Marcin P. Joachimiak - Publications, H-index & Citations

Marcin P. Joachimiak

lawrence berkeley national laboratory

29H指数

104论文数

6.1K被引数

收录论文 37

发表时间

KG-Microbe: Building modular and scalable knowledge graphs for microbiome and microbial sciences KG-Microbe：构建用于微生物组和微生物科学的模块化和可扩展知识图谱

GigaScience

IF3.9

2026-07-10

OAAI

Brook E Santangelo; Harshad Hegde; J Harry Caufield; Justin Reese; Tomas Kliegr; Lawrence E Hunter; Catherine A Lozupone; Christopher J Mungall; Marcin P Joachimiak

Representing dental caries and dysbiosis within the oral microbiome in the Oral Health and Disease Ontology 在口腔健康与疾病本体论中表征口腔微生物组内的龋齿和菌群失调

Journal of Biomedical Semantics

IF2

2026-04-24

PREAI

Duncan, William D.; Sabharwal, Amarpreet; Diehl, Alexander D.; Dutta, Nivedita; Diller, Matthew; Joachimiak, Marcin P.; Chandrasekharan, Gopikrishnan M.

Explaining word embeddings with perfect fidelity: a case study in predicting research impact 解释词嵌入的完美保真度：一项预测研究影响的案例研究

Machine Learning

IF2.9

2025-10-30

PREAI

Lucie Dvořáčková; Marcin P. Joachimiak; Michal Černý; Adriana Kubecová; Vilém Sklenák; Tomáš Kliegr

Explainable rule-based prediction of cultivation media for microbes 基于可解释规则的微生物培养基预测

Computational and Structural Biotechnology Journal

IF4.1

2025-10-14

OAAI

Petr Máša; Tomáš Kliegr; Marcin P. Joachimiak

The Artificial Intelligence Ontology: LLM-Assisted Construction of AI Concept Hierarchies 人工智能本体：LLM辅助构建AI概念层级

APPLIED ONTOLOGY

IF3.5

2025-03-02

OAAI

Joachimiak, Marcin P.; Miller, Mark A.; Caufield, J. Harry; Ly, Ryan; Harris, Nomi L.; Tritt, Andrew; Mungall, Christopher J.; Bouchard, Kristofer E.

Estimating geographic variation of infection fatality ratios during epidemics 估计流行期间感染死亡率的地理变化

INFECTIOUS DISEASE MODELLING

IF2.5

2024-06-01

OAAI

Ladau, Joshua; Brodie, Eoin L.; Falco, Nicola; Bansal, Ishan; Hoffman, Elijah B.; Joachimiak, Marcin P.; Mora, Ana M.; Walker, Angelica M.; Wainwright, Haruko M.; Wu, Yulun; Pavicic, Mirko; Jacobson, Daniel; Hess, Matthias; Brown, James B.; Abuabara, Katrina

Integrating biological knowledge for mechanistic inference in the host-associated microbiome

FRONTIERS IN MICROBIOLOGY

IF4.5

2024-04-04

OAAI

Santangelo, Brook E.; Apgar, Madison; Colorado, Angela Sofia Burkhart; Martin, Casey G.; Sterrett, John; Wall, Elena; Joachimiak, Marcin P.; Hunter, Lawrence E.; Lozupone, Catherine A.

A bacterial sensor taxonomy across earth ecosystems for machine learning applications 用于机器学习应用的跨地球生态系统的细菌传感器分类法

MSYSTEMS

IF4.6

2024-01-23

OAAI

Park, Helen; Joachimiak, Marcin P.; Jungbluth, Sean P.; Yang, Ziming; Riehl, William J.; Canon, R. Shane; Arkin, Adam P.; Dehal, Paramvir S.

GRAPE for fast and scalable graph processing and random-walk-based embedding GRAPE用于快速和可扩展的图形处理和基于随机游走的嵌入

NATURE COMPUTATIONAL SCIENCE

IF18.3

2023-06-26

OAAI

Cappelletti, Luca; Fontana, Tommaso; Casiraghi, Elena; Ravanmehr, Vida; Callahan, Tiffany J. J.; Cano, Carlos; Joachimiak, Marcin P. P.; Mungall, Christopher J. J.; Robinson, Peter N. N.; Reese, Justin; Valentini, Giorgio

Developing a Knowledge Graph for Pharmacokinetic Natural Product-Drug Interactions 开发药代动力学天然产物-药物相互作用的知识图谱

JOURNAL OF BIOMEDICAL INFORMATICS

IF4.5

2023-04-01

OAAI

Taneja, Sanya B.; Callahan, Tiffany J.; Paine, Mary F.; Kane-Gill, Sandra L.; Kilicoglu, Halil; Joachimiak, Marcin P.; Boyce, Richard D.

