---
title: "Molecular Biology — papers, page 2"
description: "Molecular Biology: 85 papers of the Elamur Research library · page 2 of 2 · 26–85, the most cited first — our summary of each, its ideas, references and…"
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---
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# 🧬 Molecular Biology

85 papers · page 2 of 2 · 26–85 · the most cited first · [all shelves](https://md.research.elamur.ai/free/en/shelves/)

Molecular Biology is a subfield of Biochemistry, Genetics and Molecular Biology in the OpenAlex classification of science. The topics most of its papers here are on: «Biomedical Text Mining and Ontologies», «Machine Learning in Bioinformatics», «Genomics and Phylogenetic Studies».

## Papers

[← prev](https://md.research.elamur.ai/free/en/shelves/biochemistry-genetics-and-molecular-biology/molecular-biology/) [1](https://md.research.elamur.ai/free/en/shelves/biochemistry-genetics-and-molecular-biology/molecular-biology/) **2**

26. [**A Neural Layered Model for Nested Named Entity Recognition**Meizhi Ju, Makoto Miwa, Sophia Ananiadou*2018 · 378 citations*](https://md.research.elamur.ai/free/en/papers/ju-2018-neural-layered-model-nested-named/)
27. [**Temporal Annotation in the Clinical Domain**William F. Styler IV, Steven Bethard, Sean Finan, et al.*2014 · 349 citations*](https://md.research.elamur.ai/free/en/papers/iv-2014-temporal-annotation-clinical-domain/)
28. [**Lessons from Natural Language Inference in the Clinical Domain**Alexey Romanov, Chaitanya Shivade*2018 · 343 citations*](https://md.research.elamur.ai/free/en/papers/romanov-2018-lessons-natural-language-inference-clinical/)
29. [**A Corpus with Multi-Level Annotations of Patients, Interventions and Outcomes to Support Language Processing for Medical Literature**Benjamin Nye, Junyi Jessy Li, Roma Patel, et al.*2018 · 293 citations*](https://md.research.elamur.ai/free/en/papers/nye-2018-corpus-multi-level-annotations-patients/)
30. [**Modeling Biological Processes for Reading Comprehension**Jonathan Berant, Vivek Srikumar, Pei-Chun Chen, et al.*2014 · 288 citations*](https://md.research.elamur.ai/free/en/papers/berant-2014-modeling-biological-processes-reading-comprehension/)
31. [**emrQA: A Large Corpus for Question Answering on Electronic Medical Records**Anusri Pampari, Preethi Raghavan, Jennifer Liang, et al.*2018 · 285 citations*](https://md.research.elamur.ai/free/en/papers/pampari-2018-emrqa-large-corpus-question-answering/)
32. [**Weakly Supervised Learning for Hedge Classification in Scientific Literature**Ben Medlock, Ted Briscoe*2007 · 266 citations*](https://md.research.elamur.ai/free/en/papers/medlock-2007-weakly-supervised-learning-hedge-classification/)
33. [**An Analysis of Simple Data Augmentation for Named Entity Recognition**Xiang Dai, Heike Adel*2020 · 264 citations*](https://md.research.elamur.ai/free/en/papers/dai-2020-analysis-simple-data-augmentation-named/)
34. [**SemEval-2016 Task 12: Clinical TempEval**Steven Bethard, Guergana Savova, Wei-Te Chen, et al.*2016 · 263 citations*](https://md.research.elamur.ai/free/en/papers/bethard-2016-semeval-2016-task-12-clinical/)
35. [**From Light to Rich ERE: Annotation of Entities, Relations, and Events**Zhiyi Song, Ann Bies, Stephanie Strassel, et al.*2015 · 263 citations*](https://md.research.elamur.ai/free/en/papers/song-2015-light-rich-ere-annotation-entities/)
36. [**Pretrained Language Models for Biomedical and Clinical Tasks: Understanding and Extending the State-of-the-Art**Patrick Lewis, Myle Ott, Jingfei Du, et al.*2020 · 240 citations*](https://md.research.elamur.ai/free/en/papers/lewis-2020-pretrained-language-models-biomedical-clinical/)
37. [**The BioScope corpus: annotation for negation, uncertainty and their scope in biomedical texts**György Szarvas, Veronika Vincze, Richárd Farkas, et al.*2008 · 240 citations*](https://md.research.elamur.ai/free/en/papers/szarvas-2008-bioscope-corpus-annotation-negation-uncertainty/)
