Index by Author

August 2025; 35 (8)
  1. A
  2. B
  3. C
  4. D
  5. E
  6. F
  7. G
  8. H
  9. I
  10. J
  11. K
  12. L
  13. M
  14. N
  15. O
  16. P
  17. Q
  18. R
  19. S
  20. T
  21. U
  22. V
  23. W
  24. X
  25. Y
  26. Z

A

  1. Aaltonen, Niina

    • Androgen receptor–mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells Genome Res. August 2025 35: 1717-1732; Published in Advance June 2, 2025, doi:10.1101/gr.280224.124
      OPEN ACCESS ARTICLE

  2. Amundsen, Susan K.

    • Lambdoid phages with abundant Chi recombination hotspots reflect diverse viral strategies for recombination-dependent growth Genome Res. August 2025 35: 1767-1780; Published in Advance July 10, 2025, doi:10.1101/gr.280248.124
      OPEN ACCESS ARTICLE

  3. Antonsson, Sindri Emmanúel

    • Batch correction methods used in single-cell RNA sequencing analyses are often poorly calibrated Genome Res. August 2025 35: 1832-1841; Published in Advance July 7, 2025, doi:10.1101/gr.279886.124
      OPEN ACCESS ARTICLE

  4. Anwer, Ayad G.

    • Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq Genome Res. August 2025 35: 1809-1820; Published in Advance July 8, 2025, doi:10.1101/gr.280014.124
      OPEN ACCESS ARTICLE

  5. Artiles, Karen L.

B

  1. Bailey, Jacqueline

    • Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq Genome Res. August 2025 35: 1809-1820; Published in Advance July 8, 2025, doi:10.1101/gr.280014.124
      OPEN ACCESS ARTICLE

  2. Bouchez, Valérie

  3. Brisse, Sylvain

C

  1. Cantù, Claudio

    • Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes Genome Res. August 2025 35: 1701-1716; Published in Advance June 23, 2025, doi:10.1101/gr.279684.124
      OPEN ACCESS ARTICLE

  2. Casjens, Sherwood R.

    • Lambdoid phages with abundant Chi recombination hotspots reflect diverse viral strategies for recombination-dependent growth Genome Res. August 2025 35: 1767-1780; Published in Advance July 10, 2025, doi:10.1101/gr.280248.124
      OPEN ACCESS ARTICLE

  3. Chakraborty, Chaitali

    • Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes Genome Res. August 2025 35: 1701-1716; Published in Advance June 23, 2025, doi:10.1101/gr.279684.124
      OPEN ACCESS ARTICLE

  4. Chen, Yuhang

  5. Chen, Zhanlin

  6. Cheng, Lijun

  7. Chtanova, Tatyana

    • Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq Genome Res. August 2025 35: 1809-1820; Published in Advance July 8, 2025, doi:10.1101/gr.280014.124
      OPEN ACCESS ARTICLE

  8. Crestani, Chiara

D

  1. Dano, Orgena

    • Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes Genome Res. August 2025 35: 1701-1716; Published in Advance June 23, 2025, doi:10.1101/gr.279684.124
      OPEN ACCESS ARTICLE

  2. Davidson, Alan R.

    • Lambdoid phages with abundant Chi recombination hotspots reflect diverse viral strategies for recombination-dependent growth Genome Res. August 2025 35: 1767-1780; Published in Advance July 10, 2025, doi:10.1101/gr.280248.124
      OPEN ACCESS ARTICLE

  3. Dekker, Job

    • Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation Genome Res. August 2025 35: 1733-1744; Published in Advance June 6, 2025, doi:10.1101/gr.280648.125
      OPEN ACCESS ARTICLE

  4. Du, Heng

    • A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
      OPEN ACCESS ARTICLE

E

  1. Ehrlich, Michelle E.

    • QuadST identifies cell–cell interaction–changed genes in spatially resolved transcriptomics data Genome Res. August 2025 35: 1821-1831; Published in Advance June 23, 2025, doi:10.1101/gr.279859.124
      OPEN ACCESS ARTICLE

F

  1. Fire, Andrew Z.

  2. Flaherty, Mary

  3. Fox, A. Nicole

    • Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation Genome Res. August 2025 35: 1733-1744; Published in Advance June 6, 2025, doi:10.1101/gr.280648.125
      OPEN ACCESS ARTICLE

  4. Fudenberg, Geoffrey

G

  1. Gatt, Catherine

    • Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq Genome Res. August 2025 35: 1809-1820; Published in Advance July 8, 2025, doi:10.1101/gr.280014.124
      OPEN ACCESS ARTICLE