Why was this cited? Explainable machine learning applied to COVID-19 research literature

SCIENTOMETRICS

IF3.5

2022-04-09

OAAI

Beranova, Lucie; Joachimiak, Marcin P.; Kliegr, Tomas; Rabby, Gollam; Sklenak, Vilem

Supervised learning with word embeddings derived from PubMed captures latent knowledge about protein kinases and cancer

genomics proteomics bioinformatics

IF2.8

2021-12-08

OAAI

Ravanmehr, Vida; Blau, Hannah; Cappelletti, Luca; Fontana, Tommaso; Carmody, Leigh; Coleman, Ben; George, Joshy; Reese, Justin; Joachimiak, Marcin; Bocci, Giovanni; Hansen, Peter; Bult, Carol; Rueter, Jens; Casiraghi, Elena; Valentini, Giorgio; Mungall, Christopher; Oprea, Tudor, I; Robinson, Peter N.

A KBase case study on genome-wide transcriptomics and plant primary metabolism in response to drought stress in Sorghum

current opinion in plant biology

IF4.5

2021-12-01

OAAI

Kumari, Sunita; Kumar, Vivek; Beilsmith, Kathleen; Seaver, Samuel M. D.; Canon, Shane; Dehal, Paramvir; Gu, Tian; Joachimiak, Marcin; Lerma-Ortiz, Claudia; Liu, Filipe; Lu, Zhenyuan; Pearson, Eric; Ranjan, Priya; Riel, William; Henry, Christopher S.; Arkin, Adam P.; Ware, Doreen

Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities (vol 6, e01194-20, 2021)微生物组元数据标准: 国家微生物组数据协作研讨会和后续活动的报告 (第6卷，e01194-20，2021)

MSYSTEMS

IF4.6

2021-06-29

OAAI

Vangay, Pajau; Burgin, Josephine; Johnston, Anjanette; Beck, Kristen L.; Berrios, Daniel C.; Blumberg, Kai; Canon, Shane; Chain, Patrick; Chandonia, John-Marc; Christianson, Danielle; Costes, Sylvain V.; Damerow, Joan; Duncan, William D.; Dundore-Arias, Jose Pablo; Fagnan, Kjiersten; Galazka, Jonathan M.; Gibbons, Sean M.; Hays, David; Hervey, Judson; Hu, Bin; Hurwitz, Bonnie L.; Jaiswal, Pankaj; Joachimiak, Marcin P.; Kinkel, Linda; Ladau, Joshua; Martin, Stanton L.; McCue, Lee Ann; Miller, Kayd; Mouncey, Nigel; Mungall, Chris; Pa, Evangelos; Reddy, T. B. K.; Richardson, Lorna; Roux, Simon; Schriml, Lynn M.; Shaffer, Justin P.; Sundaramurthi, Jagadish Chandrabose; Thompson, Luke R.; Timme, Ruth E.; Zheng, Jie; Wood-Charlson, Elisha M.; Eloe-Fadrosh, Emiley A.

Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities 微生物组元数据标准: 国家微生物组数据协作研讨会和后续活动的报告

MSYSTEMS

IF4.6

2021-02-23

OAAI

Vangay, Pajau; Burgin, Josephine; Johnston, Anjanette; Beck, Kristen L.; Berrios, Daniel C.; Blumberg, Kai; Canon, Shane; Chain, Patrick; Chandonia, John-Marc; Christianson, Danielle; Costes, Sylvain V.; Damerow, Joan; Duncan, William D.; Dundore-Arias, Jose Pablo; Fagnan, Kjiersten; Galazka, Jonathan M.; Gibbons, Sean M.; Hays, David; Hervey, Judson; Hu, Bin; Hurwitz, Bonnie L.; Jaiswal, Pankaj; Joachimiak, Marcin P.; Kinkel, Linda; Ladau, Joshua; Martin, Stanton L.; McCue, Lee Ann; Miller, Kayd; Mouncey, Nigel; Mungall, Chris; Pafilis, Evangelos; Reddy, T. B. K.; Richardson, Lorna; Roux, Simon; Schriml, Lynn M.; Shaffer, Justin P.; Sundaramurthi, Jagadish Chandrabose; Thompson, Luke R.; Timme, Ruth E.; Zheng, Jie; Wood-Charlson, Elisha M.; Eloe-Fadrosh, Emiley A.

