Multimodal analysis of RNA sequencing data powers discovery of complex trait genetics

Authors: Daniel Munro, Nava Ehsan, Seyed Mehdi Esmaeili-Fard, Alexander Gusev, Abraham A. Palmer, Pejman Mohammadi

Source: Nature Communications, Vol 15, Iss 1, Pp 1-12 (2024)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/5333a8f7155348aa99ffa07322e30b4a

MSGene: a multistate model using genetic risk and the electronic health record applied to lifetime risk of coronary artery disease

Authors: Sarah M. Urbut, Ming Wai Yeung, Shaan Khurshid, So Mi Jemma Cho, Art Schuermans, Jakob German, Kodi Taraszka, Kaavya Paruchuri, Akl C. Fahed, Patrick T. Ellinor, Ludovic Trinquart, Giovanni Parmigiani, Alexander Gusev, Pradeep Natarajan

Source: Nature Communications, Vol 15, Iss 1, Pp 1-14 (2024)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/dbb0e85692d248568e99606b71073f1e

A Comprehensive Analysis on the Nature of the Spiral Arms in NGC 3686, NGC 4321, and NGC 2403

Authors: Valeria Kostiuk, Alexander Marchuk, Alexander Gusev, Ilia V. Chugunov

Source: Galaxies, Vol 13, Iss 2, p 27 (2025)

Subject Terms: galaxies, spiral structure, galactic dynamics and kinematics, Astronomy, QB1-991

File Description: electronic resource

Relation: https://www.mdpi.com/2075-4434/13/2/27; https://doaj.org/toc/2075-4434

Access URL: https://doaj.org/article/feaea24ded2547f0aeb235071dfc69be

Prediction and stratification of longitudinal risk for chronic obstructive pulmonary disease across smoking behaviors

Authors: Yixuan He, David C. Qian, James A. Diao, Michael H. Cho, Edwin K. Silverman, Alexander Gusev, Arjun K. Manrai, Alicia R. Martin, Chirag J. Patel

Source: Nature Communications, Vol 14, Iss 1, Pp 1-9 (2023)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/97210e4a87a7449baf7efe784bb53fc7

Additional impact of genetic ancestry over race/ethnicity to prevalence of KRAS mutations and allele-specific subtypes in non-small cell lung cancer

Authors: Xinan Wang, Kangcheng Hou, Biagio Ricciuti, Joao V. Alessi, Xihao Li, Federica Pecci, Rounak Dey, Jia Luo, Mark M. Awad, Alexander Gusev, Xihong Lin, Bruce E. Johnson, David C. Christiani

Source: HGG Advances, Vol 5, Iss 3, Pp 100320- (2024)

Subject Terms: non-small cell lung cancer (NSCLC), KRAS, somatic mutation, biomarker, race/ethnicity, genetic ancestry, Genetics, QH426-470

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2666247724000599; https://doaj.org/toc/2666-2477

Access URL: https://doaj.org/article/872f42da70b04727916e504d972d5581

A biallelic multiple nucleotide length polymorphism explains functional causality at 5p15.33 prostate cancer risk locus

Authors: Sandor Spisak, Viktoria Tisza, Pier Vitale Nuzzo, Ji-Heui Seo, Balint Pataki, Dezso Ribli, Zsofia Sztupinszki, Connor Bell, Mersedeh Rohanizadegan, David R. Stillman, Sarah Abou Alaiwi, Alan H. Bartels, Marton Papp, Anamay Shetty, Forough Abbasi, Xianzhi Lin, Kate Lawrenson, Simon A. Gayther, Mark Pomerantz, Sylvan Baca, Norbert Solymosi, Istvan Csabai, Zoltan Szallasi, Alexander Gusev, Matthew L. Freedman

Source: Nature Communications, Vol 14, Iss 1, Pp 1-13 (2023)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/56f577f878744951b0fa9132df89b32d

Epigenomic charting and functional annotation of risk loci in renal cell carcinoma

Authors: Amin H. Nassar, Sarah Abou Alaiwi, Sylvan C. Baca, Elio Adib, Rosario I. Corona, Ji-Heui Seo, Marcos A. S. Fonseca, Sandor Spisak, Talal El Zarif, Viktoria Tisza, David A. Braun, Heng Du, Monica He, Abdallah Flaifel, Michel Alchoueiry, Thomas Denize, Sayed G. Matar, Andres Acosta, Sachet Shukla, Yue Hou, John Steinharter, Gabrielle Bouchard, Jacob E. Berchuck, Edward O’Connor, Connor Bell, Pier Vitale Nuzzo, Gwo-Shu Mary Lee, Sabina Signoretti, Michelle S. Hirsch, Mark Pomerantz, Elizabeth Henske, Alexander Gusev, Kate Lawrenson, Toni K. Choueiri, David J. Kwiatkowski, Matthew L. Freedman