  2. Gaynor-Gillett, Sophia C.

  3. Gerstein, Mark

  4. Geschwind, Daniel

  5. Gilad, Yoav

    • Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids Genome Res. August 2025 35: 1689-1700; Published in Advance June 2, 2025, doi:10.1101/gr.280219.124
      OPEN ACCESS ARTICLE

  6. Goldys, Ewa

    • Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq Genome Res. August 2025 35: 1809-1820; Published in Advance July 8, 2025, doi:10.1101/gr.280014.124
      OPEN ACCESS ARTICLE

  7. Gonzalez, Inma

    • Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation Genome Res. August 2025 35: 1733-1744; Published in Advance June 6, 2025, doi:10.1101/gr.280648.125
      OPEN ACCESS ARTICLE

  8. Gu, Mengting

  9. Guo, Qiuyu

H

  1. Habibalahi, Abbas

    • Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq Genome Res. August 2025 35: 1809-1820; Published in Advance July 8, 2025, doi:10.1101/gr.280014.124
      OPEN ACCESS ARTICLE

  2. Helminen, Laura

    • Androgen receptor–mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells Genome Res. August 2025 35: 1717-1732; Published in Advance June 2, 2025, doi:10.1101/gr.280224.124
      OPEN ACCESS ARTICLE

  3. Hiltunen, Johannes

    • Androgen receptor–mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells Genome Res. August 2025 35: 1717-1732; Published in Advance June 2, 2025, doi:10.1101/gr.280224.124
      OPEN ACCESS ARTICLE

  4. Holst, Jeff

    • Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq Genome Res. August 2025 35: 1809-1820; Published in Advance July 8, 2025, doi:10.1101/gr.280014.124
      OPEN ACCESS ARTICLE

  5. Huang, Shaodong

  6. Hwang, Ahyeon

I

  1. Ichikawa, Kazuki

  2. Iino, Yuichi

J

  1. Jeong, Dae-Eun

  2. Johansson, Emma M.V.

    • Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq Genome Res. August 2025 35: 1809-1820; Published in Advance July 8, 2025, doi:10.1101/gr.280014.124
      OPEN ACCESS ARTICLE

  3. Jonasson, Mattias

    • Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes Genome Res. August 2025 35: 1701-1716; Published in Advance June 23, 2025, doi:10.1101/gr.279684.124
      OPEN ACCESS ARTICLE

K

  1. Kalleberg, Jenna

    • Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain Genome Res. August 2025 35: 1859-1874; Published in Advance June 2, 2025, doi:10.1101/gr.279542.124
      OPEN ACCESS ARTICLE

  2. Kanamori, Manami

  3. Kobayashi, Haruka

L

  1. Laakso, Hanna

    • Androgen receptor–mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells Genome Res. August 2025 35: 1717-1732; Published in Advance June 2, 2025, doi:10.1101/gr.280224.124
      OPEN ACCESS ARTICLE

  2. Lan, Xun

    • A novel multislice framework for precision 3D spatial domain reconstruction and disease pathology analysis Genome Res. August 2025 35: 1794-1808; Published in Advance July 14, 2025, doi:10.1101/gr.280281.124

  3. Launonen, Kaisa-Mari

    • Androgen receptor–mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells Genome Res. August 2025 35: 1717-1732; Published in Advance June 2, 2025, doi:10.1101/gr.280224.124
      OPEN ACCESS ARTICLE

  4. Lea, Amanda J.

    • Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes Genome Res. August 2025 35: 1781-1793; Published in Advance July 14, 2025, doi:10.1101/gr.279957.124
      OPEN ACCESS ARTICLE

  5. Lee, Donghoon

  6. Li, Wanying

    • A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
      OPEN ACCESS ARTICLE

  7. Lin, Francis

    • Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq Genome Res. August 2025 35: 1809-1820; Published in Advance July 8, 2025, doi:10.1101/gr.280014.124
      OPEN ACCESS ARTICLE

  8. Lin, Xia

  9. Liu, Bin

    • A novel multislice framework for precision 3D spatial domain reconstruction and disease pathology analysis Genome Res. August 2025 35: 1794-1808; Published in Advance July 14, 2025, doi:10.1101/gr.280281.124

  10. Liu, Jason

  11. Liu, Jian-Feng

    • A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
      OPEN ACCESS ARTICLE

  12. Liu, Zhen

    • A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
      OPEN ACCESS ARTICLE

M

  1. Malinen, Marjo

    • Androgen receptor–mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells Genome Res. August 2025 35: 1717-1732; Published in Advance June 2, 2025, doi:10.1101/gr.280224.124
      OPEN ACCESS ARTICLE