Zinc against COVID-19? Symptom surveillance and deficiency risk groups

PLOS NEGLECTED TROPICAL DISEASES

IF3.4

2021-01-04

OAAI

Joachimiak, Marcin P.

KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response KG-COVID-19: 一种生成用于新型冠状病毒肺炎响应的定制知识图的框架

PATTERNS

IF7.4

2021-01-01

OAAI

Reese, Justin T.; Unni, Deepak; Callahan, Tiffany J.; Cappelletti, Luca; Ravanmehr, Vida; Carbon, Seth; Shefchek, Kent A.; Good, Benjamin M.; Balhoff, James P.; Fontana, Tommaso; Blau, Hannah; Matentzoglu, Nicolas; Harris, Nomi L.; Munoz-Torres, Monica C.; Haendel, Melissa A.; Robinson, Peter N.; Joachimiak, Marcin P.; Mungall, Christopher J.

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species 君主倡议2019年: 一个将表型与跨物种基因型联系起来的综合数据和分析平台

NUCLEIC ACIDS RESEARCH

IF13.1

2019-11-08

151

OAAI

Shefchek, Kent A.; Harris, Nomi L.; Gargano, Michael; Matentzoglu, Nicolas; Unni, Deepak; Brush, Matthew; Keith, Daniel; Conlin, Tom; Vasilevsky, Nicole; Zhang, Xingmin Aaron; Balhoff, James P.; Babb, Larry; Bello, Susan M.; Blau, Hannah; Bradford, Yvonne; Carbon, Seth; Carmody, Leigh; Chan, Lauren E.; Cipriani, Valentina; Cuzick, Alayne; Della Rocca, Maria; Dunn, Nathan; Essaid, Shahim; Fey, Petra; Grove, Chris; Gourdine, Jean-Phillipe; Hamosh, Ada; Harris, Midori; Helbig, Ingo; Hoatlin, Maureen; Joachimiak, Marcin; Jupp, Simon; Lett, Kenneth B.; Lewis, Suzanna E.; McNamara, Craig; Pendlington, Zoe M.; Pilgrim, Clare; Putman, Tim; Ravanmehr, Vida; Reese, Justin; Riggs, Erin; Robb, Sofia; Roncaglia, Paola; Seager, James; Segerdell, Erik; Similuk, Morgan; Storm, Andrea L.; Thaxon, Courtney; Thessen, Anne; Jacobsen, Julius O. B.; McMurry, Julie A.; Groza, Tudor; Koehler, Sebastian; Smedley, Damian; Robinson, Peter N.; Mungall, Christopher J.; Haendel, Melissa A.; Munoz-Torres, Monica C.; Osumi-Sutherland, David

How many rare diseases are there?罕见病有多少种？

NATURE REVIEWS DRUG DISCOVERY

IF101.8

2019-11-05

235

OAAI

Haendel, Melissa; Vasilevsky, Nicole; Unni, Deepak; Bologa, Cristian; Harris, Nomi; Rehm, Heidi; Hamosh, Ada; Baynam, Gareth; Groza, Tudor; McMurry, Julie; Dawkins, Hugh; Rath, Ana; Thaxon, Courtney; Bocci, Giovanni; Joachimiak, Marcin P.; Koehler, Sebastian; Robinson, Peter N.; Mungall, Chris; Oprea, Tudor I.

Semantic integration of clinical laboratory tests from electronic health records for deep phenotyping and biomarker discovery

NPJ DIGITAL MEDICINE

IF15.1

2019-05-02

OAAI

Zhang, Xingmin Aaron; Yates, Amy; Vasilevsky, Nicole; Gourdine, J. P.; Callahan, Tiffany J.; Carmody, Leigh C.; Danis, Daniel; Joachimiak, Marcin P.; Ravanmehr, Vida; Pfaff, Emily R.; Champion, James; Robasky, Kimberly; Xu, Hao; Fecho, Karamarie; Walton, Nephi A.; Zhu, Richard L.; Ramsdill, Justin; Mungall, Christopher J.; Koehler, Sebastian; Haendel, Melissa A.; McDonald, Clement J.; Vreeman, Daniel J.; Peden, David B.; Bennett, Tellen D.; Feinstein, James A.; Martin, Blake; Stefanski, Adrianne L.; Hunter, Lawrence E.; Chute, Christopher G.; Robinson, Peter N.

研究方向