Source: Nature Communications, Vol 14, Iss 1, Pp 1-16 (2023)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/5c45bbe4ef1e4b0b9d9d760011ce2040

1273 Effect of systemic immunosuppression timing on overall survival among immune checkpoint inhibitor recipients

Authors: Kun-Hsing Yu, Shijia Zhang, Nga Nguyen, Feng Liu, Nikolai Klebanov, Alexander Gusev, Shawn Kwatra, Yevgeniy R Semenov, Genevieve M Boland, Nicole R LeBoeuf, Kimberly Tang, Guihong Wan, Boshen Yan, Munachimso Amadife, Bonnie W Leung

Source: Journal for ImmunoTherapy of Cancer, Vol 11, Iss Suppl 1 (2023)

Subject Terms: Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

File Description: electronic resource

Relation: https://doaj.org/toc/2051-1426

Access URL: https://doaj.org/article/2ad08a751a01468f9fc0646d71cb3c63

1241 Clusters of multi-organ toxicities are associated with improved survival among immune checkpoint inhibitor recipients: a population-level study

Authors: Kun-Hsing Yu, Shadmehr Demehri, Nga Nguyen, Leyre Zubiri, Kerry Reynolds, Alexander Gusev, Shawn Kwatra, Yevgeniy R Semenov, Nicole R LeBoeuf, Jayhyun Seo, William Lotter, Katie Roster, Wenxin Chen, Guihong Wan, Ahmad Rajesh, Hannah Rashdan

Source: Journal for ImmunoTherapy of Cancer, Vol 11, Iss Suppl 1 (2023)

Subject Terms: Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

File Description: electronic resource

Relation: https://doaj.org/toc/2051-1426

Access URL: https://doaj.org/article/2db26149663644138c8caab863d52e03

1252 Immune checkpoint inhibitor-induced diabetes mellitus comprises multiple clinical endotypes with distinct immunologic features

Authors: John McGuire, Hoang Tran, Dejan Juric, Leyre Zubiri, Kerry Reynolds, Alexander Gusev, Genevieve M Boland, Caitlin Colling, Sidney Martin, Alexandra-Chloe Villani, Michelle Rengarajan, Alice Tirard, Benjamin Arnold, Karina Ruiz Esteves, Sergio Aguilar Fernandez, Kaitlyn Shank, Aaron Deutsch, Alekhya Gunturi, Nandini Samanta, Katherine Perlman, Tianqi Ouyang, Meghan Sise

Source: Journal for ImmunoTherapy of Cancer, Vol 11, Iss Suppl 1 (2023)

Subject Terms: Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

File Description: electronic resource

Relation: https://doaj.org/toc/2051-1426

Access URL: https://doaj.org/article/445420564ece4a1b87d180b24d253f57

The impact of stage-related features in melanoma recurrence prediction: A machine learning approach

Authors: Guihong Wan, PhD, Bonnie Leung, BS, Nga Nguyen, MD, MPH, Mia S. DeSimone, MD, MPH, Feng Liu, PhD, Min Seok Choi, MS, Diane Ho, RHIA, CTR, Valerie Laucks, BS, Stacey Duey, MCPH, Ryan J. Sullivan, MD, Genevieve M. Boland, MD, PhD, Nicole R. LeBoeuf, MD, MPH, David Liu, MD, MPH, Alexander Gusev, PhD, Shawn G. Kwatra, MD, Peter K. Sorger, PhD, Kun-Hsing Yu, MD, PhD, Yevgeniy R. Semenov, MD, MA

Source: JAAD International, Vol 10, Iss , Pp 28-30 (2023)

Subject Terms: Dermatology, RL1-803

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S266632872200116X; https://doaj.org/toc/2666-3287

Access URL: https://doaj.org/article/1709f0a0574d4ee0b85d69947c217674

Prediction of early-stage melanoma recurrence using clinical and histopathologic features

Authors: Guihong Wan, Nga Nguyen, Feng Liu, Mia S. DeSimone, Bonnie W. Leung, Ahmad Rajeh, Michael R. Collier, Min Seok Choi, Munachimso Amadife, Kimberly Tang, Shijia Zhang, Jordan S. Phillipps, Ruple Jairath, Nora A. Alexander, Yining Hua, Meng Jiao, Wenxin Chen, Diane Ho, Stacey Duey, István Balázs Németh, Gyorgy Marko-Varga, Jeovanis Gil Valdés, David Liu, Genevieve M. Boland, Alexander Gusev, Peter K. Sorger, Kun-Hsing Yu, Yevgeniy R. Semenov

Source: npj Precision Oncology, Vol 6, Iss 1, Pp 1-16 (2022)

Subject Terms: Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

File Description: electronic resource

Relation: https://doaj.org/toc/2397-768X

Access URL: https://doaj.org/article/677b9e82a3af4455b315991c7f27eef6

Multi-context genetic modeling of transcriptional regulation resolves novel disease loci