38. [**Richer Event Description: Integrating event coreference with temporal, causal and bridging annotation**Tim O'Gorman, Kristin Wright-Bettner, Martha Palmer*2016 · 223 citations*](https://md.research.elamur.ai/free/en/papers/gorman-2016-richer-event-description-integrating-event/)
39. [**Loosely Tree-Based Alignment for Machine Translation**Daniel Gildea*2003 · 220 citations*](https://md.research.elamur.ai/free/en/papers/gildea-2003-loosely-tree-based-alignment-machine/)
40. [**SciREX: A Challenge Dataset for Document-Level Information Extraction**Sarthak Jain, Madeleine van Zuylen, Hannaneh Hajishirzi, et al.*2020 · 217 citations*](https://md.research.elamur.ai/free/en/papers/jain-2020-scirex-challenge-dataset-document-level/)
41. [**Learning Word-Class Lattices for Definition and Hypernym Extraction**Roberto Navigli, Paola Velardi*2010 · 201 citations*](https://md.research.elamur.ai/free/en/papers/navigli-2010-learning-word-class-lattices-definition/)
42. [**Appendix F: MUC-7 Coreference Task Definition (version 3.0)**Lynette Hirschman, Nancy Chinchor*1998 · 186 citations*](https://md.research.elamur.ai/free/en/papers/hirschman-1998-appendix-f-muc-7-coreference/)
43. [**Learning the Scope of Hedge Cues in Biomedical Texts**Roser Morante, Walter Daelemans*2009 · 175 citations*](https://md.research.elamur.ai/free/en/papers/morante-2009-learning-scope-hedge-cues-biomedical/)
44. [**Task-oriented Evaluation of Syntactic Parsers and Their Representations**Yusuke Miyao, Rune Sætre, Kenji Sagae, et al.*2008 · 129 citations*](https://md.research.elamur.ai/free/en/papers/miyao-2008-task-oriented-evaluation-syntactic-parsers/)
45. [**Hedge Classification in Biomedical Texts with a Weakly Supervised Selection of Keywords**György Szarvas*2008 · 107 citations*](https://md.research.elamur.ai/free/en/papers/szarvas-2008-hedge-classification-biomedical-texts-weakly/)
46. [**Identifying the Information Structure of Scientific Abstracts: An Investigation of Three Different Schemes**Yufan Guo, Anna Korhonen, Maria Liakata, et al.*2010 · 93 citations*](https://md.research.elamur.ai/free/en/papers/guo-2010-identifying-information-structure-scientific-abstracts/)
47. [**Statistical Anaphora Resolution in Biomedical Texts**Caroline Gasperin, Ted Briscoe*2008 · 66 citations*](https://md.research.elamur.ai/free/en/papers/gasperin-2008-statistical-anaphora-resolution-biomedical-texts/)
48. [**A Linguistic Resource for Discovering Event Structures and Resolving Event Coreference**Cosmin Bejan, Sanda Harabagiu*2008 · 64 citations*](https://md.research.elamur.ai/free/en/papers/bejan-2008-linguistic-resource-discovering-event-structures/)
49. [**The Arabic Ontology — An Arabic Wordnet with Ontologically Clean Content**Mustafa Jarrar*2021 · 61 citations*](https://md.research.elamur.ai/free/en/papers/jarrar-2022-arabic-ontology-arabic-wordnet-ontologically/)
50. [**Joint Event Trigger Identification and Event Coreference Resolution with Structured Perceptron**Jun Araki, Teruko Mitamura*2015 · 56 citations*](https://md.research.elamur.ai/free/en/papers/araki-2015-joint-event-trigger-identification-event/)
51. [**Findings of the WMT 2019 Biomedical Translation Shared Task: Evaluation for MEDLINE Abstracts and Biomedical Terminologies**Rachel Bawden, Kevin Bretonnel Cohen, Cristian Grozea, et al.*2019 · 54 citations*](https://md.research.elamur.ai/free/en/papers/bawden-2019-findings-wmt-2019-biomedical-translation/)
52. [**Overview of BioNLP 2011 Protein Coreference Shared Task**Ngan Nguyen, Jin-Dong Kim, Jun'ichi Tsujii*2011 · 32 citations*](https://md.research.elamur.ai/free/en/papers/nguyen-2011-overview-bionlp-2011-protein-coreference/)
53. [**ChEMU-Ref: A Corpus for Modeling Anaphora Resolution in the Chemical Domain**Biaoyan Fang, Christian Druckenbrodt, Saber A Akhondi, et al.*2021 · 27 citations*](https://md.research.elamur.ai/free/en/papers/fang-2021-chemu-ref-corpus-modeling-anaphora/)
