virkud, Ehud Dahan, Hannah Seay, Dvir Itzkovits, Hera Vlamakis +5 more

Lectin-Seq: a method to profile lectin-microbe interactions in native communities

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.12.14.520458

N/A

0DataRank · unranked

2 citations

Christine R. Isabella, Rebecca L. Walker, Dallis Sergio, Tony Gaca, Smrithi Raman +13 more

Gut microbiome and metabolome profiling in Framingham heart study reveals cholesterol-metabolizing bacteria

Cell(2024)10.1016/j.cell.2024.03.014

N/A

0DataRank · unranked

226 citations

Martin Stražar, Ahmed M. Mohamed, Julián Ávila-Pacheco, Rebecca L. Walker, Tina Lebar +21 more

Linking microbial genes to plasma and stool metabolites uncovers host-microbial interactions underlying ulcerative colitis disease course

Cell Host & Microbe(2024)10.1016/j.chom.2023.12.013

N/A

0DataRank · unranked

72 citations

Martin Stražar, Julián Ávila-Pacheco, Daniel F. Rojas‐Tapias, Eric M. Brown, Emily R. Temple +19 more

Integrated annotation prioritizes metabolites with bioactivity in inflammatory bowel disease

Molecular Systems Biology(2024)10.1038/s44320-024-00027-8

N/A

0DataRank · unranked

11 citations

Sena Bae, Yancong Zhang, Eunyoung Chun, Julián Ávila-Pacheco, Ludwig Geistlinger +11 more

Remodeling of human colon plasma cell repertoire in ulcerative colitis

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.02.14.480403

N/A

0DataRank · unranked

0 citations

Basak Eraslan, Andrew Hudak, Eric M. Brown, Dallis Sergio, Toni Marie Delorey +12 more