  2. Melsted, Páll

    • Batch correction methods used in single-cell RNA sequencing analyses are often poorly calibrated Genome Res. August 2025 35: 1832-1841; Published in Advance July 7, 2025, doi:10.1101/gr.279886.124
      OPEN ACCESS ARTICLE

  3. Molliex, Amandine

    • Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation Genome Res. August 2025 35: 1733-1744; Published in Advance June 6, 2025, doi:10.1101/gr.280648.125
      OPEN ACCESS ARTICLE

  4. Moran, Jennifer R.

  5. Morishita, Shinichi

N

  1. Navarro, Pablo

    • Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation Genome Res. August 2025 35: 1733-1744; Published in Advance June 6, 2025, doi:10.1101/gr.280648.125
      OPEN ACCESS ARTICLE

  2. Niskanen, Einari A.

    • Androgen receptor–mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells Genome Res. August 2025 35: 1717-1732; Published in Advance June 2, 2025, doi:10.1101/gr.280224.124
      OPEN ACCESS ARTICLE

  3. Nordin, Anna

    • Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes Genome Res. August 2025 35: 1701-1716; Published in Advance June 23, 2025, doi:10.1101/gr.279684.124
      OPEN ACCESS ARTICLE

O

  1. Ochman, Howard

    • De novo gene birth and the conundrum of ORFan genes in bacteria Genome Res. August 2025 35: 1679-1688; Published in Advance July 10, 2025, doi:10.1101/gr.280157.124

  2. Oomen, Marlies E.

    • Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation Genome Res. August 2025 35: 1733-1744; Published in Advance June 6, 2025, doi:10.1101/gr.280648.125
      OPEN ACCESS ARTICLE

  3. Owa, Chie

P

  1. Paakinaho, Ville

    • Androgen receptor–mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells Genome Res. August 2025 35: 1717-1732; Published in Advance June 2, 2025, doi:10.1101/gr.280224.124
      OPEN ACCESS ARTICLE

  2. Pagella, Pierfrancesco

    • Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes Genome Res. August 2025 35: 1701-1716; Published in Advance June 23, 2025, doi:10.1101/gr.279684.124
      OPEN ACCESS ARTICLE

  3. Palvimo, Jorma J.

    • Androgen receptor–mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells Genome Res. August 2025 35: 1717-1732; Published in Advance June 2, 2025, doi:10.1101/gr.280224.124
      OPEN ACCESS ARTICLE

  4. Papadopoulou, Thaleia

    • Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation Genome Res. August 2025 35: 1733-1744; Published in Advance June 6, 2025, doi:10.1101/gr.280648.125
      OPEN ACCESS ARTICLE

  5. Passet, Virginie

  6. Petersen, Rachel M.

    • Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes Genome Res. August 2025 35: 1781-1793; Published in Advance July 14, 2025, doi:10.1101/gr.279957.124
      OPEN ACCESS ARTICLE

  7. PsychENCODE Consortium

Q

  1. Qi, Le

  2. Qi, Ren

    • A novel multislice framework for precision 3D spatial domain reconstruction and disease pathology analysis Genome Res. August 2025 35: 1794-1808; Published in Advance July 14, 2025, doi:10.1101/gr.280281.124

R

  1. Rahmaninejad, Hadi

  2. Rao, Ziyan

  3. Remeseiro, Silvia

    • Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes Genome Res. August 2025 35: 1701-1716; Published in Advance June 23, 2025, doi:10.1101/gr.279684.124
      OPEN ACCESS ARTICLE

  4. Rethoret-Pasty, Martin

  5. Rissman, Jacob

    • Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain Genome Res. August 2025 35: 1859-1874; Published in Advance June 2, 2025, doi:10.1101/gr.279542.124
      OPEN ACCESS ARTICLE

  6. Rodrigues, Carla

  7. Rougvie, Ann E.

  8. Roussos, Panos

    • QuadST identifies cell–cell interaction–changed genes in spatially resolved transcriptomics data Genome Res. August 2025 35: 1821-1831; Published in Advance June 23, 2025, doi:10.1101/gr.279859.124
      OPEN ACCESS ARTICLE

S

  1. Schnabel, Robert D.

    • Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain Genome Res. August 2025 35: 1859-1874; Published in Advance June 2, 2025, doi:10.1101/gr.279542.124
      OPEN ACCESS ARTICLE

  2. Schwarz, Erich M.

  3. Shang, Yuqing

    • QuadST identifies cell–cell interaction–changed genes in spatially resolved transcriptomics data Genome Res. August 2025 35: 1821-1831; Published in Advance June 23, 2025, doi:10.1101/gr.279859.124
      OPEN ACCESS ARTICLE