54. [**The Taming of Reconcile as a Biomedical Coreference Resolver**Youngjun Kim, Ellen Riloff, Nathan Gilbert*2011 · 27 citations*](https://md.research.elamur.ai/free/en/papers/kim-2011-taming-reconcile-as-biomedical-coreference/)
55. [**Pronominal and Sortal Anaphora Resolution for Biomedical Literature**Yu-Hsiang Lin, Tyne Liang*2004 · 23 citations*](https://md.research.elamur.ai/free/en/papers/lin-2004-pronominal-sortal-anaphora-resolution-biomedical/)
56. [**Cross-Document, Cross-Language Event Coreference Annotation Using Event Hoppers**Zhiyi Song, Ann Bies, Justin Mott, et al.*2018 · 18 citations*](https://md.research.elamur.ai/free/en/papers/song-2018-cross-document-cross-language-event/)
57. [**An NP-Cluster Based Approach to Coreference Resolution**Xiaofeng Yang, Jian Su, GuoDong Zhou, et al.*2004 · 18 citations*](https://md.research.elamur.ai/free/en/papers/yang-2004-np-cluster-based-approach-coreference/)
58. [**Coreference Resolution for the Biomedical Domain: A Survey**Pengcheng Lu, Massimo Poesio*2021 · 17 citations*](https://md.research.elamur.ai/free/en/papers/lu-2021-coreference-resolution-biomedical-domain-survey/)
59. [**Al –-Khalil : The Arabic Linguistic Ontology Project**Hassina Aliane, Zaia Alimazighi, Ahmed Cherif Mazari*2010 · 16 citations*](https://md.research.elamur.ai/free/en/papers/aliane-2010-al-khalil-arabic-linguistic-ontology/)
60. [**Exploiting Coreference Annotations for Text-to-Hypertext Conversion**Anke Holler, Jan Frederik Maas, Angelika Storrer*2004 · 16 citations*](https://md.research.elamur.ai/free/en/papers/holler-2004-exploiting-coreference-annotations-text-hypertext/)
61. [**Cross-document coreference: An approach to capturing coreference without context**Kristin Wright-Bettner, Martha Palmer, Guergana Savova, et al.*2019 · 15 citations*](https://md.research.elamur.ai/free/en/papers/bettner-2019-cross-document-coreference-approach-capturing/)
62. [**Towards Cross-Domain PDTB-Style Discourse Parsing**Evgeny Stepanov, Giuseppe Riccardi*2014 · 15 citations*](https://md.research.elamur.ai/free/en/papers/stepanov-2014-cross-domain-pdtb-style-discourse/)
63. [**New Arabic Medical Dataset for Diseases Classification**Jaafar Hammoud, Aleksandra Vatian, Natalia Dobrenko, et al.*2021 · 14 citations*](https://md.research.elamur.ai/free/en/papers/hammoud-2021-new-arabic-medical-dataset-diseases/)
64. [**Medical Term Extraction in an Arabic Medical Corpus**Doaa Samy, Antonio Moreno-Sandoval, Conchi Bueno-Díaz, et al.*2012 · 13 citations*](https://md.research.elamur.ai/free/en/papers/samy-2012-medical-term-extraction-arabic-medical/)
65. [**Towards Ontology Construction with Language Models**Maurice Funk, Simon Hosemann, Jean Christoph Jung, et al.*2023 · 12 citations*](https://md.research.elamur.ai/free/en/papers/funk-2023-towards-ontology-construction-language-models/)
66. [**Domain Adaptation of Coreference Resolution for Radiology Reports**Emilia Apostolova, Noriko Tomuro, Pattanasak Mongkolwat, et al.*2012 · 12 citations*](https://md.research.elamur.ai/free/en/papers/apostolova-2012-domain-adaptation-coreference-resolution-radiology/)
67. [**SciCorp: A Corpus of English Scientific Articles Annotated for Information Status Analysis**Ina Roesiger*2016 · 11 citations*](https://md.research.elamur.ai/free/en/papers/roesiger-2016-scicorp-corpus-english-scientific-articles/)
68. [**Negation scope and spelling variation for text-mining of Danish electronic patient records**Cecilia Engel Thomas, Peter Bjødstrup Jensen, Thomas Werge, et al.*2014 · 9 citations*](https://md.research.elamur.ai/free/en/papers/thomas-2014-negation-scope-spelling-variation-text/)
69. [**Developing an Arabic Infectious Disease Ontology to Include Non-Standard Terminology**Lama Alsudias, Paul Rayson*2020 · 5 citations*](https://md.research.elamur.ai/free/en/papers/alsudias-2020-developing-arabic-infectious-disease-ontology/)
70. [**Agent-Based Uncertainty Awareness Improves Automated Radiology Report Labeling with an Open-Source Large Language Model**Hadas Ben-Atya, Naama Gavrielov, Zvi Badash, et al.*2025 · 3 citations*](https://md.research.elamur.ai/free/en/papers/ben-atya-2025-agent-based-uncertainty-awareness-improves/)
