Publications by authors named "Amir Karger"

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DeNoFo: a file format and toolkit for standardized, comparable de novo gene annotation.
Elias Dohmen, Margaux Aubel, Lars A Eicholt, Paul Roginski, Victor Luria, Amir Karger

Bioinformatics· October 2025

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De Novo Gene Emergence: Summary, Classification, and Challenges of Current Methods.
Anna Grandchamp, Margaux Aubel, Lars A Eicholt, Paul Roginski, Victor Luria, Amir Karger

Genome Biol Evol· October 2025

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Human-specific features of the cerebellum and ZP2-regulated synapse development.
Suel-Kee Kim, Adriana Cherskov, Aastha Sindhwani, Sang-Hun Choi, Hyojin Kim, Amir Karger

bioRxiv· September 2025

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Adaptive Evolution of Gene Regulatory Networks in Mammalian Neocortical Neurons.
Zhuo Li, Navjot Kaur, Gabriel Santpere, Sydney K Muchnik, Suvimal Kumar Sindhu, Amir Karger

bioRxiv· May 2025

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DeNoFo: a file format and toolkit for standardised, comparable de novo gene annotation.
Elias Dohmen, Margaux Aubel, Lars A Eicholt, Paul Roginski, Victor Luria, Amir Karger

bioRxiv· April 2025

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Expression of Random Sequences and de novo Evolved Genes From the Mouse in Human Cells Reveals Functional Diversity and Specificity.
Silvia Aldrovandi, Johana Fajardo Castro, Kristian Ullrich, Amir Karger, Victor Luria

Genome Biol Evol· December 2024

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Functional associations of evolutionarily recent human genes exhibit sensitivity to the 3D genome landscape and disease.
Katherine Fleck, Victor Luria, Nitanta Garag, Amir Karger, Trevor Hunter

bioRxiv· November 2024

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Individual variation in the emergence of anterior-to-posterior neural fates from human pluripotent stem cells.
Suel-Kee Kim, Seungmae Seo, Genevieve Stein-O'Brien, Amritha Jaishankar, Kazuya Ogawa, Amir Karger

Stem Cell Reports· September 2024

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Human-specific features and developmental dynamics of the brain N-glycome.
Thomas S Klarić, Ivan Gudelj, Gabriel Santpere, Mislav Novokmet, Frano Vučković, Amir Karger

Sci Adv· December 2023

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Developmental dynamics of RNA translation in the human brain.
Erin E Duffy, Benjamin Finander, GiHun Choi, Ava C Carter, Iva Pritisanac, Amir Karger

Nat Neurosci· October 2022

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Molecular and cellular evolution of the primate dorsolateral prefrontal cortex.
Shaojie Ma, Mario Skarica, Qian Li, Chuan Xu, Ryan D Risgaard, Amir Karger

Science· September 2022

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Phylogenomic analyses of the genus Drosophila reveals genomic signals of climate adaptation.
Fang Li, Rahul V Rane, Victor Luria, Zijun Xiong, Jiawei Chen, Amir Karger

Mol Ecol Resour· May 2022

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Noncanonical open reading frames encode functional proteins essential for cancer cell survival.
John R Prensner, Oana M Enache, Victor Luria, Karsten Krug, Karl R Clauser, Amir Karger

Nat Biotechnol· June 2021

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Apcdd1 is a dual BMP/Wnt inhibitor in the developing nervous system and skin.
Alin Vonica, Neha Bhat, Keith Phan, Jinbai Guo, Lăcrimioara Iancu, Amir Karger

Dev Biol· August 2020

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The whale shark genome reveals how genomic and physiological properties scale with body size.
Jessica A Weber, Seung Gu Park, Victor Luria, Sungwon Jeon, Hak-Min Kim, Amir Karger

Proc Natl Acad Sci U S A· August 2020

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The genome of the giant Nomura's jellyfish sheds light on the early evolution of active predation.
Hak-Min Kim, Jessica A Weber, Nayoung Lee, Seung Gu Park, Yun Sung Cho, Amir Karger

BMC Biol· March 2019

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The Gonium pectorale genome demonstrates co-option of cell cycle regulation during the evolution of multicellularity.
Erik R Hanschen, Tara N Marriage, Patrick J Ferris, Takashi Hamaji, Atsushi Toyoda, Amir Karger

Nat Commun· April 2016

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Somatic mutation in single human neurons tracks developmental and transcriptional history.
Michael A Lodato, Mollie B Woodworth, Semin Lee, Gilad D Evrony, Bhaven K Mehta, Amir Karger

Science· October 2015

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Peptidomic discovery of short open reading frame-encoded peptides in human cells.
Sarah A Slavoff, Andrew J Mitchell, Adam G Schwaid, Moran N Cabili, Jiao Ma, Amir D Karger

Nat Chem Biol· January 2013

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Deep annotation of Populus trichocarpa microRNAs from diverse tissue sets.
Joshua R Puzey, Amir Karger, Michael Axtell, Elena M Kramer

PLoS One· July 2012

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