  4. Shi, Manman

  5. Shoura, Massa J.

  6. Smith, Gerald R.

    • Lambdoid phages with abundant Chi recombination hotspots reflect diverse viral strategies for recombination-dependent growth Genome Res. August 2025 35: 1767-1780; Published in Advance July 10, 2025, doi:10.1101/gr.280248.124
      OPEN ACCESS ARTICLE

  7. Song, Xiaoyu

    • QuadST identifies cell–cell interaction–changed genes in spatially resolved transcriptomics data Genome Res. August 2025 35: 1821-1831; Published in Advance June 23, 2025, doi:10.1101/gr.279859.124
      OPEN ACCESS ARTICLE

  8. Spector, Megan

  9. Suzuki, Yoshihiko

T

  1. Tortora, Maxime M.C.

  2. Toyoshima, Yu

U

  1. Umans, Benjamin D.

    • Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids Genome Res. August 2025 35: 1689-1700; Published in Advance June 2, 2025, doi:10.1101/gr.280219.124
      OPEN ACCESS ARTICLE

  2. uz-Zaman, Md. Hassan

    • De novo gene birth and the conundrum of ORFan genes in bacteria Genome Res. August 2025 35: 1679-1688; Published in Advance July 10, 2025, doi:10.1101/gr.280157.124

V

  1. Vockley, Christopher M.

    • Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes Genome Res. August 2025 35: 1781-1793; Published in Advance July 14, 2025, doi:10.1101/gr.279957.124
      OPEN ACCESS ARTICLE

W

  1. Wahba, Lamia

  2. Wahi, Kanu

    • Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq Genome Res. August 2025 35: 1809-1820; Published in Advance July 8, 2025, doi:10.1101/gr.280014.124
      OPEN ACCESS ARTICLE

  3. Wall, Martha

  4. Wang, Gaoyuan

  5. Wang, Pei

    • QuadST identifies cell–cell interaction–changed genes in spatially resolved transcriptomics data Genome Res. August 2025 35: 1821-1831; Published in Advance June 23, 2025, doi:10.1101/gr.279859.124
      OPEN ACCESS ARTICLE

  6. White, Kevin P.

  7. Wu, Chenyang

X

  1. Xiao, Yao

  2. Xie, Yike

    • Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq Genome Res. August 2025 35: 1809-1820; Published in Advance July 8, 2025, doi:10.1101/gr.280014.124
      OPEN ACCESS ARTICLE

  3. Xue, Yahui

    • A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
      OPEN ACCESS ARTICLE

Y

  1. Yuan, Guo-Cheng

    • QuadST identifies cell–cell interaction–changed genes in spatially resolved transcriptomics data Genome Res. August 2025 35: 1821-1831; Published in Advance June 23, 2025, doi:10.1101/gr.279859.124
      OPEN ACCESS ARTICLE

Z

  1. Zambanini, Gianluca

    • Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes Genome Res. August 2025 35: 1701-1716; Published in Advance June 23, 2025, doi:10.1101/gr.279684.124
      OPEN ACCESS ARTICLE

  2. Zanini, Fabio

    • Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq Genome Res. August 2025 35: 1809-1820; Published in Advance July 8, 2025, doi:10.1101/gr.280014.124
      OPEN ACCESS ARTICLE

  3. Zhang, Daijun

    • A novel multislice framework for precision 3D spatial domain reconstruction and disease pathology analysis Genome Res. August 2025 35: 1794-1808; Published in Advance July 14, 2025, doi:10.1101/gr.280281.124

  4. Zhang, Jing

  5. Zhang, Meilin

    • A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
      OPEN ACCESS ARTICLE

  6. Zhang, Min

  7. Zhang, Weijie

  8. Zhang, Yu

    • A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
      OPEN ACCESS ARTICLE

  9. Zhao, Dongyu

  10. Zheng, Clarence

    • Lambdoid phages with abundant Chi recombination hotspots reflect diverse viral strategies for recombination-dependent growth Genome Res. August 2025 35: 1767-1780; Published in Advance July 10, 2025, doi:10.1101/gr.280248.124
      OPEN ACCESS ARTICLE

  11. Zhou, Lei

    • A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
      OPEN ACCESS ARTICLE

  12. Zhou, Sixuan

    • A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
      OPEN ACCESS ARTICLE

  13. Zhou, Yuheng

  14. Zhuo, Yue

    • A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
      OPEN ACCESS ARTICLE

  15. Zidane, Nora

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