71. [**Automatic Suggestions Help Extending Eventive Ontology: A Case Study on SynSemClass**Jana Straková, Eva Fučíková, Zdenka Uresova, et al.*2026 · 1 citation*](https://md.research.elamur.ai/free/en/papers/strakova-2026-automatic-suggestions-help-extending-eventive/)
72. [**EPOP: A Benchmark Corpus for Assessing NLP Models on Structured Information Extraction in Plant Health**Claire Nedellec, Marine Courtin, Xinzhi Yao, et al.*2026 · 1 citation*](https://md.research.elamur.ai/free/en/papers/nedellec-2026-epop-benchmark-corpus-assessing-nlp/)
73. [**Unsupervised Labelling of Mutation Triggers in Welsh**Nicolás Gutiérrez-Rolón, Fernando Alva-Manchego*2026 · 1 citation*](https://md.research.elamur.ai/free/en/papers/rolon-2026-unsupervised-labelling-mutation-triggers-welsh/)
74. [**How to construct a multi-lingual domain ontology**Nitsan Chrizman, Alon Itai*2014 · 1 citation*](https://md.research.elamur.ai/free/en/papers/chrizman-2014-how-construct-multi-lingual-domain/)
75. [**Effect of Out Of Vocabulary Terms on Inferring Eligibility Criteria for a Retrospective Study in Hebrew EHR**Raphael Cohen, Michael Elhadad*2013 · 1 citation*](https://md.research.elamur.ai/free/en/papers/cohen-2013-effect-out-vocabulary-terms-inferring/)
76. [**A Dataset of Psychiatric Hospital Notes with Temporal Information Annotations**Timothy A. Miller, Gaby Dinh, David Harris, et al.*2026*](https://md.research.elamur.ai/free/en/papers/miller-2026-dataset-psychiatric-hospital-notes-temporal/)
77. [**Extracting Medical Image-Related Entities from Spanish Electronic Health Records Using NER Methods**Alexander Platas, Marcos Merino, Elena Zotova, et al.*2026*](https://md.research.elamur.ai/free/en/papers/platas-2026-extracting-medical-image-related-entities/)
78. [**JPPB: Automatic Construction of a Soft-Labeled Japanese Patient Phrase Bank for Symptom Normalization**Tomohiro Nishiyama, Mana Kuramoto, Shoko Wakamiya, et al.*2026*](https://md.research.elamur.ai/free/en/papers/nishiyama-2026-jppb-automatic-construction-soft-labeled/)
79. [**MUC-4 Revisited: Document-level Event Analysis beyond Span-based Arguments**Helene Bøsei Olsen, Erik Velldal, Lilja Øvrelid*2026*](https://md.research.elamur.ai/free/en/papers/olsen-2026-muc-4-revisited-document-level/)
80. [**Towards Corpus-Based Population and Visualization of ISO 24617-8 Ontology (Short Paper)**Maciej Ogrodniczuk, Dariusz Czerski*2026*](https://md.research.elamur.ai/free/en/papers/ogrodniczuk-2026-corpus-based-population-visualization-iso/)
81. [**Trustworthy NLP for Low-Resource Languages: Agent-Based Uncertainty Modeling for Hebrew Radiology Report Structuring**Hadas Ben Atya, Naama Gavrielov, Zvi Badash, et al.*2026*](https://md.research.elamur.ai/free/en/papers/atya-2026-trustworthy-nlp-low-resource-languages/)
82. [**Building Patient Journeys in Hebrew: A Language Model for Clinical Timeline Extraction**Kai Golan Hashiloni, Brenda Kasabe Nokai, Michal Shevach, et al.*2025*](https://md.research.elamur.ai/free/en/papers/hashiloni-2025-building-patient-journeys-hebrew-language/)
83. [**Hierarchical Section Matching Prediction (HSMP) BERT for Fine-Grained Extraction of Structured Data from Hebrew Free-Text Radiology Reports in Crohn's Disease**Zvi Badash; Hadas Ben-Atya; Naama Gavrielov; Liam Hazan; Gili Focht; Ruth Cytter-Kuint; Talar Hagopian; Dan Turner;, Moti Freiman*2025*](https://md.research.elamur.ai/free/en/papers/badash-2025-hierarchical-section-matching-prediction-hsmp/)
84. [**Rdgai: Classifying transcriptional changes using Large Language Models with a test case from an Arabic Gospel tradition**Robert Turnbull*2025*](https://md.research.elamur.ai/free/en/papers/turnbull-2025-rdgai-classifying-transcriptional-changes-using/)
85. [**Using English for commonsense knowledge**Allan Ramsay, Debora Field*2009*](https://md.research.elamur.ai/free/en/papers/ramsay-2009-english-commonsense-knowledge/)

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