Authors: Mike Thompson, Mary Grace Gordon, Andrew Lu, Anchit Tandon, Eran Halperin, Alexander Gusev, Chun Jimmie Ye, Brunilda Balliu, Noah Zaitlen

Source: Nature Communications, Vol 13, Iss 1, Pp 1-15 (2022)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/a40a64f23b1e496faf8be74f3f60563c

DeCAF: a novel method to identify cell-type specific regulatory variants and their role in cancer risk

Authors: Cynthia A. Kalita, Alexander Gusev

Source: Genome Biology, Vol 23, Iss 1, Pp 1-22 (2022)

Subject Terms: Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/a2fd4c6f9fa543ae8b9a902944c5992c

Variation in targetable genomic alterations in non-small cell lung cancer by genetic ancestry, sex, smoking history, and histology

Authors: Elio Adib, Amin H. Nassar, Sarah Abou Alaiwi, Stefan Groha, Elie W. Akl, Lynette M. Sholl, Kesi S. Michael, Mark M. Awad, Pasi A. Jӓnne, Alexander Gusev, David J. Kwiatkowski

Source: Genome Medicine, Vol 14, Iss 1, Pp 1-10 (2022)

Subject Terms: Non-small cell lung cancer, Targeted therapies, Targetable genomic alterations, Genetic ancestry, Smoking, Medicine, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1756-994X

Access URL: https://doaj.org/article/c4e87f114ea24bebb735210ae5f0e899

The lingering effects of Neanderthal introgression on human complex traits

Authors: Xinzhu Wei, Christopher R Robles, Ali Pazokitoroudi, Andrea Ganna, Alexander Gusev, Arun Durvasula, Steven Gazal, Po-Ru Loh, David Reich, Sriram Sankararaman

Source: eLife, Vol 12 (2023)

Subject Terms: complex trait, Neanderthal introgression, heritability, fine mapping, selection, Medicine, Science, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://elifesciences.org/articles/80757; https://doaj.org/toc/2050-084X

Access URL: https://doaj.org/article/d9bc395d35c846718dd9f8c95194e3f7

Somatic mutational profiles and germline polygenic risk scores in human cancer

Authors: Yuxi Liu, Alexander Gusev, Yujing J. Heng, Ludmil B. Alexandrov, Peter Kraft

Source: Genome Medicine, Vol 14, Iss 1, Pp 1-16 (2022)

Subject Terms: Somatic mutation, Mutational signature, Single-base substitution signature, Polygenic risk score, Cancer, Medicine, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1756-994X

Access URL: https://doaj.org/article/31efe95b91134ea5bd40e4797f7cb13a

Functional characterisation of the amyotrophic lateral sclerosis risk locus GPX3/TNIP1

Authors: Restuadi Restuadi, Frederik J. Steyn, Edor Kabashi, Shyuan T. Ngo, Fei-Fei Cheng, Marta F. Nabais, Mike J. Thompson, Ting Qi, Yang Wu, Anjali K. Henders, Leanne Wallace, Chris R. Bye, Bradley J. Turner, Laura Ziser, Susan Mathers, Pamela A. McCombe, Merrilee Needham, David Schultz, Matthew C. Kiernan, Wouter van Rheenen, Leonard H. van den Berg, Jan H. Veldink, Roel Ophoff, Alexander Gusev, Noah Zaitlen, Allan F. McRae, Robert D. Henderson, Naomi R. Wray, Jean Giacomotto, Fleur C. Garton

Source: Genome Medicine, Vol 14, Iss 1, Pp 1-22 (2022)

Subject Terms: Motor neurone disease, MND, Genome-wide association study, Computational biology, Zebrafish, Neurodegenerative diseases, Medicine, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1756-994X

Access URL: https://doaj.org/article/554d6d92682e49b2a277f81cb79542d2

Artificial intelligence-aided clinical annotation of a large multi-cancer genomic dataset

Authors: Kenneth L. Kehl, Wenxin Xu, Alexander Gusev, Ziad Bakouny, Toni K. Choueiri, Irbaz Bin Riaz, Haitham Elmarakeby, Eliezer M. Van Allen, Deborah Schrag

Source: Nature Communications, Vol 12, Iss 1, Pp 1-9 (2021)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/723f47f007e84b058d8d369a5c28f480

Constructing germline research cohorts from the discarded reads of clinical tumor sequences

Authors: Alexander Gusev, Stefan Groha, Kodi Taraszka, Yevgeniy R. Semenov, Noah Zaitlen

Source: Genome Medicine, Vol 13, Iss 1, Pp 1-14 (2021)

Subject Terms: Medicine, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1756-994X

Access URL: https://doaj.org/article/dfd1ed628f8e4314b50a12954fd90ff0